diff --git a/packages/apollo-collaboration-server/.development.env b/packages/apollo-collaboration-server/.development.env index 829a80e03..88e149bc1 100644 --- a/packages/apollo-collaboration-server/.development.env +++ b/packages/apollo-collaboration-server/.development.env @@ -11,7 +11,7 @@ MICROSOFT_CLIENT_ID=fabdd045-163c-4712-9d40-dbbb043b3090 MICROSOFT_CLIENT_SECRET=~Gr8Q~h6RTU7SMC-fjNxXy_~nabTD-ME_rFyLa.M DESCRIPTION=A server for Apollo development purposes PLUGIN_LOCATION=http://localhost:9000/dist/jbrowse-plugin-apollo.umd.development.js -FEATURE_TYPE_ONTOLOGY_LOCATION=http://localhost:9000/test_data/so-v3.1.json +FEATURE_TYPE_ONTOLOGY_LOCATION=http://localhost:9000/test_data/so-2024-11-18.json LOG_LEVELS=error,warn,log,debug ALLOW_ROOT_USER=true ROOT_USER_PASSWORD=password diff --git a/packages/apollo-mst/src/AnnotationFeatureModel.ts b/packages/apollo-mst/src/AnnotationFeatureModel.ts index cc7d38bf7..00e76e266 100644 --- a/packages/apollo-mst/src/AnnotationFeatureModel.ts +++ b/packages/apollo-mst/src/AnnotationFeatureModel.ts @@ -291,40 +291,6 @@ export const AnnotationFeatureModel = types transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'), ) }, - get looksLikeGene(): boolean { - // eslint-disable-next-line @typescript-eslint/no-explicit-any - const session = getSession(self) as any - const { apolloDataStore } = session - const { featureTypeOntology } = apolloDataStore.ontologyManager - if (!featureTypeOntology) { - return false - } - const children = self.children as Children - if (!children?.size) { - return false - } - const isGene = - featureTypeOntology.isTypeOf(self.type, 'gene') || - featureTypeOntology.isTypeOf(self.type, 'pseudogene') - if (!isGene) { - return false - } - for (const [, child] of children) { - if ( - featureTypeOntology.isTypeOf(child.type, 'transcript') || - featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript') - ) { - const { children: grandChildren } = child - if (!grandChildren?.size) { - return false - } - return [...grandChildren.values()].some((grandchild) => - featureTypeOntology.isTypeOf(grandchild.type, 'exon'), - ) - } - } - return false - }, })) .actions((self) => ({ setAttributes(attributes: Map) { diff --git a/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-gene-model.png b/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-gene-model.png new file mode 100755 index 000000000..f88443d3e Binary files /dev/null and b/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-gene-model.png differ diff --git a/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-linear-apollo-display-canvas.png b/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-linear-apollo-display-canvas.png new file mode 100755 index 000000000..42ca01252 Binary files 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b/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-seq-track-canvas.png differ diff --git a/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-headless.png b/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-headless.png deleted file mode 100755 index 380fcb39c..000000000 Binary files a/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-headless.png and /dev/null differ diff --git a/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-interactive.png b/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-interactive.png deleted file mode 100755 index c17a4a0ae..000000000 Binary files a/packages/jbrowse-plugin-apollo/cypress/cypress-image-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-interactive.png and /dev/null differ diff --git a/packages/jbrowse-plugin-apollo/cypress/data/so.json.gz b/packages/jbrowse-plugin-apollo/cypress/data/so.json.gz index 4056964bb..18ec2bf77 100644 Binary files a/packages/jbrowse-plugin-apollo/cypress/data/so.json.gz and b/packages/jbrowse-plugin-apollo/cypress/data/so.json.gz differ diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/renderTrack.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/renderTrack.cy.ts new file mode 100644 index 000000000..68d8b5369 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/cypress/e2e/renderTrack.cy.ts @@ -0,0 +1,69 @@ +/* eslint-disable cypress/no-unnecessary-waiting */ +describe('Simple tests for visuals', () => { + beforeEach(() => { + cy.loginAsGuest() + }) + afterEach(() => { + cy.deleteAssemblies() + }) + it('Shows correct gene model', () => { + cy.addAssemblyFromGff('so_types.gff3', 'test_data/so_types.gff3') + cy.selectAssemblyToView('so_types.gff3') + cy.get('body').then(($body) => { + if ($body.find('button[aria-label="Close drawer"]').length > 0) { + cy.get('button[aria-label="Close drawer"]').click() + } + }) + + cy.searchFeatures('TGGT1_200010', 1) + cy.wait(5000) + // This may fail locally due to differences in runtime such as installed + // fonts on. The snapshots used in this test are generated on GitHub Actions + cy.get('canvas[data-testid="overlayCanvas"]').compareSnapshot('gene-model') + }) + it('Shows different glyph types', () => { + cy.addAssemblyFromGff('glyph_types.gff3', 'test_data/glyph_types.gff3') + cy.selectAssemblyToView('glyph_types.gff3') + cy.contains('Open track selector').click() + cy.contains('Reference sequence (').click() + cy.contains('Annotations (').click() + + cy.get('body').then(($body) => { + if ($body.find('button[aria-label="Close drawer"]').length > 0) { + cy.get('button[aria-label="Close drawer"]').click() + } + }) + cy.wait(2000) // Wait for render + // This may fail locally due to differences in runtime such as installed + // fonts on. The snapshots used in this test are generated on GitHub Actions + cy.get('canvas[data-testid="seqTrackCanvas"]').compareSnapshot( + 'seq-track-canvas', + ) + + cy.get('[data-testid="track_menu_icon"]').last().click() + cy.contains('Display types').trigger('mouseover') + cy.contains('LinearApolloSixFrameDisplay').click() + cy.wait(2000) // Wait for render + // This may fail locally due to differences in runtime such as installed + // fonts on. The snapshots used in this test are generated on GitHub Actions + cy.get('canvas[data-testid="canvas"]').compareSnapshot( + 'linear-apollo-six-frame-display-canvas', + ) + + cy.get('[data-testid="track_menu_icon"]').last().click() + cy.contains('Display types').trigger('mouseover') + cy.contains('LinearApolloDisplay').click() + cy.get('button[data-testid="view_menu_icon"]', { timeout: 10_000 }).click({ + force: true, + timeout: 10_000, + }) + cy.contains('Show...', { timeout: 10_000 }).click() + cy.contains('Show all regions in assembly', { timeout: 10_000 }).click() + cy.wait(2000) // Wait for render + // This may fail locally due to differences in runtime such as installed + // fonts on. The snapshots used in this test are generated on GitHub Actions + cy.get('canvas[data-testid="canvas"]').compareSnapshot( + 'linear-apollo-display-canvas', + ) + }) +}) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/visualGeneModel.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/visualGeneModel.cy.ts deleted file mode 100644 index 0f1e641f4..000000000 --- a/packages/jbrowse-plugin-apollo/cypress/e2e/visualGeneModel.cy.ts +++ /dev/null @@ -1,28 +0,0 @@ -/* eslint-disable cypress/no-unnecessary-waiting */ -describe('Simple tests for visuals', () => { - beforeEach(() => { - cy.loginAsGuest() - }) - afterEach(() => { - cy.deleteAssemblies() - }) - it('Shows correct gene model', () => { - cy.addAssemblyFromGff('so_types.gff3', 'test_data/so_types.gff3') - cy.selectAssemblyToView('so_types.gff3', 'TGGT1_200010') - - cy.get('body').then(($body) => { - if ($body.find('button[aria-label="Close drawer"]').length > 0) { - cy.get('button[aria-label="Close drawer"]').click() - } - }) - - cy.wait(5000) - - // NB: The size of the image differs between headless and interactive execution of cypress. - // Use *headless for pushing to gihub - cy.get('canvas[data-testid="overlayCanvas"]').compareSnapshot( - 'gene-model-headless', - ) - // cy.get('canvas[data-testid="overlayCanvas"]').compareSnapshot('gene-model-interactive') - }) -}) diff --git a/packages/jbrowse-plugin-apollo/cypress/support/commands.ts b/packages/jbrowse-plugin-apollo/cypress/support/commands.ts index e93a033d9..6539c2ddb 100644 --- a/packages/jbrowse-plugin-apollo/cypress/support/commands.ts +++ b/packages/jbrowse-plugin-apollo/cypress/support/commands.ts @@ -76,7 +76,7 @@ Cypress.Commands.add('addOntologies', () => { name: 'Sequence Ontology', version: 'unversioned', source: { - uri: 'http://localhost:9000/test_data/so-v3.1.json', + uri: 'http://localhost:9000/test_data/so-2024-11-18.json', locationType: 'UriLocation', }, }, @@ -86,6 +86,8 @@ Cypress.Commands.add('addOntologies', () => { }, { collection: 'jbrowseconfigs' }, ) + // so.json.gz was generated from an IndexedDB dump using the script found at + // https://gist.github.com/loilo/ed43739361ec718129a15ae5d531095b cy.readFile('cypress/data/so.json.gz', null).then((soGZip: Buffer) => { cy.wrap>( loadOntology( diff --git a/packages/jbrowse-plugin-apollo/jbrowse_config.json b/packages/jbrowse-plugin-apollo/jbrowse_config.json index 150606613..24d7d872b 100644 --- a/packages/jbrowse-plugin-apollo/jbrowse_config.json +++ b/packages/jbrowse-plugin-apollo/jbrowse_config.json @@ -30,7 +30,7 @@ "name": "Sequence Ontology", "version": "3.1", "source": { - "uri": "test_data/so-v3.1.json", + "uri": "test_data/so-2024-11-18.json", "locationType": "UriLocation" } } diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts index d891708b8..8e614b2ba 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts @@ -1,5 +1,6 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import { type MenuItem } from '@jbrowse/core/ui' +import { type ContentBlock } from '@jbrowse/core/util/blockTypes' import { alpha } from '@mui/material' import { @@ -15,70 +16,86 @@ import { type LinearApolloDisplayRendering } from '../stateModel/rendering' import { type CanvasMouseEvent } from '../types' import { type Glyph } from './Glyph' +import { getLeftPx, strokeRectInner } from './util' -function drawBoxOutline( - ctx: CanvasRenderingContext2D, - x: number, - y: number, - width: number, - height: number, - color: string, +/** @returns undefined if mouse not on the edge of this feature, otherwise 'start' or 'end' depending on which edge */ +function isMouseOnFeatureEdge( + mousePosition: MousePosition, + feature: AnnotationFeature, + stateModel: LinearApolloDisplay, ) { - drawBox(ctx, x, y, width, height, color) - if (width <= 2) { - return + const { refName, regionNumber, x } = mousePosition + const { lgv } = stateModel + const { offsetPx } = lgv + const minPxInfo = lgv.bpToPx({ refName, coord: feature.min, regionNumber }) + const maxPxInfo = lgv.bpToPx({ refName, coord: feature.max, regionNumber }) + if (minPxInfo !== undefined && maxPxInfo !== undefined) { + const minPx = minPxInfo.offsetPx - offsetPx + const maxPx = maxPxInfo.offsetPx - offsetPx + if (Math.abs(maxPx - minPx) < 8) { + return + } + if (Math.abs(minPx - x) < 4) { + return 'min' + } + if (Math.abs(maxPx - x) < 4) { + return 'max' + } } - ctx.clearRect(x + 1, y + 1, width - 2, height - 2) + return } -function drawBoxFill( +function drawHighlight( + stateModel: LinearApolloDisplayRendering, ctx: CanvasRenderingContext2D, - x: number, - y: number, - width: number, - height: number, - color: string, + feature: AnnotationFeature, + selected = false, ) { - drawBox(ctx, x + 1, y + 1, width - 2, height - 2, color) + const { apolloRowHeight, lgv, theme } = stateModel + const position = stateModel.getFeatureLayoutPosition(feature) + if (!position) { + return + } + const { bpPerPx, displayedRegions, offsetPx } = lgv + const { layoutIndex, layoutRow } = position + const displayedRegion = displayedRegions[layoutIndex] + const { refName, reversed } = displayedRegion + const { length, max, min } = feature + const startPx = + (lgv.bpToPx({ + refName, + coord: reversed ? max : min, + regionNumber: layoutIndex, + })?.offsetPx ?? 0) - offsetPx + const top = layoutRow * apolloRowHeight + const widthPx = length / bpPerPx + ctx.fillStyle = selected + ? theme.palette.action.disabled + : theme.palette.action.focus + ctx.fillRect(startPx, top, widthPx, apolloRowHeight) } function draw( + display: LinearApolloDisplay, ctx: CanvasRenderingContext2D, feature: AnnotationFeature, row: number, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, + block: ContentBlock, ) { - const { apolloRowHeight: heightPx, lgv, selectedFeature, theme } = stateModel - const { bpPerPx, displayedRegions, offsetPx } = lgv - const displayedRegion = displayedRegions[displayedRegionIndex] - const minX = - (lgv.bpToPx({ - refName: displayedRegion.refName, - coord: feature.min, - regionNumber: displayedRegionIndex, - })?.offsetPx ?? 0) - offsetPx - const { reversed } = displayedRegion - const widthPx = feature.length / bpPerPx - const startPx = reversed ? minX - widthPx : minX - const top = row * heightPx - const backgroundColor = theme.palette.background.default - const textColor = theme.palette.text.primary - const featureBox: [number, number, number, number] = [ - startPx, - top, - widthPx, - heightPx, - ] - drawBoxOutline(ctx, ...featureBox, textColor) - if (widthPx <= 2) { - // Don't need to add details if the feature is too small to see them - return + const { apolloRowHeight, lgv, selectedFeature, theme } = display + const { bpPerPx } = lgv + const left = Math.round(getLeftPx(display, feature, block)) + const top = row * apolloRowHeight + const width = Math.round(feature.length / bpPerPx) + const height = apolloRowHeight + if (width > 2) { + ctx.fillStyle = theme.palette.background.default + ctx.fillRect(left, top, width, apolloRowHeight) } + strokeRectInner(ctx, left, top, width, height, theme.palette.text.primary) - drawBoxFill(ctx, startPx, top, widthPx, heightPx, backgroundColor) if (isSelectedFeature(feature, selectedFeature)) { - drawHighlight(stateModel, ctx, feature, true) + drawHighlight(display, ctx, feature, true) } } @@ -95,7 +112,7 @@ function drawDragPreview( const row = Math.floor(start.y / apolloRowHeight) const region = displayedRegions[start.regionNumber] - const rowCount = getRowCount(feature) + const rowCount = getRowCount() const featureEdgeBp = region.reversed ? region.end - feature[edge] @@ -112,36 +129,6 @@ function drawDragPreview( overlayCtx.fillRect(rectX, rectY, rectWidth, rectHeight) } -function drawHighlight( - stateModel: LinearApolloDisplayRendering, - ctx: CanvasRenderingContext2D, - feature: AnnotationFeature, - selected = false, -) { - const { apolloRowHeight, lgv, theme } = stateModel - const position = stateModel.getFeatureLayoutPosition(feature) - if (!position) { - return - } - const { bpPerPx, displayedRegions, offsetPx } = lgv - const { layoutIndex, layoutRow } = position - const displayedRegion = displayedRegions[layoutIndex] - const { refName, reversed } = displayedRegion - const { length, max, min } = feature - const startPx = - (lgv.bpToPx({ - refName, - coord: reversed ? max : min, - regionNumber: layoutIndex, - })?.offsetPx ?? 0) - offsetPx - const top = layoutRow * apolloRowHeight - const widthPx = length / bpPerPx - ctx.fillStyle = selected - ? theme.palette.action.disabled - : theme.palette.action.focus - ctx.fillRect(startPx, top, widthPx, apolloRowHeight) -} - function drawHover( stateModel: LinearApolloDisplay, ctx: CanvasRenderingContext2D, @@ -216,18 +203,6 @@ function drawTooltip( context.fillText(location, startPx + 2, textTop) } -export function drawBox( - ctx: CanvasRenderingContext2D, - x: number, - y: number, - width: number, - height: number, - color: string, -) { - ctx.fillStyle = color - ctx.fillRect(x, y, width, height) -} - function getContextMenuItems( display: LinearApolloDisplayMouseEvents, ): MenuItem[] { @@ -238,23 +213,34 @@ function getContextMenuItems( return getContextMenuItemsForFeature(display, hoveredFeature.feature) } -function getFeatureFromLayout( - feature: AnnotationFeature, - _bp: number, - _row: number, -): AnnotationFeature { - return feature +function getRowCount() { + return 1 } -function getRowCount(_feature: AnnotationFeature) { - return 1 +function getFeatureFromLayout( + _display: LinearApolloDisplay, + feature: AnnotationFeature, + bp: number, + row: number, +) { + if (row > 0) { + return + } + if (bp >= feature.min && bp <= feature.max) { + return feature + } + return } function getRowForFeature( - _feature: AnnotationFeature, - _childFeature: AnnotationFeature, -): number | undefined { - return 0 + _display: LinearApolloDisplay, + feature: AnnotationFeature, + childFeature: AnnotationFeature, +) { + if (feature._id === childFeature._id) { + return 0 + } + return } function onMouseDown( @@ -307,33 +293,6 @@ function onMouseUp( stateModel.showFeatureDetailsWidget(feature) } -/** @returns undefined if mouse not on the edge of this feature, otherwise 'start' or 'end' depending on which edge */ -function isMouseOnFeatureEdge( - mousePosition: MousePosition, - feature: AnnotationFeature, - stateModel: LinearApolloDisplay, -) { - const { refName, regionNumber, x } = mousePosition - const { lgv } = stateModel - const { offsetPx } = lgv - const minPxInfo = lgv.bpToPx({ refName, coord: feature.min, regionNumber }) - const maxPxInfo = lgv.bpToPx({ refName, coord: feature.max, regionNumber }) - if (minPxInfo !== undefined && maxPxInfo !== undefined) { - const minPx = minPxInfo.offsetPx - offsetPx - const maxPx = maxPxInfo.offsetPx - offsetPx - if (Math.abs(maxPx - minPx) < 8) { - return - } - if (Math.abs(minPx - x) < 4) { - return 'min' - } - if (Math.abs(maxPx - x) < 4) { - return 'max' - } - } - return -} - export const boxGlyph: Glyph = { draw, drawDragPreview, diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/CDSGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/CDSGlyph.ts new file mode 100644 index 000000000..ac156f89c --- /dev/null +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/CDSGlyph.ts @@ -0,0 +1,192 @@ +import { + type AnnotationFeature, + type TranscriptPartCoding, +} from '@apollo-annotation/mst' +import { type MenuItem } from '@jbrowse/core/ui' +import { getFrame } from '@jbrowse/core/util' +import { type ContentBlock } from '@jbrowse/core/util/blockTypes' + +import { type LinearApolloDisplay } from '../stateModel' + +import { type Glyph } from './Glyph' +import { getLeftPx, strokeRectInner } from './util' + +function drawCDSLocation( + display: LinearApolloDisplay, + ctx: CanvasRenderingContext2D, + cdsLocation: TranscriptPartCoding, + strand: 1 | -1 | undefined, + row: number, + block: ContentBlock, +) { + const { apolloRowHeight, canvasPatterns, lgv, theme } = display + const { bpPerPx } = lgv + const left = Math.round(getLeftPx(display, cdsLocation, block)) + const width = Math.round((cdsLocation.max - cdsLocation.min) / bpPerPx) + const halfHeight = Math.round(apolloRowHeight / 2) + const top = row * apolloRowHeight + if (width > 2) { + const frame = getFrame( + cdsLocation.min, + cdsLocation.max, + strand ?? 1, + cdsLocation.phase, + ) + const frameColor = theme.palette.framesCDS.at(frame)?.main + ctx.fillStyle = frameColor ?? 'black' + ctx.fillRect(left, top, width, apolloRowHeight) + const forwardFill = canvasPatterns.forward + const backwardFill = canvasPatterns.backward + if (forwardFill && backwardFill && strand) { + const { reversed } = block + const reversal = reversed ? -1 : 1 + const [topFill, bottomFill] = + strand * reversal === 1 + ? [forwardFill, backwardFill] + : [backwardFill, forwardFill] + ctx.fillStyle = topFill + ctx.fillRect(left, top, width, halfHeight) + ctx.fillStyle = bottomFill + ctx.fillRect(left, top + halfHeight, width, halfHeight) + } + } + strokeRectInner( + ctx, + left, + top, + width, + apolloRowHeight, + theme.palette.text.primary, + ) +} + +function draw( + display: LinearApolloDisplay, + ctx: CanvasRenderingContext2D, + cds: AnnotationFeature, + row: number, + block: ContentBlock, +) { + const transcript = cds.parent + if (!transcript) { + return + } + const { cdsLocations } = transcript + const thisCDSLocations = cdsLocations.find((loc) => { + const min = loc.at(cds.strand === 1 ? 0 : -1)?.min + const max = loc.at(cds.strand === 1 ? -1 : 0)?.max + return cds.min === min && cds.max === max + }) + if (!thisCDSLocations) { + return + } + for (const cdsLocation of thisCDSLocations) { + drawCDSLocation(display, ctx, cdsLocation, cds.strand, row, block) + } +} + +function getRowCount() { + return 1 +} + +function getFeatureFromLayout( + _display: LinearApolloDisplay, + feature: AnnotationFeature, + bp: number, + row: number, +) { + if (row > 0) { + return + } + if (bp >= feature.min && bp <= feature.max) { + return feature + } + return +} + +function getRowForFeature( + _display: LinearApolloDisplay, + feature: AnnotationFeature, + childFeature: AnnotationFeature, +) { + if (feature._id === childFeature._id) { + return 0 + } + return +} + +function drawHover() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// overlayCtx: CanvasRenderingContext2D, + +function drawDragPreview() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// ctx: CanvasRenderingContext2D, + +function onMouseDown() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseMove() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseLeave() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseUp() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function drawTooltip() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// context: CanvasRenderingContext2D, + +function getContextMenuItemsForFeature(): MenuItem[] { + return [] + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// sourceFeature: AnnotationFeature, + +function getContextMenuItems(): MenuItem[] { + return [] + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, + +export const cdsGlyph: Glyph = { + draw, + drawDragPreview, + drawHover, + drawTooltip, + getContextMenuItems, + getContextMenuItemsForFeature, + getFeatureFromLayout, + getRowCount, + getRowForFeature, + onMouseDown, + onMouseLeave, + onMouseMove, + onMouseUp, +} diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts new file mode 100644 index 000000000..047563bee --- /dev/null +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts @@ -0,0 +1,150 @@ +import { type AnnotationFeature } from '@apollo-annotation/mst' +import { type MenuItem } from '@jbrowse/core/ui' +import { type ContentBlock } from '@jbrowse/core/util/blockTypes' + +import { type LinearApolloDisplay } from '../stateModel' + +import { type Glyph } from './Glyph' +import { getLeftPx, strokeRectInner } from './util' + +function draw( + display: LinearApolloDisplay, + ctx: CanvasRenderingContext2D, + exon: AnnotationFeature, + row: number, + block: ContentBlock, +) { + const { apolloRowHeight, canvasPatterns, lgv, theme } = display + const { bpPerPx } = lgv + const left = Math.round(getLeftPx(display, exon, block)) + const width = Math.round(exon.length / bpPerPx) + const height = Math.round(0.6 * apolloRowHeight) + const halfHeight = Math.round(height / 2) + const top = Math.round(halfHeight / 2) + row * apolloRowHeight + if (width > 2) { + ctx.fillStyle = 'rgb(211,211,211)' + ctx.fillRect(left, top, width, height) + const forwardFill = canvasPatterns.forward + const backwardFill = canvasPatterns.backward + const { strand } = exon + if (forwardFill && backwardFill && strand) { + const { reversed } = block + const reversal = reversed ? -1 : 1 + const [topFill, bottomFill] = + strand * reversal === 1 + ? [forwardFill, backwardFill] + : [backwardFill, forwardFill] + ctx.fillStyle = topFill + ctx.fillRect(left, top, width, halfHeight) + ctx.fillStyle = bottomFill + ctx.fillRect(left, top + halfHeight, width, halfHeight) + } + } + strokeRectInner(ctx, left, top, width, height, theme.palette.text.primary) +} + +function getRowCount() { + return 1 +} + +function getFeatureFromLayout( + _display: LinearApolloDisplay, + feature: AnnotationFeature, + bp: number, + row: number, +) { + if (row > 0) { + return + } + if (bp >= feature.min && bp <= feature.max) { + return feature + } + return +} + +function getRowForFeature( + _display: LinearApolloDisplay, + feature: AnnotationFeature, + childFeature: AnnotationFeature, +) { + if (feature._id === childFeature._id) { + return 0 + } + return +} + +function drawHover() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// overlayCtx: CanvasRenderingContext2D, + +function drawDragPreview() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// ctx: CanvasRenderingContext2D, + +function onMouseDown() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseMove() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseLeave() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseUp() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function drawTooltip() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// context: CanvasRenderingContext2D, + +function getContextMenuItemsForFeature(): MenuItem[] { + return [] + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// sourceFeature: AnnotationFeature, + +function getContextMenuItems(): MenuItem[] { + return [] + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, + +export const exonGlyph: Glyph = { + draw, + drawDragPreview, + drawHover, + drawTooltip, + getContextMenuItems, + getContextMenuItemsForFeature, + getFeatureFromLayout, + getRowCount, + getRowForFeature, + onMouseDown, + onMouseLeave, + onMouseMove, + onMouseUp, +} diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts index 394b34220..c763b7157 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts @@ -5,14 +5,13 @@ import { type MenuItem } from '@jbrowse/core/ui' import { type AbstractSessionModel, getContainingView, - getFrame, intersection2, isSessionModelWithWidgets, } from '@jbrowse/core/util' +import { type ContentBlock } from '@jbrowse/core/util/blockTypes' import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import { alpha } from '@mui/material' -import { type OntologyRecord } from '../../OntologyManager' import { MergeExons, MergeTranscripts, SplitExon } from '../../components' import { type MousePosition, @@ -32,431 +31,187 @@ import { import { getRelatedFeatures } from '../../util/annotationFeatureUtils' import { type LinearApolloDisplay } from '../stateModel' import { type LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents' -import { type LinearApolloDisplayRendering } from '../stateModel/rendering' import { type CanvasMouseEvent } from '../types' import { boxGlyph } from './BoxGlyph' import { type Glyph } from './Glyph' +import { transcriptGlyph } from './TranscriptGlyph' +import { getLeftPx, strokeRectInner } from './util' -let forwardFillLight: CanvasPattern | null = null -let backwardFillLight: CanvasPattern | null = null -let forwardFillDark: CanvasPattern | null = null -let backwardFillDark: CanvasPattern | null = null -const canvas = globalThis.document.createElement('canvas') -// @ts-expect-error getContext is undefined in the web worker -// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition -if (canvas?.getContext) { - for (const direction of ['forward', 'backward']) { - for (const themeMode of ['light', 'dark']) { - const canvas = document.createElement('canvas') - const canvasSize = 10 - canvas.width = canvas.height = canvasSize - const ctx = canvas.getContext('2d') - if (ctx) { - const stripeColor1 = - themeMode === 'light' ? 'rgba(0,0,0,0)' : 'rgba(0,0,0,0.75)' - const stripeColor2 = - themeMode === 'light' ? 'rgba(255,255,255,0.25)' : 'rgba(0,0,0,0.50)' - const gradient = - direction === 'forward' - ? ctx.createLinearGradient(0, canvasSize, canvasSize, 0) - : ctx.createLinearGradient(0, 0, canvasSize, canvasSize) - gradient.addColorStop(0, stripeColor1) - gradient.addColorStop(0.25, stripeColor1) - gradient.addColorStop(0.25, stripeColor2) - gradient.addColorStop(0.5, stripeColor2) - gradient.addColorStop(0.5, stripeColor1) - gradient.addColorStop(0.75, stripeColor1) - gradient.addColorStop(0.75, stripeColor2) - gradient.addColorStop(1, stripeColor2) - ctx.fillStyle = gradient - ctx.fillRect(0, 0, 10, 10) - if (direction === 'forward') { - if (themeMode === 'light') { - forwardFillLight = ctx.createPattern(canvas, 'repeat') - } else { - forwardFillDark = ctx.createPattern(canvas, 'repeat') - } - } else { - if (themeMode === 'light') { - backwardFillLight = ctx.createPattern(canvas, 'repeat') - } else { - backwardFillDark = ctx.createPattern(canvas, 'repeat') - } - } - } - } - } -} - -function drawBackground( - ctx: CanvasRenderingContext2D, +function getDraggableFeatureInfo( + mousePosition: MousePosition, feature: AnnotationFeature, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, - row: number, - color?: string, -) { - const { apolloRowHeight, lgv, session, theme } = stateModel - const { bpPerPx, displayedRegions, offsetPx } = lgv - const displayedRegion = displayedRegions[displayedRegionIndex] - const { refName, reversed } = displayedRegion + stateModel: LinearApolloDisplay, +): { feature: AnnotationFeature; edge: 'min' | 'max' } | undefined { + const { session } = stateModel const { apolloDataStore } = session const { featureTypeOntology } = apolloDataStore.ontologyManager if (!featureTypeOntology) { throw new Error('featureTypeOntology is undefined') } - - const topLevelFeatureMinX = - (lgv.bpToPx({ - refName, - coord: feature.min, - regionNumber: displayedRegionIndex, - })?.offsetPx ?? 0) - offsetPx - const topLevelFeatureWidthPx = feature.length / bpPerPx - const topLevelFeatureStartPx = reversed - ? topLevelFeatureMinX - topLevelFeatureWidthPx - : topLevelFeatureMinX - const topLevelFeatureTop = row * apolloRowHeight - const topLevelFeatureHeight = - getRowCount(feature, featureTypeOntology) * apolloRowHeight - - let selectedColor - if (color) { - selectedColor = color - } else { - selectedColor = readConfObject( - session.getPluginConfiguration(), - 'geneBackgroundColor', - { featureType: feature.type }, - ) as string - if (!selectedColor) { - selectedColor = alpha(theme.palette.background.paper, 0.6) - } - } - ctx.fillStyle = selectedColor - ctx.fillRect( - topLevelFeatureStartPx, - topLevelFeatureTop, - topLevelFeatureWidthPx, - topLevelFeatureHeight, - ) -} - -function draw( - ctx: CanvasRenderingContext2D, - feature: AnnotationFeature, - row: number, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, -): void { - const { apolloRowHeight, lgv, selectedFeature, session, theme } = stateModel - const { bpPerPx, displayedRegions, offsetPx } = lgv - const displayedRegion = displayedRegions[displayedRegionIndex] - const { refName, reversed } = displayedRegion - const rowHeight = apolloRowHeight - const cdsHeight = Math.round(0.9 * rowHeight) - const { children, strand } = feature - if (!children) { + const isGene = + featureTypeOntology.isTypeOf(feature.type, 'gene') || + featureTypeOntology.isTypeOf(feature.type, 'pseudogene') + const isTranscript = + featureTypeOntology.isTypeOf(feature.type, 'transcript') || + featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript') + const isCDS = featureTypeOntology.isTypeOf(feature.type, 'CDS') + if (isGene || isTranscript) { + // For gene glyphs, the sizes of genes and transcripts are determined by + // their child exons, so we don't make them draggable return } - const { apolloDataStore } = session - const { featureTypeOntology } = apolloDataStore.ontologyManager - if (!featureTypeOntology) { - throw new Error('featureTypeOntology is undefined') - } - - // Draw background for gene - drawBackground(ctx, feature, stateModel, displayedRegionIndex, row) - - // Draw lines on different rows for each transcript - let currentRow = 0 - for (const [, transcript] of children) { - const isTranscript = - featureTypeOntology.isTypeOf(transcript.type, 'transcript') || - featureTypeOntology.isTypeOf(transcript.type, 'pseudogenic_transcript') - if (!isTranscript) { - currentRow += 1 - continue + // So now the type of feature is either CDS or exon. If an exon and CDS edge + // are in the same place, we want to prioritize dragging the exon. If the + // feature we're on is a CDS, let's find any exon it may overlap. + const { bp, refName, regionNumber, x } = mousePosition + const { lgv } = stateModel + if (isCDS) { + const transcript = feature.parent + if (!transcript?.children) { + return } - const { children: transcriptChildren } = transcript - if (!transcriptChildren) { - continue + const exonChildren: AnnotationFeature[] = [] + for (const child of transcript.children.values()) { + const childIsExon = featureTypeOntology.isTypeOf(child.type, 'exon') + if (childIsExon) { + exonChildren.push(child) + } } - const cdsCount = getCDSCount(transcript, featureTypeOntology) - - for (const [, childFeature] of transcriptChildren) { - if (!featureTypeOntology.isTypeOf(childFeature.type, 'CDS')) { - continue + const overlappingExon = exonChildren.find((child) => { + const [start, end] = intersection2(bp - 1, bp, child.min, child.max) + return start !== undefined && end !== undefined + }) + if (overlappingExon) { + // We are on an exon, are we on the edge of it? + const minMax = getMinAndMaxPx(overlappingExon, refName, regionNumber, lgv) + if (minMax) { + const overlappingEdge = getOverlappingEdge(overlappingExon, x, minMax) + if (overlappingEdge) { + return overlappingEdge + } } - drawLine( - ctx, - stateModel, - displayedRegionIndex, - row, - transcript, - currentRow, - ) - currentRow += 1 } - - if (cdsCount === 0) { - drawLine( - ctx, - stateModel, - displayedRegionIndex, - row, - transcript, - currentRow, - ) - currentRow += 1 + } + // End of special cases, let's see if we're on the edge of this CDS or exon + const minMax = getMinAndMaxPx(feature, refName, regionNumber, lgv) + if (minMax) { + const overlappingEdge = getOverlappingEdge(feature, x, minMax) + if (overlappingEdge) { + return overlappingEdge } } + return +} - const forwardFill = - theme.palette.mode === 'dark' ? forwardFillDark : forwardFillLight - const backwardFill = - theme.palette.mode === 'dark' ? backwardFillDark : backwardFillLight - // Draw exon and CDS for each transcript - currentRow = 0 - for (const [, child] of children) { - if ( - !( - featureTypeOntology.isTypeOf(child.type, 'transcript') || - featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript') - ) - ) { - boxGlyph.draw(ctx, child, row, stateModel, displayedRegionIndex) - currentRow += 1 - continue - } - const cdsCount = getCDSCount(child, featureTypeOntology) - if (cdsCount != 0) { - for (const cdsRow of child.cdsLocations) { - const { children: transcriptChildren } = child - if (!transcriptChildren) { - continue - } - for (const [, exon] of transcriptChildren) { - if (!featureTypeOntology.isTypeOf(exon.type, 'exon')) { - continue - } - drawExon( - ctx, - stateModel, - displayedRegionIndex, - row, - exon, - currentRow, - strand, - forwardFill, - backwardFill, - ) - } - for (const cds of cdsRow) { - const cdsWidthPx = (cds.max - cds.min) / bpPerPx - const minX = - (lgv.bpToPx({ - refName, - coord: cds.min, - regionNumber: displayedRegionIndex, - })?.offsetPx ?? 0) - offsetPx - const cdsStartPx = reversed ? minX - cdsWidthPx : minX - ctx.fillStyle = theme.palette.text.primary - const cdsTop = - (row + currentRow) * rowHeight + (rowHeight - cdsHeight) / 2 - ctx.fillRect(cdsStartPx, cdsTop, cdsWidthPx, cdsHeight) - if (cdsWidthPx > 2) { - ctx.clearRect( - cdsStartPx + 1, - cdsTop + 1, - cdsWidthPx - 2, - cdsHeight - 2, - ) - const frame = getFrame( - cds.min, - cds.max, - child.strand ?? 1, - cds.phase, - ) - const frameColor = theme.palette.framesCDS.at(frame)?.main - ctx.fillStyle = frameColor ?? 'black' - ctx.fillRect( - cdsStartPx + 1, - cdsTop + 1, - cdsWidthPx - 2, - cdsHeight - 2, - ) - if (forwardFill && backwardFill && strand) { - const reversal = reversed ? -1 : 1 - const [topFill, bottomFill] = - strand * reversal === 1 - ? [forwardFill, backwardFill] - : [backwardFill, forwardFill] - ctx.fillStyle = topFill - ctx.fillRect( - cdsStartPx + 1, - cdsTop + 1, - cdsWidthPx - 2, - (cdsHeight - 2) / 2, - ) - ctx.fillStyle = bottomFill - ctx.fillRect( - cdsStartPx + 1, - cdsTop + (cdsHeight - 2) / 2, - cdsWidthPx - 2, - (cdsHeight - 2) / 2, - ) - } - } - } - currentRow += 1 - } - } +interface LayoutRow { + feature: AnnotationFeature + glyph: Glyph + rowInFeature: number +} - const { children: transcriptChildren } = child - // Draw exons for non-coding genes - if (cdsCount === 0 && transcriptChildren) { - for (const [, exon] of transcriptChildren) { - if (!featureTypeOntology.isTypeOf(exon.type, 'exon')) { - continue - } - drawExon( - ctx, - stateModel, - displayedRegionIndex, - row, - exon, - currentRow, - strand, - forwardFill, - backwardFill, - ) - } - currentRow += 1 - } +function getLayoutRows( + display: LinearApolloDisplay, + feature: AnnotationFeature, +): LayoutRow[] { + const { children } = feature + if (!children) { + return [] } - if (selectedFeature && containsSelectedFeature(feature, selectedFeature)) { - drawHighlight(stateModel, ctx, selectedFeature, true) + const rows: LayoutRow[] = [] + const { session } = display + for (const [, child] of children) { + const isTranscript = isTranscriptFeature(child, session) + const glyph = isTranscript ? transcriptGlyph : boxGlyph + const newRowCount = glyph.getRowCount(display, child) + for (let i = 0; i < newRowCount; i++) { + rows.push({ feature: child, glyph, rowInFeature: i }) + } } + + return rows } -function drawExon( +function drawHighlight( + stateModel: LinearApolloDisplay, ctx: CanvasRenderingContext2D, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, - row: number, - exon: AnnotationFeature, - currentRow: number, - strand: number | undefined, - forwardFill: CanvasPattern | null, - backwardFill: CanvasPattern | null, + feature: AnnotationFeature, + selected = false, ) { const { apolloRowHeight, lgv, theme } = stateModel + + const position = stateModel.getFeatureLayoutPosition(feature) + if (!position) { + return + } const { bpPerPx, displayedRegions, offsetPx } = lgv - const displayedRegion = displayedRegions[displayedRegionIndex] + const { featureRow, layoutIndex, layoutRow } = position + const displayedRegion = displayedRegions[layoutIndex] const { refName, reversed } = displayedRegion - - const minX = + const { length, max, min } = feature + const startPx = (lgv.bpToPx({ refName, - coord: exon.min, - regionNumber: displayedRegionIndex, + coord: reversed ? max : min, + regionNumber: layoutIndex, })?.offsetPx ?? 0) - offsetPx - const widthPx = exon.length / bpPerPx - const startPx = reversed ? minX - widthPx : minX + const row = layoutRow + featureRow + const top = row * apolloRowHeight + const widthPx = length / bpPerPx + ctx.fillStyle = selected + ? theme.palette.action.disabled + : theme.palette.action.focus - const top = (row + currentRow) * apolloRowHeight - const exonHeight = Math.round(0.6 * apolloRowHeight) - const exonTop = top + (apolloRowHeight - exonHeight) / 2 - ctx.fillStyle = theme.palette.text.primary - ctx.fillRect(startPx, exonTop, widthPx, exonHeight) - if (widthPx > 2) { - ctx.clearRect(startPx + 1, exonTop + 1, widthPx - 2, exonHeight - 2) - ctx.fillStyle = 'rgb(211,211,211)' - ctx.fillRect(startPx + 1, exonTop + 1, widthPx - 2, exonHeight - 2) - if (forwardFill && backwardFill && strand) { - const reversal = reversed ? -1 : 1 - const [topFill, bottomFill] = - strand * reversal === 1 - ? [forwardFill, backwardFill] - : [backwardFill, forwardFill] - ctx.fillStyle = topFill - ctx.fillRect(startPx + 1, exonTop + 1, widthPx - 2, (exonHeight - 2) / 2) - ctx.fillStyle = bottomFill - ctx.fillRect( - startPx + 1, - exonTop + 1 + (exonHeight - 2) / 2, - widthPx - 2, - (exonHeight - 2) / 2, - ) - } - } + ctx.fillRect( + startPx, + top, + widthPx, + apolloRowHeight * getRowCount(stateModel, feature), + ) } -function* range(start: number, stop: number, step = 1): Generator { - if (start === stop) { - return +function draw( + display: LinearApolloDisplay, + ctx: CanvasRenderingContext2D, + gene: AnnotationFeature, + row: number, + block: ContentBlock, +): void { + const { apolloRowHeight, lgv, theme, selectedFeature, session } = display + const { bpPerPx } = lgv + const left = Math.round(getLeftPx(display, gene, block)) + const width = Math.round(gene.length / bpPerPx) + const top = row * apolloRowHeight + const height = getRowCount(display, gene) * apolloRowHeight + if (width > 2) { + let selectedColor = readConfObject( + session.getPluginConfiguration(), + 'geneBackgroundColor', + { featureType: gene.type }, + ) as string + selectedColor = alpha(theme.palette.background.paper, 0.6) + ctx.fillStyle = selectedColor + ctx.fillRect(left, top, width, height) } - if (start < stop) { - for (let i = start; i < stop; i += step) { - yield i - } + strokeRectInner(ctx, left, top, width, height, theme.palette.text.primary) + const { children } = gene + if (!children) { return } - for (let i = start; i > stop; i -= step) { - yield i + + // Draw lines on different rows for each transcript + const rows = getLayoutRows(display, gene) + for (const [idx, layoutRow] of rows.entries()) { + const { feature: rowFeature, glyph, rowInFeature } = layoutRow + if (rowInFeature > 1) { + continue + } + glyph.draw(display, ctx, rowFeature, row + idx, block) } -} -function drawLine( - ctx: CanvasRenderingContext2D, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, - row: number, - transcript: AnnotationFeature, - currentRow: number, -) { - const { apolloRowHeight, lgv, theme } = stateModel - const { bpPerPx, displayedRegions, offsetPx } = lgv - const displayedRegion = displayedRegions[displayedRegionIndex] - const { refName, reversed } = displayedRegion - const minX = - (lgv.bpToPx({ - refName, - coord: transcript.min, - regionNumber: displayedRegionIndex, - })?.offsetPx ?? 0) - offsetPx - const widthPx = Math.round(transcript.length / bpPerPx) - const startPx = reversed ? minX - widthPx : minX - const height = - Math.round((currentRow + 1 / 2) * apolloRowHeight) + row * apolloRowHeight - ctx.strokeStyle = theme.palette.text.primary - const { strand = 1 } = transcript - ctx.beginPath() - // If view is reversed, draw forward as reverse and vice versa - const effectiveStrand = strand * (reversed ? -1 : 1) - // Draw the transcript line, and extend it out a bit on the 3` end - const lineStart = startPx - (effectiveStrand === -1 ? 5 : 0) - const lineEnd = startPx + widthPx + (effectiveStrand === -1 ? 0 : 5) - ctx.moveTo(lineStart, height) - ctx.lineTo(lineEnd, height) - // Now to draw arrows every 20 pixels along the line - // Make the arrow range a bit shorter to avoid an arrow hanging off the 5` end - const arrowsStart = lineStart + (effectiveStrand === -1 ? 0 : 3) - const arrowsEnd = lineEnd - (effectiveStrand === -1 ? 3 : 0) - // Offset determines if the arrows face left or right - const offset = effectiveStrand === -1 ? 3 : -3 - const arrowRange = - effectiveStrand === -1 - ? range(arrowsStart, arrowsEnd, 20) - : range(arrowsEnd, arrowsStart, 20) - for (const arrowLocation of arrowRange) { - ctx.moveTo(arrowLocation + offset, height + offset) - ctx.lineTo(arrowLocation, height) - ctx.lineTo(arrowLocation + offset, height - offset) + if (selectedFeature && containsSelectedFeature(gene, selectedFeature)) { + drawHighlight(display, ctx, selectedFeature, true) } - ctx.stroke() } function drawDragPreview( @@ -488,48 +243,6 @@ function drawDragPreview( overlayCtx.fillRect(rectX, rectY, rectWidth, rectHeight) } -function drawHighlight( - stateModel: LinearApolloDisplayRendering, - ctx: CanvasRenderingContext2D, - feature: AnnotationFeature, - selected = false, -) { - const { apolloRowHeight, lgv, session, theme } = stateModel - const { featureTypeOntology } = session.apolloDataStore.ontologyManager - - const position = stateModel.getFeatureLayoutPosition(feature) - if (!position) { - return - } - const { bpPerPx, displayedRegions, offsetPx } = lgv - const { featureRow, layoutIndex, layoutRow } = position - const displayedRegion = displayedRegions[layoutIndex] - const { refName, reversed } = displayedRegion - const { length, max, min } = feature - const startPx = - (lgv.bpToPx({ - refName, - coord: reversed ? max : min, - regionNumber: layoutIndex, - })?.offsetPx ?? 0) - offsetPx - const row = layoutRow + featureRow - const top = row * apolloRowHeight - const widthPx = length / bpPerPx - ctx.fillStyle = selected - ? theme.palette.action.disabled - : theme.palette.action.focus - - if (!featureTypeOntology) { - throw new Error('featureTypeOntology is undefined') - } - ctx.fillRect( - startPx, - top, - widthPx, - apolloRowHeight * getRowCount(feature, featureTypeOntology), - ) -} - function drawHover( stateModel: LinearApolloDisplay, ctx: CanvasRenderingContext2D, @@ -542,161 +255,61 @@ function drawHover( drawHighlight(stateModel, ctx, hoveredFeature.feature) } -function getFeatureFromLayout( - feature: AnnotationFeature, - bp: number, - row: number, - featureTypeOntology: OntologyRecord, -): AnnotationFeature | undefined { - const featureInThisRow: AnnotationFeature[] = - featuresForRow(feature, featureTypeOntology)[row] || [] - for (const f of featureInThisRow) { - let featureObj - if (bp >= f.min && bp <= f.max && f.parent) { - featureObj = f - } - if (!featureObj) { - continue - } - if ( - featureTypeOntology.isTypeOf(featureObj.type, 'CDS') && - featureObj.parent && - (featureTypeOntology.isTypeOf(featureObj.parent.type, 'transcript') || - featureTypeOntology.isTypeOf( - featureObj.parent.type, - 'pseudogenic_transcript', - )) - ) { - const { cdsLocations } = featureObj.parent - for (const cdsLoc of cdsLocations) { - for (const loc of cdsLoc) { - if (bp >= loc.min && bp <= loc.max) { - return featureObj - } - } - } - - // If mouse position is in the intron region, return the transcript - return featureObj.parent - } - // If mouse position is in a feature that is not a CDS, return the feature - return featureObj - } - return feature -} - -function getCDSCount( - feature: AnnotationFeature, - featureTypeOntology: OntologyRecord, -): number { - const { children, type } = feature - if (!children) { - return 0 - } - const isMrna = featureTypeOntology.isTypeOf(type, 'transcript') - let cdsCount = 0 - if (isMrna) { - for (const [, child] of children) { - if (featureTypeOntology.isTypeOf(child.type, 'CDS')) { - cdsCount += 1 - } - } - } - return cdsCount -} - function getRowCount( + display: LinearApolloDisplay, feature: AnnotationFeature, - featureTypeOntology: OntologyRecord, - _bpPerPx?: number, ): number { - const { children, type } = feature - if (!children) { + const layoutRows = getLayoutRows(display, feature) + if (layoutRows.length === 0) { return 1 } - const isTranscript = - featureTypeOntology.isTypeOf(type, 'transcript') || - featureTypeOntology.isTypeOf(type, 'pseudogenic_transcript') - let rowCount = 0 - if (isTranscript) { - for (const [, child] of children) { - if (featureTypeOntology.isTypeOf(child.type, 'CDS')) { - rowCount += 1 - } - } - - // return 1 if there are no CDSs for non coding genes - return rowCount === 0 ? 1 : rowCount - } - for (const [, child] of children) { - rowCount += getRowCount(child, featureTypeOntology) - } - return rowCount + return layoutRows.length } -/** - * A list of all the subfeatures for each row for a given feature, as well as - * the feature itself. - * If the row contains a transcript, the order is CDS -\> exon -\> transcript -\> gene - * If the row does not contain an transcript, the order is subfeature -\> gene - */ -function featuresForRow( +function getFeatureFromLayout( + display: LinearApolloDisplay, feature: AnnotationFeature, - featureTypeOntology: OntologyRecord, -): AnnotationFeature[][] { - const isGene = - featureTypeOntology.isTypeOf(feature.type, 'gene') || - featureTypeOntology.isTypeOf(feature.type, 'pseudogene') - if (!isGene) { - throw new Error('Top level feature for GeneGlyph must have type "gene"') + bp: number, + row: number, +) { + const layoutRow = getLayoutRows(display, feature).at(row) + if (!layoutRow) { + return } - const { children } = feature - if (!children) { - return [[feature]] + const { feature: rowFeature, glyph, rowInFeature } = layoutRow + const subFeature = glyph.getFeatureFromLayout( + display, + rowFeature, + bp, + rowInFeature, + ) + if (subFeature) { + return subFeature } - const features: AnnotationFeature[][] = [] - for (const [, child] of children) { - if ( - !( - featureTypeOntology.isTypeOf(child.type, 'transcript') || - featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript') - ) - ) { - features.push([child, feature]) - continue - } - if (!child.children) { - continue - } - const cdss: AnnotationFeature[] = [] - const exons: AnnotationFeature[] = [] - for (const [, grandchild] of child.children) { - if (featureTypeOntology.isTypeOf(grandchild.type, 'CDS')) { - cdss.push(grandchild) - } else if (featureTypeOntology.isTypeOf(grandchild.type, 'exon')) { - exons.push(grandchild) - } - } - for (const cds of cdss) { - features.push([cds, ...exons, child, feature]) - } - if (cdss.length === 0) { - features.push([...exons, child, feature]) - } + if (bp >= feature.min && bp <= feature.max) { + return feature } - return features + return } function getRowForFeature( + display: LinearApolloDisplay, feature: AnnotationFeature, childFeature: AnnotationFeature, - featureTypeOntology: OntologyRecord, ) { - const rows = featuresForRow(feature, featureTypeOntology) + const rows = getLayoutRows(display, feature) for (const [idx, row] of rows.entries()) { - if (row.some((feature) => feature._id === childFeature._id)) { + if (row.feature._id === childFeature._id) { return idx } + const subFeatureRow = row.glyph.getRowForFeature( + display, + row.feature, + childFeature, + ) + if (subFeatureRow !== undefined) { + return subFeatureRow + idx + } } return } @@ -759,72 +372,6 @@ function onMouseUp( selectFeatureAndOpenWidget(stateModel, feature) } -function getDraggableFeatureInfo( - mousePosition: MousePosition, - feature: AnnotationFeature, - stateModel: LinearApolloDisplay, -): { feature: AnnotationFeature; edge: 'min' | 'max' } | undefined { - const { session } = stateModel - const { apolloDataStore } = session - const { featureTypeOntology } = apolloDataStore.ontologyManager - if (!featureTypeOntology) { - throw new Error('featureTypeOntology is undefined') - } - const isGene = - featureTypeOntology.isTypeOf(feature.type, 'gene') || - featureTypeOntology.isTypeOf(feature.type, 'pseudogene') - const isTranscript = - featureTypeOntology.isTypeOf(feature.type, 'transcript') || - featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript') - const isCDS = featureTypeOntology.isTypeOf(feature.type, 'CDS') - if (isGene || isTranscript) { - // For gene glyphs, the sizes of genes and transcripts are determined by - // their child exons, so we don't make them draggable - return - } - // So now the type of feature is either CDS or exon. If an exon and CDS edge - // are in the same place, we want to prioritize dragging the exon. If the - // feature we're on is a CDS, let's find any exon it may overlap. - const { bp, refName, regionNumber, x } = mousePosition - const { lgv } = stateModel - if (isCDS) { - const transcript = feature.parent - if (!transcript?.children) { - return - } - const exonChildren: AnnotationFeature[] = [] - for (const child of transcript.children.values()) { - const childIsExon = featureTypeOntology.isTypeOf(child.type, 'exon') - if (childIsExon) { - exonChildren.push(child) - } - } - const overlappingExon = exonChildren.find((child) => { - const [start, end] = intersection2(bp - 1, bp, child.min, child.max) - return start !== undefined && end !== undefined - }) - if (overlappingExon) { - // We are on an exon, are we on the edge of it? - const minMax = getMinAndMaxPx(overlappingExon, refName, regionNumber, lgv) - if (minMax) { - const overlappingEdge = getOverlappingEdge(overlappingExon, x, minMax) - if (overlappingEdge) { - return overlappingEdge - } - } - } - } - // End of special cases, let's see if we're on the edge of this CDS or exon - const minMax = getMinAndMaxPx(feature, refName, regionNumber, lgv) - if (minMax) { - const overlappingEdge = getOverlappingEdge(feature, x, minMax) - if (overlappingEdge) { - return overlappingEdge - } - } - return -} - function getContextMenuItems( display: LinearApolloDisplayMouseEvents, mousePosition: MousePositionWithFeature, diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts index 76769d145..607b6609e 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts @@ -1,5 +1,6 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import { type MenuItem } from '@jbrowse/core/ui' +import { type ContentBlock } from '@jbrowse/core/util/blockTypes' import { alpha } from '@mui/material' import { @@ -10,87 +11,42 @@ import { import { getRelatedFeatures } from '../../util/annotationFeatureUtils' import { type LinearApolloDisplay } from '../stateModel' import { type LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents' -import { type LinearApolloDisplayRendering } from '../stateModel/rendering' -import { boxGlyph, drawBox } from './BoxGlyph' +import { boxGlyph } from './BoxGlyph' import { type Glyph } from './Glyph' +import { getLeftPx, strokeRectInner } from './util' -function featuresForRow(feature: AnnotationFeature): AnnotationFeature[][] { - const features = [[feature]] - if (feature.children) { - for (const [, child] of feature.children) { - features.push(...featuresForRow(child)) - } - } - return features -} - -function getRowCount(feature: AnnotationFeature) { - return featuresForRow(feature).length +interface LayoutRow { + feature: AnnotationFeature + glyph: Glyph + rowInFeature: number } -function draw( - ctx: CanvasRenderingContext2D, +function getLayoutRows( + display: LinearApolloDisplay, feature: AnnotationFeature, - row: number, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, -) { - const { selectedFeature } = stateModel - for (let i = 0; i < getRowCount(feature); i++) { - drawRow(ctx, feature, row + i, row, stateModel, displayedRegionIndex) - } - if (selectedFeature && containsSelectedFeature(feature, selectedFeature)) { - drawHighlight(stateModel, ctx, selectedFeature) +): LayoutRow[] { + const rows: LayoutRow[] = [ + { feature, glyph: genericChildGlyph, rowInFeature: 0 }, + ] + const { children } = feature + if (!children) { + return rows } -} - -function drawRow( - ctx: CanvasRenderingContext2D, - topLevelFeature: AnnotationFeature, - row: number, - topRow: number, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, -) { - const features = featuresForRow(topLevelFeature)[row - topRow] - for (const feature of features) { - drawFeature(ctx, feature, row, stateModel, displayedRegionIndex) - } -} - -function drawFeature( - ctx: CanvasRenderingContext2D, - feature: AnnotationFeature, - row: number, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, -) { - const { apolloRowHeight: heightPx, lgv, theme } = stateModel - const { bpPerPx, displayedRegions, offsetPx } = lgv - const displayedRegion = displayedRegions[displayedRegionIndex] - const minX = - (lgv.bpToPx({ - refName: displayedRegion.refName, - coord: feature.min, - regionNumber: displayedRegionIndex, - })?.offsetPx ?? 0) - offsetPx - const { reversed } = displayedRegion - const widthPx = feature.length / bpPerPx - const startPx = reversed ? minX - widthPx : minX - const top = row * heightPx - const rowCount = getRowCount(feature) - const groupingColor = alpha(theme.palette.background.paper, 0.6) - if (rowCount > 1) { - // draw background that encapsulates all child features - const featureHeight = rowCount * heightPx - drawBox(ctx, startPx, top, widthPx, featureHeight, groupingColor) + // eslint-disable-next-line @typescript-eslint/unbound-method + const { getGlyph } = display + for (const [, child] of children) { + const glyph = getGlyph(child) + const newRowCount = glyph.getRowCount(display, child) + for (let i = 0; i < newRowCount; i++) { + rows.push({ feature: child, glyph, rowInFeature: i }) + } } - boxGlyph.draw(ctx, feature, row, stateModel, displayedRegionIndex) + return rows } function drawHighlight( - stateModel: LinearApolloDisplayRendering, + stateModel: LinearApolloDisplay, ctx: CanvasRenderingContext2D, feature: AnnotationFeature, selected = false, @@ -117,7 +73,53 @@ function drawHighlight( ctx.fillStyle = selected ? theme.palette.action.disabled : theme.palette.action.focus - ctx.fillRect(startPx, top, widthPx, apolloRowHeight * getRowCount(feature)) + ctx.fillRect( + startPx, + top, + widthPx, + apolloRowHeight * getRowCount(stateModel, feature), + ) +} + +function draw( + display: LinearApolloDisplay, + ctx: CanvasRenderingContext2D, + feature: AnnotationFeature, + row: number, + block: ContentBlock, +) { + const { apolloRowHeight, lgv, selectedFeature, theme } = display + const { bpPerPx } = lgv + const left = Math.round(getLeftPx(display, feature, block)) + const top = row * apolloRowHeight + const width = Math.round(feature.length / bpPerPx) + const height = getRowCount(display, feature) * apolloRowHeight + if (width > 2) { + ctx.fillStyle = alpha(theme.palette.background.paper, 0.6) + ctx.fillRect(left, top, width, height) + } + strokeRectInner(ctx, left, top, width, height, theme.palette.text.primary) + boxGlyph.draw(display, ctx, feature, row, block) + strokeRectInner(ctx, left, top, width, height, theme.palette.text.primary) + const { children } = feature + if (!children) { + return + } + const childRows = getLayoutRows(display, feature).slice(1) + let rowOffset = 1 + for (const childRow of childRows) { + const { feature: childFeature, glyph, rowInFeature } = childRow + if (rowInFeature > 0) { + rowOffset += 1 + continue + } + glyph.draw(display, ctx, childFeature, row + rowOffset, block) + rowOffset += 1 + } + + if (selectedFeature && containsSelectedFeature(feature, selectedFeature)) { + drawHighlight(display, ctx, selectedFeature) + } } function drawHover( @@ -131,22 +133,41 @@ function drawHover( drawHighlight(stateModel, ctx, hoveredFeature.feature) } +function getRowCount(display: LinearApolloDisplay, feature: AnnotationFeature) { + const rows = getLayoutRows(display, feature) + return rows.length +} + function getFeatureFromLayout( + display: LinearApolloDisplay, feature: AnnotationFeature, bp: number, row: number, ) { - const layoutRow = featuresForRow(feature)[row] - return layoutRow.find((f) => bp >= f.min && bp <= f.max) + const layoutRows = getLayoutRows(display, feature) + const layoutRow = layoutRows.at(row) + if (!layoutRow) { + return + } + const { feature: rowFeature, glyph, rowInFeature } = layoutRow + if (rowInFeature === 0) { + if (bp >= rowFeature.min && bp <= rowFeature.max) { + return rowFeature + } + return + } + return glyph.getFeatureFromLayout(display, rowFeature, bp, rowInFeature) } function getRowForFeature( + display: LinearApolloDisplay, feature: AnnotationFeature, childFeature: AnnotationFeature, ) { - const rows = featuresForRow(feature) + const rows = getLayoutRows(display, feature) for (const [idx, row] of rows.entries()) { - if (row.some((feature) => feature._id === childFeature._id)) { + const { feature: rowFeature } = row + if (rowFeature._id === childFeature._id) { return idx } } diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/Glyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/Glyph.ts index 3c0004513..df8e7900b 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/Glyph.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/Glyph.ts @@ -1,39 +1,21 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import { type MenuItem } from '@jbrowse/core/ui' +import { type ContentBlock } from '@jbrowse/core/util/blockTypes' -import { type OntologyRecord } from '../../OntologyManager' import { type MousePositionWithFeature } from '../../util' +import { type LinearApolloDisplay } from '../stateModel' import { type LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents' -import { type LinearApolloDisplayRendering } from '../stateModel/rendering' import { type CanvasMouseEvent } from '../types' export interface Glyph { - /** @returns number of layout rows used by this glyph with this feature and zoom level */ - getRowCount( - feature: AnnotationFeature, - featureTypeOntology: OntologyRecord, - bpPerPx: number, - ): number /** draw the feature's primary rendering on the canvas */ draw( + display: LinearApolloDisplay, ctx: CanvasRenderingContext2D, feature: AnnotationFeature, row: number, - stateModel: LinearApolloDisplayRendering, - displayedRegionIndex: number, + block: ContentBlock, ): void - /** @returns the feature or subfeature at the given bp and row number in this glyph's layout */ - getFeatureFromLayout( - feature: AnnotationFeature, - bp: number, - row: number, - featureTypeOntology: OntologyRecord, - ): AnnotationFeature | undefined - getRowForFeature( - feature: AnnotationFeature, - childFeature: AnnotationFeature, - featureTypeOntology: OntologyRecord, - ): number | undefined drawHover( display: LinearApolloDisplayMouseEvents, @@ -45,6 +27,28 @@ export interface Glyph { ctx: CanvasRenderingContext2D, ): void + /** @returns number of layout rows used by this glyph with this feature and zoom level */ + getRowCount(display: LinearApolloDisplay, feature: AnnotationFeature): number + /** + * @returns the feature or subfeature at the given bp and row number in this + * glyph's layout, or undefined if one does not exist + */ + getFeatureFromLayout( + display: LinearApolloDisplay, + feature: AnnotationFeature, + bp: number, + row: number, + ): AnnotationFeature | undefined + /** + * @returns the row in this glyph where a child feature appears, or undefined + * if the feature does not appear + */ + getRowForFeature( + display: LinearApolloDisplay, + feature: AnnotationFeature, + childFeature: AnnotationFeature, + ): number | undefined + onMouseDown( display: LinearApolloDisplayMouseEvents, currentMousePosition: MousePositionWithFeature, diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts new file mode 100644 index 000000000..54174df40 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts @@ -0,0 +1,321 @@ +import { type AnnotationFeature } from '@apollo-annotation/mst' +import { type MenuItem } from '@jbrowse/core/ui' +import { type ContentBlock } from '@jbrowse/core/util/blockTypes' + +import { type MousePositionWithFeature } from '../../util' +import { isCDSFeature, isExonFeature } from '../../util/glyphUtils' +import { type LinearApolloDisplay } from '../stateModel' + +import { cdsGlyph } from './CDSGlyph' +import { exonGlyph } from './ExonGlyph' +import { type Glyph } from './Glyph' +import { getLeftPx } from './util' + +function* range(start: number, stop: number, step = 1): Generator { + if (start === stop) { + return + } + if (start < stop) { + for (let i = start; i < stop; i += step) { + yield i + } + return + } + for (let i = start; i > stop; i -= step) { + yield i + } +} + +function drawTranscriptLine( + display: LinearApolloDisplay, + ctx: CanvasRenderingContext2D, + transcript: AnnotationFeature, + row: number, + block: ContentBlock, +) { + const { apolloRowHeight, lgv, theme } = display + const { bpPerPx } = lgv + const { reversed } = block + const left = Math.round(getLeftPx(display, transcript, block)) + const width = Math.round(transcript.length / bpPerPx) + const top = Math.round(apolloRowHeight / 2) + row * apolloRowHeight + ctx.strokeStyle = theme.palette.text.primary + const { strand = 1 } = transcript + ctx.beginPath() + // If view is reversed, draw forward as reverse and vice versa + const effectiveStrand = strand * (reversed ? -1 : 1) + // Draw the transcript line, and extend it out a bit on the 3` end + const lineStart = left - (effectiveStrand === -1 ? 5 : 0) + const lineEnd = left + width + (effectiveStrand === -1 ? 0 : 5) + ctx.moveTo(lineStart, top) + ctx.lineTo(lineEnd, top) + // Now to draw arrows every 20 pixels along the line + // Make the arrow range a bit shorter to avoid an arrow hanging off the 5` end + const arrowsStart = lineStart + (effectiveStrand === -1 ? 0 : 3) + const arrowsEnd = lineEnd - (effectiveStrand === -1 ? 3 : 0) + // Offset determines if the arrows face left or right + const offset = effectiveStrand === -1 ? 3 : -3 + const arrowRange = + effectiveStrand === -1 + ? range(arrowsStart, arrowsEnd, 20) + : range(arrowsEnd, arrowsStart, 20) + for (const arrowLocation of arrowRange) { + ctx.moveTo(arrowLocation + offset, top + offset) + ctx.lineTo(arrowLocation, top) + ctx.lineTo(arrowLocation + offset, top - offset) + } + ctx.stroke() +} + +function getExonChildren( + display: LinearApolloDisplay, + transcript: AnnotationFeature, +): AnnotationFeature[] { + const { children } = transcript + if (!children) { + return [] + } + const { session } = display + return [...children.values()].filter((child) => isExonFeature(child, session)) +} + +function getNonExonChildren( + display: LinearApolloDisplay, + transcript: AnnotationFeature, +): AnnotationFeature[] { + const { children } = transcript + if (!children) { + return [] + } + const { session } = display + return [...children.values()].filter( + (child) => !isExonFeature(child, session), + ) +} + +interface LayoutRowFeature { + feature: AnnotationFeature + glyph: Glyph + rowInFeature: number +} + +type LayoutRow = LayoutRowFeature[] + +function getLayoutRows( + display: LinearApolloDisplay, + transcript: AnnotationFeature, +): LayoutRow[] { + const { children } = transcript + if (!children) { + return [] + } + const rows: LayoutRow[] = [] + const exons = getExonChildren(display, transcript) + const nonExonChildren = getNonExonChildren(display, transcript) + // Usually non-coding (no CDS) transcript + if (nonExonChildren.length === 0) { + const row: LayoutRow = [] + for (const exon of exons) { + row.push({ feature: exon, glyph: exonGlyph, rowInFeature: 0 }) + } + rows.push(row) + return rows + } + // eslint-disable-next-line @typescript-eslint/unbound-method + const { getGlyph, session } = display + let extraOffset = 0 + for (const [idx, child] of nonExonChildren.entries()) { + const row: LayoutRow = [] + if (isCDSFeature(child, session)) { + for (const exon of exons) { + row.push({ + feature: exon, + glyph: exonGlyph, + rowInFeature: idx + extraOffset, + }) + } + row.push({ + feature: child, + glyph: cdsGlyph, + rowInFeature: idx + extraOffset, + }) + } else { + const glyph = getGlyph(child) + const rowCount = glyph.getRowCount(display, child) + for (let i = 0; i < rowCount; i++) { + row.push({ feature: child, glyph, rowInFeature: i }) + } + extraOffset += rowCount - 1 + } + rows.push(row) + } + return rows +} + +function draw( + display: LinearApolloDisplay, + ctx: CanvasRenderingContext2D, + transcript: AnnotationFeature, + row: number, + block: ContentBlock, +) { + const rows = getLayoutRows(display, transcript) + if (rows.length === 0) { + drawTranscriptLine(display, ctx, transcript, row, block) + return + } + for (const [idx, layoutRow] of rows.entries()) { + drawTranscriptLine(display, ctx, transcript, row + idx, block) + for (const layoutFeature of layoutRow) { + const { feature, glyph, rowInFeature } = layoutFeature + if (rowInFeature > 1) { + continue + } + glyph.draw(display, ctx, feature, row + rowInFeature, block) + } + } +} + +function getRowCount(display: LinearApolloDisplay, feature: AnnotationFeature) { + const rows = getLayoutRows(display, feature) + if (rows.length === 0) { + return 1 + } + return rows.length +} + +function getFeatureFromLayout( + display: LinearApolloDisplay, + transcript: AnnotationFeature, + bp: number, + row: number, +) { + const layoutRow = getLayoutRows(display, transcript).at(row) + if (!layoutRow) { + return + } + // If it's in an intron, return the transcript + // Then if it's in an exon and the CDS, return the CDS + // Then if it's in an exon, return the exon + const isInTranscript = bp >= transcript.min && bp <= transcript.max + if (!isInTranscript) { + return + } + const { session } = display + const matchingExonLayout = layoutRow.find((layoutRowFeature) => { + const { feature } = layoutRowFeature + const isExon = isExonFeature(feature, session) + if (!isExon) { + return false + } + return bp >= feature.min && bp <= feature.max + }) + if (!matchingExonLayout) { + return transcript + } + const matchingCDSLayout = layoutRow.find((layoutRowFeature) => { + const { feature } = layoutRowFeature + const isCDS = isCDSFeature(feature, session) + if (!isCDS) { + return false + } + return bp >= feature.min && bp <= feature.max + }) + if (matchingCDSLayout) { + return matchingCDSLayout.feature + } + return matchingExonLayout.feature +} + +function getRowForFeature( + display: LinearApolloDisplay, + feature: AnnotationFeature, + childFeature: AnnotationFeature, +) { + const rows = getLayoutRows(display, feature) + for (const [idx, row] of rows.entries()) { + for (const rowFeature of row) { + if (rowFeature.feature._id === childFeature._id) { + return idx + } + } + } + return +} + +function drawHover() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// overlayCtx: CanvasRenderingContext2D, + +function drawDragPreview() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// ctx: CanvasRenderingContext2D, + +function onMouseDown() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseMove( + display: LinearApolloDisplay, + mousePosition: MousePositionWithFeature, +) { + const { feature, bp } = mousePosition + display.setHoveredFeature({ feature, bp }) +} + +function onMouseLeave() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function onMouseUp() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, +// event: CanvasMouseEvent, + +function drawTooltip() { + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// context: CanvasRenderingContext2D, + +function getContextMenuItemsForFeature(): MenuItem[] { + return [] + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// sourceFeature: AnnotationFeature, + +function getContextMenuItems(): MenuItem[] { + return [] + // Not implemented +} +// display: LinearApolloDisplayMouseEvents, +// currentMousePosition: MousePositionWithFeature, + +export const transcriptGlyph: Glyph = { + draw, + drawDragPreview, + drawHover, + drawTooltip, + getContextMenuItems, + getContextMenuItemsForFeature, + getFeatureFromLayout, + getRowCount, + getRowForFeature, + onMouseDown, + onMouseLeave, + onMouseMove, + onMouseUp, +} diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/index.ts index 35d65c9ca..097e07d3e 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/index.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/index.ts @@ -1,3 +1,4 @@ export * from './BoxGlyph' export * from './GeneGlyph' export * from './GenericChildGlyph' +export * from './TranscriptGlyph' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/util.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/util.ts index fba827d02..8e67d9fab 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/util.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/util.ts @@ -17,3 +17,20 @@ export function getLeftPx( featureLeftBpDistanceFromBlockLeftBp / bpPerPx return blockLeftPx + featureLeftPxDistanceFromBlockLeftPx } + +/** + * Perform a canvas strokeRect, but have the stroke be contained within the + * given rect instead of centered on it. + */ +export function strokeRectInner( + ctx: CanvasRenderingContext2D, + left: number, + top: number, + width: number, + height: number, + color: string, +) { + ctx.strokeStyle = color + ctx.lineWidth = 1 + ctx.strokeRect(left + 0.5, top + 0.5, width - 1, height - 1) +} diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts index 12c467570..e26779e60 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts @@ -8,7 +8,20 @@ import { autorun, observable } from 'mobx' import { addDisposer, isAlive } from 'mobx-state-tree' import { type ApolloSessionModel } from '../../session' -import { boxGlyph, geneGlyph, genericChildGlyph } from '../glyphs' +import { + isCDSFeature, + isExonFeature, + isGeneFeature, + isTranscriptFeature, +} from '../../util/glyphUtils' +import { + boxGlyph, + geneGlyph, + genericChildGlyph, + transcriptGlyph, +} from '../glyphs' +import { cdsGlyph } from '../glyphs/CDSGlyph' +import { exonGlyph } from '../glyphs/ExonGlyph' import { baseModelFactory } from './base' @@ -64,9 +77,18 @@ export function layoutsModelFactory( }, getGlyph(feature: AnnotationFeature) { const { topLevelFeature } = feature - if (topLevelFeature.looksLikeGene) { + if (isGeneFeature(topLevelFeature, self.session)) { return geneGlyph } + if (isTranscriptFeature(topLevelFeature, self.session)) { + return transcriptGlyph + } + if (isExonFeature(topLevelFeature, self.session)) { + return exonGlyph + } + if (isCDSFeature(topLevelFeature, self.session)) { + return cdsGlyph + } if (topLevelFeature.children?.size) { return genericChildGlyph } @@ -111,7 +133,8 @@ export function layoutsModelFactory( } const rowCount = self .getGlyph(feature) - .getRowCount(feature, featureTypeOntology, self.lgv.bpPerPx) + // @ts-expect-error ts doesn't understand mst extension + .getRowCount(self, feature) let startingRow = 0 let placed = false while (!placed) { @@ -153,8 +176,6 @@ export function layoutsModelFactory( }, getFeatureLayoutPosition(feature: AnnotationFeature) { const { featureLayouts } = this - const { featureTypeOntology } = - self.session.apolloDataStore.ontologyManager for (const [idx, layout] of featureLayouts.entries()) { for (const [layoutRowNum, layoutRow] of layout) { for (const [featureRowNum, layoutFeatureId] of layoutRow) { @@ -176,12 +197,10 @@ export function layoutsModelFactory( } } if (layoutFeature.hasDescendant(feature._id)) { - if (!featureTypeOntology) { - throw new Error('featureTypeOntology is undefined') - } const row = self .getGlyph(layoutFeature) - .getRowForFeature(layoutFeature, feature, featureTypeOntology) + // @ts-expect-error ts doesn't understand mst extension + .getRowForFeature(self, layoutFeature, feature) if (row !== undefined) { return { layoutIndex: idx, diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts index d575e280f..b0466ede4 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts @@ -71,10 +71,11 @@ export function mouseEventsModelIntermediateFactory( throw new Error('featureTypeOntology is undefined') } const feature = glyph.getFeatureFromLayout( + // @ts-expect-error ts doesn't understand mst extension + self, topLevelFeature, bp, featureRow, - featureTypeOntology, ) if (!feature) { return mousePosition diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts index dddc3dec5..7d80b7189 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts @@ -41,6 +41,49 @@ export function renderingModelFactory( self.lastRowTooltipBufferHeight ) }, + get canvasPatterns(): Record< + 'forward' | 'backward', + CanvasPattern | null + > { + const patterns: Record<'forward' | 'backward', CanvasPattern | null> = { + forward: null, + backward: null, + } + const canvas = document.createElement('canvas') + const ctx = canvas?.getContext('2d') + if (!ctx) { + return patterns + } + const canvasSize = 10 + canvas.width = canvas.height = canvasSize + const { theme } = self + const stripeColor1 = + theme.palette.mode === 'light' ? 'rgba(0,0,0,0)' : 'rgba(0,0,0,0.75)' + const stripeColor2 = + theme.palette.mode === 'light' + ? 'rgba(255,255,255,0.25)' + : 'rgba(0,0,0,0.50)' + const directions = ['forward', 'backward'] as const + for (const direction of directions) { + const gradient = + direction === 'forward' + ? ctx.createLinearGradient(0, canvasSize, canvasSize, 0) + : ctx.createLinearGradient(0, 0, canvasSize, canvasSize) + gradient.addColorStop(0, stripeColor1) + gradient.addColorStop(0.25, stripeColor1) + gradient.addColorStop(0.25, stripeColor2) + gradient.addColorStop(0.5, stripeColor2) + gradient.addColorStop(0.5, stripeColor1) + gradient.addColorStop(0.75, stripeColor1) + gradient.addColorStop(0.75, stripeColor2) + gradient.addColorStop(1, stripeColor2) + ctx.fillStyle = gradient + ctx.clearRect(0, 0, canvasSize, canvasSize) + ctx.fillRect(0, 0, canvasSize, canvasSize) + patterns[direction] = ctx.createPattern(canvas, 'repeat') + } + return patterns + }, })) .actions((self) => ({ toggleShown() { @@ -132,19 +175,27 @@ export function renderingModelFactory( self, autorun( () => { - const { canvas, featureLayouts, featuresHeight, lgv } = self - if (!lgv.initialized || self.regionCannotBeRendered()) { + const { canvas, featureLayouts, lgv } = self + if ( + !lgv.initialized || + self.regionCannotBeRendered() || + !canvas + ) { return } - const { displayedRegions, dynamicBlocks } = lgv + const { dynamicBlocks, offsetPx } = lgv - const ctx = canvas?.getContext('2d') + const ctx = canvas.getContext('2d') if (!ctx) { return } - ctx.clearRect(0, 0, dynamicBlocks.totalWidthPx, featuresHeight) + ctx.clearRect(0, 0, canvas.width, canvas.height) for (const [idx, featureLayout] of featureLayouts.entries()) { - const displayedRegion = displayedRegions[idx] + const block = dynamicBlocks.contentBlocks.at(idx) + if (!block) { + continue + } + const blockLeftPx = block.offsetPx - offsetPx for (const [row, featureLayoutRow] of featureLayout.entries()) { for (const [featureRow, featureId] of featureLayoutRow) { const feature = self.getAnnotationFeatureById(featureId) @@ -153,15 +204,21 @@ export function renderingModelFactory( } if ( !doesIntersect2( - displayedRegion.start, - displayedRegion.end, + block.start, + block.end, feature.min, feature.max, ) ) { continue } - self.getGlyph(feature).draw(ctx, feature, row, self, idx) + ctx.save() + ctx.beginPath() + ctx.rect(blockLeftPx, 0, block.widthPx, canvas.height) + ctx.clip() + // @ts-expect-error ts doesn't understand mst extension + self.getGlyph(feature).draw(self, ctx, feature, row, block) + ctx.restore() } } } diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx index dbcd03bf3..8cec44c78 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx @@ -21,6 +21,7 @@ import { clusterResultByMessage, useStyles, } from '../../util/displayUtils' +import { looksLikeGene } from '../../util/glyphUtils' import { type LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from '../stateModel' import { TrackLines } from './TrackLines' @@ -181,7 +182,11 @@ export const LinearApolloSixFrameDisplay = observer( regionNumber: idx, })?.offsetPx ?? 0) - lgv.offsetPx const [feature] = checkResult.featureIds - if (!feature || !feature.parent?.looksLikeGene) { + if ( + !feature || + !feature.parent || + !looksLikeGene(feature.parent, session) + ) { return null } diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts index 3c2a0e461..b1947f7de 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts @@ -12,6 +12,7 @@ import { autorun, observable } from 'mobx' import { addDisposer, isAlive } from 'mobx-state-tree' import { type ApolloSessionModel } from '../../session' +import { looksLikeGene } from '../../util/glyphUtils' import { geneGlyph } from '../glyphs' import { baseModelFactory } from './base' @@ -123,7 +124,7 @@ export function layoutsModelFactory( if (!featureTypeOntology) { throw new Error('featureTypeOntology is undefined') } - if (feature.looksLikeGene) { + if (looksLikeGene(feature, self.session)) { const rowNum = feature.strand == 1 ? self.geneTrackRowNums[0] diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts index 5d5622709..21c40e845 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts @@ -13,6 +13,7 @@ import { type Instance, addDisposer, types } from 'mobx-state-tree' import { type ApolloSessionModel } from '../../session' import { codonColorCode } from '../../util/displayUtils' +import { looksLikeGene } from '../../util/glyphUtils' import { layoutsModelFactory } from './layouts' @@ -209,7 +210,7 @@ export function renderingModelFactory( const displayedRegion = displayedRegions[idx] for (const [row, featureLayoutRow] of featureLayout.entries()) { for (const { feature } of featureLayoutRow) { - if (!feature.looksLikeGene) { + if (!looksLikeGene(feature, self.session)) { continue } if ( diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/__snapshots__/index.test.ts.snap b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/__snapshots__/index.test.ts.snap index cdf528dcb..cdb48be65 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/__snapshots__/index.test.ts.snap +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/__snapshots__/index.test.ts.snap @@ -4,13 +4,17 @@ exports[`OntologyStore SO clone_insert_end is among valid subparts of BAC_cloned [ { "fullTextWords": [ - "so:0000103", + "so:0000785", + "cloned", + "region", + "segment", + "sequence", + "inserted", + "propagated", "clone", - "insert", - "end", ], - "id": "http://purl.obolibrary.org/obo/SO_0000103", - "lbl": "clone_insert_end", + "id": "http://purl.obolibrary.org/obo/SO_0000785", + "lbl": "cloned_region", "meta": { "basicPropertyValues": [ { @@ -18,19 +22,23 @@ exports[`OntologyStore SO clone_insert_end is among valid subparts of BAC_cloned "val": "sequence", }, ], + "comments": [ + "Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.", + ], "definition": { - "val": "The end of the clone insert.", - "xrefs": [ - "SO:ke", - ], + "val": "The region of sequence that has been inserted and is being propagated by the clone.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "clone insert end", + "val": "cloned segment", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cloned region", + "xrefs": [], }, ], }, @@ -65,6 +73,7 @@ exports[`OntologyStore SO clone_insert_end is among valid subparts of BAC_cloned { "pred": "hasExactSynonym", "val": "clone insert start", + "xrefs": [], }, ], }, @@ -72,13 +81,13 @@ exports[`OntologyStore SO clone_insert_end is among valid subparts of BAC_cloned }, { "fullTextWords": [ - "so:0000785", - "cloned", - "region", - "segment", + "so:0000103", + "clone", + "insert", + "end", ], - "id": "http://purl.obolibrary.org/obo/SO_0000785", - "lbl": "cloned_region", + "id": "http://purl.obolibrary.org/obo/SO_0000103", + "lbl": "clone_insert_end", "meta": { "basicPropertyValues": [ { @@ -86,17 +95,20 @@ exports[`OntologyStore SO clone_insert_end is among valid subparts of BAC_cloned "val": "sequence", }, ], - "comments": [ - "Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.", + "definition": { + "val": "The end of the clone insert.", + "xrefs": [ + "SO:ke", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "cloned region", - }, - { - "pred": "hasExactSynonym", - "val": "cloned segment", + "val": "clone insert end", + "xrefs": [], }, ], }, @@ -1058,9 +1070,9 @@ exports[`OntologyStore can load goslim generic 2`] = ` ] `; -exports[`OntologyStore can query SO 1`] = `2629`; +exports[`OntologyStore can query SO 1`] = `2826`; -exports[`OntologyStore can query SO features not part of something else 1`] = `1147`; +exports[`OntologyStore can query SO features not part of something else 1`] = `1179`; exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` [ @@ -1109,6 +1121,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` { "pred": "hasExactSynonym", "val": "INSDC_feature:gene", + "xrefs": [], }, ], "xrefs": [ @@ -1121,35 +1134,51 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000087", - "nuclear", + "so:0001867", + "candidate", "gene", - "sequence", + "target", + "suspected", + "involved", + "expression", + "trait", ], - "id": "http://purl.obolibrary.org/obo/SO_0000087", - "lbl": "nuclear_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001867", + "lbl": "candidate_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-01-17T02:53:03Z", + }, + ], + "comments": [ + "Requested by Bayer Cropscience December, 2011.", ], "definition": { - "val": "A gene from nuclear sequence.", + "val": "A gene suspected of being involved in the expression of a trait.", "xrefs": [ - "SO:xp", + "GMOD:ea", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "nuclear gene", + "val": "target gene", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Nuclear_gene", + "pred": "hasExactSynonym", + "val": "candidate gene", + "xrefs": [], }, ], }, @@ -1157,15 +1186,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000088", - "mt", + "so:0000111", + "transposable", + "element", "gene", - "mitochondrial", - "located", - "sequence", + "encoded", + "within", + "example", + "gag", + "int", + "env", + "pol", + "genes", + "ty", + "yeast", ], - "id": "http://purl.obolibrary.org/obo/SO_0000088", - "lbl": "mt_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000111", + "lbl": "transposable_element_gene", "meta": { "basicPropertyValues": [ { @@ -1174,24 +1211,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene located in mitochondrial sequence.", + "val": "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "mitochondrial gene", - }, - { - "pred": "hasExactSynonym", - "val": "mt gene", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Mitochondrial_gene", + "val": "transposable element gene", + "xrefs": [], }, ], }, @@ -1199,13 +1228,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000090", - "plastid", + "so:0000690", "gene", - "sequence", + "polycistronic", + "transcript", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000090", - "lbl": "plastid_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000690", + "lbl": "gene_with_polycistronic_transcript", "meta": { "basicPropertyValues": [ { @@ -1214,7 +1244,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from plastid sequence.", + "val": "A gene that encodes a polycistronic transcript.", "xrefs": [ "SO:xp", ], @@ -1222,7 +1252,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "plastid gene", + "val": "gene with polycistronic transcript", + "xrefs": [], }, ], }, @@ -1230,13 +1261,18 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000097", - "nucleomorph", + "so:0001219", + "retrogene", "gene", - "sequence", + "produced", + "product", + "reverse", + "transcriptase", + "mediated", + "event", ], - "id": "http://purl.obolibrary.org/obo/SO_0000097", - "lbl": "nucleomorph_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001219", + "lbl": "retrogene", "meta": { "basicPropertyValues": [ { @@ -1245,29 +1281,24 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from nucleomorph sequence.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene that has been produced as the product of a reverse transcriptase mediated event.", + "xrefs": [], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "nucleomorph gene", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000098", - "plasmid", + "so:0001217", + "protein", + "coding", "gene", - "sequence", + "codes", + "rna", + "translated", ], - "id": "http://purl.obolibrary.org/obo/SO_0000098", - "lbl": "plasmid_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001217", + "lbl": "protein_coding_gene", "meta": { "basicPropertyValues": [ { @@ -1276,15 +1307,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from plasmid sequence.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene that codes for an RNA that can be translated into a protein.", + "xrefs": [], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#Alliance_of_Genome_Resources", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "plasmid gene", + "val": "protein coding gene", + "xrefs": [], }, ], }, @@ -1292,13 +1325,18 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000099", - "proviral", + "so:0001431", + "cryptic", "gene", - "sequence", + "transcribed", + "normal", + "conditions", + "critical", + "cellular", + "functioning", ], - "id": "http://purl.obolibrary.org/obo/SO_0000099", - "lbl": "proviral_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001431", + "lbl": "cryptic_gene", "meta": { "basicPropertyValues": [ { @@ -1307,15 +1345,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from proviral sequence.", + "val": "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "proviral gene", + "val": "cryptic gene", + "xrefs": [], }, ], }, @@ -1323,23 +1362,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000111", - "transposable", - "element", + "so:0001263", + "ncrna", "gene", - "encoded", - "within", - "example", - "gag", - "int", - "env", - "pol", - "genes", - "ty", - "yeast", + "non", + "coding", + "rna", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000111", - "lbl": "transposable_element_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001263", + "lbl": "ncRNA_gene", "meta": { "basicPropertyValues": [ { @@ -1348,15 +1380,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene that encodes a non-coding RNA.", + "xrefs": [], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#Alliance_of_Genome_Resources", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "transposable element gene", + "val": "ncRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "non-coding RNA gene", + "xrefs": [], }, ], }, @@ -1364,12 +1403,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000127", - "silenced", + "so:0000280", + "engineered", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000127", - "lbl": "silenced_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000280", + "lbl": "engineered_gene", "meta": { "basicPropertyValues": [ { @@ -1378,7 +1417,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is silenced.", + "val": "A gene that is engineered.", "xrefs": [ "SO:xp", ], @@ -1386,7 +1425,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "silenced gene", + "val": "engineered gene", + "xrefs": [], }, ], }, @@ -1394,12 +1434,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000280", - "engineered", + "so:0000890", + "post", + "translationally", + "regulated", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000280", - "lbl": "engineered_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000890", + "lbl": "post_translationally_regulated_gene", "meta": { "basicPropertyValues": [ { @@ -1408,7 +1450,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is engineered.", + "val": "A gene that is post translationally regulated.", "xrefs": [ "SO:xp", ], @@ -1416,7 +1458,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "engineered gene", + "val": "post translationally regulated gene", + "xrefs": [], }, ], }, @@ -1424,12 +1467,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000285", - "foreign", + "so:0000459", "gene", + "trans", + "spliced", + "transcript", ], - "id": "http://purl.obolibrary.org/obo/SO_0000285", - "lbl": "foreign_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000459", + "lbl": "gene_with_trans_spliced_transcript", "meta": { "basicPropertyValues": [ { @@ -1438,7 +1483,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is foreign.", + "val": "A gene with a transcript that is trans-spliced.", "xrefs": [ "SO:xp", ], @@ -1446,7 +1491,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "foreign gene", + "val": "gene with trans spliced transcript", + "xrefs": [], }, ], }, @@ -1454,12 +1500,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000287", - "fusion", + "so:0000088", + "mt", "gene", + "mitochondrial", + "located", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000287", - "lbl": "fusion_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000088", + "lbl": "mt_gene", "meta": { "basicPropertyValues": [ { @@ -1468,7 +1517,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is a fusion.", + "val": "A gene located in mitochondrial sequence.", "xrefs": [ "SO:xp", ], @@ -1476,12 +1525,18 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "fusion gene", + "val": "mt gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "mitochondrial gene", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Fusion_gene", + "val": "http://en.wikipedia.org/wiki/Mitochondrial_gene", }, ], }, @@ -1489,62 +1544,65 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000456", - "recombinationally", - "rearranged", + "so:0002121", + "vertebrate", + "immune", + "system", "gene", + "configuration", + "ig", + "tr", + "variable", + "v", + "diversity", + "d", + "joining", + "j", + "germline", + "genes", + "dna", + "rearrangements", + "without", + "constant", + "c", + "undefined", + "non", + "rearranged", + "regions", + "loci", ], - "id": "http://purl.obolibrary.org/obo/SO_0000456", - "lbl": "recombinationally_rearranged_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002121", + "lbl": "vertebrate_immune_system_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "definition": { - "val": "A gene that is recombinationally rearranged.", - "xrefs": [ - "SO:ke", - ], - }, - "synonyms": [ { - "pred": "hasExactSynonym", - "val": "recombinationally rearranged gene", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T15:54:51Z", }, ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0000459", - "gene", - "trans", - "spliced", - "transcript", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000459", - "lbl": "gene_with_trans_spliced_transcript", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "A gene with a transcript that is trans-spliced.", + "val": "The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci).", "xrefs": [ - "SO:xp", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with trans spliced transcript", + "val": "immune_gene", + "xrefs": [], }, ], }, @@ -1552,14 +1610,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000690", + "so:0000456", + "recombinationally", + "rearranged", "gene", - "polycistronic", - "transcript", - "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000690", - "lbl": "gene_with_polycistronic_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000456", + "lbl": "recombinationally_rearranged_gene", "meta": { "basicPropertyValues": [ { @@ -1568,15 +1625,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that encodes a polycistronic transcript.", + "val": "A gene that is recombinationally rearranged.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with polycistronic transcript", + "val": "recombinationally rearranged gene", + "xrefs": [], }, ], }, @@ -1584,13 +1642,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000816", - "rescue", + "so:0000087", + "nuclear", "gene", - "rescues", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000816", - "lbl": "rescue_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000087", + "lbl": "nuclear_gene", "meta": { "basicPropertyValues": [ { @@ -1599,7 +1657,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that rescues.", + "val": "A gene from nuclear sequence.", "xrefs": [ "SO:xp", ], @@ -1607,7 +1665,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "rescue gene", + "val": "nuclear gene", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Nuclear_gene", }, ], }, @@ -1615,14 +1679,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000890", - "post", - "translationally", - "regulated", + "so:0000898", + "epigenetically", + "modified", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000890", - "lbl": "post_translationally_regulated_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000898", + "lbl": "epigenetically_modified_gene", "meta": { "basicPropertyValues": [ { @@ -1631,15 +1694,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is post translationally regulated.", + "val": "A gene that is epigenetically modified.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "post translationally regulated gene", + "val": "epigenetically modified gene", + "xrefs": [], }, ], }, @@ -1647,14 +1711,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000891", - "negatively", - "autoregulated", + "so:0000285", + "foreign", "gene", - "autoreguated", ], - "id": "http://purl.obolibrary.org/obo/SO_0000891", - "lbl": "negatively_autoregulated_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000285", + "lbl": "foreign_gene", "meta": { "basicPropertyValues": [ { @@ -1663,7 +1725,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is negatively autoreguated.", + "val": "A gene that is foreign.", "xrefs": [ "SO:xp", ], @@ -1671,7 +1733,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "negatively autoregulated gene", + "val": "foreign gene", + "xrefs": [], }, ], }, @@ -1679,13 +1742,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000892", - "positively", - "autoregulated", + "so:0000896", + "translationally", + "regulated", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000892", - "lbl": "positively_autoregulated_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000896", + "lbl": "translationally_regulated_gene", "meta": { "basicPropertyValues": [ { @@ -1694,7 +1757,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is positively autoregulated.", + "val": "A gene that is translationally regulated.", "xrefs": [ "SO:xp", ], @@ -1702,7 +1765,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "positively autoregulated gene", + "val": "translationally regulated gene", + "xrefs": [], }, ], }, @@ -1710,13 +1774,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000896", - "translationally", - "regulated", + "so:0000287", + "fusion", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000896", - "lbl": "translationally_regulated_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000287", + "lbl": "fusion_gene", "meta": { "basicPropertyValues": [ { @@ -1725,7 +1788,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is translationally regulated.", + "val": "A gene that is a fusion.", "xrefs": [ "SO:xp", ], @@ -1733,7 +1796,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "translationally regulated gene", + "val": "fusion gene", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Fusion_gene", }, ], }, @@ -1741,13 +1810,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000898", - "epigenetically", - "modified", + "so:0000891", + "negatively", + "autoregulated", "gene", + "autoreguated", ], - "id": "http://purl.obolibrary.org/obo/SO_0000898", - "lbl": "epigenetically_modified_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000891", + "lbl": "negatively_autoregulated_gene", "meta": { "basicPropertyValues": [ { @@ -1756,15 +1826,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is epigenetically modified.", + "val": "A gene that is negatively autoreguated.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "epigenetically modified gene", + "val": "negatively autoregulated gene", + "xrefs": [], }, ], }, @@ -1810,85 +1881,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000996", - "predicted", + "so:0000892", + "positively", + "autoregulated", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000996", - "lbl": "predicted_gene", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], - "comments": [ - "This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "predicted gene", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0001217", - "protein", - "coding", - "gene", - ], - "id": "http://purl.obolibrary.org/obo/SO_0001217", - "lbl": "protein_coding_gene", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "protein coding gene", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0001219", - "retrogene", - ], - "id": "http://purl.obolibrary.org/obo/SO_0001219", - "lbl": "retrogene", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0001263", - "ncrna", - "gene", - "non", - "coding", - "rna", - "encodes", - ], - "id": "http://purl.obolibrary.org/obo/SO_0001263", - "lbl": "ncRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000892", + "lbl": "positively_autoregulated_gene", "meta": { "basicPropertyValues": [ { @@ -1897,16 +1896,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that encodes a non-coding RNA.", + "val": "A gene that is positively autoregulated.", + "xrefs": [ + "SO:xp", + ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "ncRNA gene", - }, - { - "pred": "hasExactSynonym", - "val": "non-coding RNA gene", + "val": "positively autoregulated gene", + "xrefs": [], }, ], }, @@ -1914,18 +1913,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001431", - "cryptic", + "so:0000996", + "predicted", "gene", - "transcribed", - "normal", - "conditions", - "critical", - "cellular", - "functioning", + "region", + "genome", + "confirmed", + "laboratory", + "experiments", ], - "id": "http://purl.obolibrary.org/obo/SO_0001431", - "lbl": "cryptic_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000996", + "lbl": "predicted_gene", "meta": { "basicPropertyValues": [ { @@ -1933,16 +1931,18 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "val": "sequence", }, ], + "comments": [ + "This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", + ], "definition": { - "val": "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.", - "xrefs": [ - "SO:ke", - ], + "val": "A region of the genome that has been predicted to be a gene but has not been confirmed by laboratory experiments.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "cryptic gene", + "val": "predicted gene", + "xrefs": [], }, ], }, @@ -1988,6 +1988,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` { "pred": "hasExactSynonym", "val": "gene with non canonical start codon", + "xrefs": [], }, ], }, @@ -1995,49 +1996,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001867", - "candidate", + "so:0000097", + "nucleomorph", "gene", - "target", - "suspected", - "involved", - "expression", - "trait", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0001867", - "lbl": "candidate_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000097", + "lbl": "nucleomorph_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-01-17T02:53:03Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Requested by Bayer Cropscience December, 2011.", - ], "definition": { - "val": "A gene suspected of being involved in the expression of a trait.", + "val": "A gene from nucleomorph sequence.", "xrefs": [ - "GMOD:ea", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "candidate gene", - }, - { - "pred": "hasExactSynonym", - "val": "target gene", + "val": "nucleomorph gene", + "xrefs": [], }, ], }, @@ -2045,64 +2028,30 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002121", - "vertebrate", - "immune", - "system", + "so:0000127", + "silenced", "gene", - "configuration", - "ig", - "tr", - "variable", - "v", - "diversity", - "d", - "joining", - "j", - "germline", - "genes", - "dna", - "rearrangements", - "without", - "constant", - "c", - "undefined", - "non", - "rearranged", - "regions", - "loci", ], - "id": "http://purl.obolibrary.org/obo/SO_0002121", - "lbl": "vertebrate_immune_system_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000127", + "lbl": "silenced_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T15:54:51Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", - ], "definition": { - "val": "The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci).", + "val": "A gene that is silenced.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "immune_gene", + "val": "silenced gene", + "xrefs": [], }, ], }, @@ -2141,6 +2090,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` { "pred": "hasExactSynonym", "val": "gene cassette", + "xrefs": [], }, ], "xrefs": [ @@ -2153,14 +2103,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000089", - "kinetoplast", + "so:0000090", + "plastid", "gene", - "located", "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000089", - "lbl": "kinetoplast_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000090", + "lbl": "plastid_gene", "meta": { "basicPropertyValues": [ { @@ -2169,7 +2118,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene located in kinetoplast sequence.", + "val": "A gene from plastid sequence.", "xrefs": [ "SO:xp", ], @@ -2177,7 +2126,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "kinetoplast gene", + "val": "plastid gene", + "xrefs": [], }, ], }, @@ -2185,13 +2135,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000091", - "apicoplast", + "so:0000816", + "rescue", "gene", - "sequence", + "rescues", ], - "id": "http://purl.obolibrary.org/obo/SO_0000091", - "lbl": "apicoplast_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000816", + "lbl": "rescue_gene", "meta": { "basicPropertyValues": [ { @@ -2200,7 +2150,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from apicoplast sequence.", + "val": "A gene that rescues.", "xrefs": [ "SO:xp", ], @@ -2208,7 +2158,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "apicoplast gene", + "val": "rescue gene", + "xrefs": [], }, ], }, @@ -2216,14 +2167,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000092", - "ct", + "so:0000099", + "proviral", "gene", - "chloroplast", "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000092", - "lbl": "ct_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000099", + "lbl": "proviral_gene", "meta": { "basicPropertyValues": [ { @@ -2232,7 +2182,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from chloroplast sequence.", + "val": "A gene from proviral sequence.", "xrefs": [ "SO:xp", ], @@ -2240,11 +2190,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "chloroplast gene", - }, - { - "pred": "hasExactSynonym", - "val": "ct gene", + "val": "proviral gene", + "xrefs": [], }, ], }, @@ -2252,13 +2199,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000093", - "chromoplast", + "so:0000098", + "plasmid", "gene", "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000093", - "lbl": "chromoplast_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000098", + "lbl": "plasmid_gene", "meta": { "basicPropertyValues": [ { @@ -2267,7 +2214,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from chromoplast_sequence.", + "val": "A gene from plasmid sequence.", "xrefs": [ "SO:xp", ], @@ -2275,7 +2222,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "chromoplast gene", + "val": "plasmid gene", + "xrefs": [], }, ], }, @@ -2283,30 +2231,54 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000094", - "cyanelle", + "so:0001868", + "positional", + "candidate", "gene", - "sequence", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000094", - "lbl": "cyanelle_gene", - "meta": { - "basicPropertyValues": [ - { + "target", + "whose", + "association", + "trait", + "based", + "location", + "chromosome", + ], + "id": "http://purl.obolibrary.org/obo/SO_0001868", + "lbl": "positional_candidate_gene", + "meta": { + "basicPropertyValues": [ + { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-01-17T02:54:42Z", + }, + ], + "comments": [ + "Requested by Bayer Cropscience December, 2011.", ], "definition": { - "val": "A gene from cyanelle sequence.", + "val": "A candidate gene whose association with a trait is based on the gene's location on a chromosome.", "xrefs": [ - "SO:xp", + "GMOD:ea", ], }, "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "positional target gene", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "cyanelle gene", + "val": "positional candidate gene", + "xrefs": [], }, ], }, @@ -2314,31 +2286,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000095", - "leucoplast", + "so:0001869", + "functional", + "candidate", "gene", - "plastid", - "sequence", + "target", + "whose", + "function", + "something", + "common", + "biologically", + "trait", + "investigation", ], - "id": "http://purl.obolibrary.org/obo/SO_0000095", - "lbl": "leucoplast_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001869", + "lbl": "functional_candidate_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-01-17T02:57:30Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + ], + "comments": [ + "Requested by Bayer Cropscience December, 2011.", ], "definition": { - "val": "A plastid gene from leucoplast sequence.", + "val": "A candidate gene whose function has something in common biologically with the trait under investigation.", "xrefs": [ - "SO:xp", + "GMOD:ea", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "leucoplast gene", + "val": "functional target gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "functional candidate gene", + "xrefs": [], }, ], }, @@ -2346,13 +2342,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000096", - "proplastid", + "so:0000283", + "engineered", + "foreign", + "transposable", + "element", "gene", - "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000096", - "lbl": "proplastid_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000283", + "lbl": "engineered_foreign_transposable_element_gene", "meta": { "basicPropertyValues": [ { @@ -2361,15 +2359,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene from proplastid sequence.", + "val": "A transposable_element that is engineered and foreign.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "proplastid gene", + "val": "engineered foreign transposable element gene", + "xrefs": [], }, ], }, @@ -2377,16 +2376,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000100", - "endogenous", - "retroviral", + "so:0000692", "gene", - "proviral", - "origin", - "retrovirus", + "dicistronic", + "transcript", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000100", - "lbl": "endogenous_retroviral_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000692", + "lbl": "gene_with_dicistronic_transcript", "meta": { "basicPropertyValues": [ { @@ -2395,7 +2392,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A proviral gene with origin endogenous retrovirus.", + "val": "A gene that encodes a dicistronic transcript.", "xrefs": [ "SO:xp", ], @@ -2403,7 +2400,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "endogenous retroviral gene", + "val": "gene with dicistronic transcript", + "xrefs": [], }, ], }, @@ -2411,15 +2409,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000283", - "engineered", - "foreign", - "transposable", - "element", + "so:0000455", "gene", + "mrna", + "frameshift", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000283", - "lbl": "engineered_foreign_transposable_element_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000455", + "lbl": "gene_with_mRNA_with_frameshift", "meta": { "basicPropertyValues": [ { @@ -2428,7 +2425,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A transposable_element that is engineered and foreign.", + "val": "A gene that encodes an mRNA with a frameshift.", "xrefs": [ "SO:xp", ], @@ -2436,7 +2433,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "engineered foreign transposable element gene", + "val": "gene with mRNA with frameshift", + "xrefs": [], }, ], }, @@ -2444,14 +2442,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000128", + "so:0000693", "gene", - "silenced", - "dna", - "modification", + "recoded", + "mrna", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000128", - "lbl": "gene_silenced_by_DNA_modification", + "id": "http://purl.obolibrary.org/obo/SO_0000693", + "lbl": "gene_with_recoded_mRNA", "meta": { "basicPropertyValues": [ { @@ -2460,7 +2458,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is silenced by DNA modification.", + "val": "A gene that encodes an mRNA that is recoded.", "xrefs": [ "SO:xp", ], @@ -2468,7 +2466,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene silenced by DNA modification", + "val": "gene with recoded mRNA", + "xrefs": [], }, ], }, @@ -2476,15 +2475,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001224", + "so:0000451", "gene", - "silenced", - "rna", - "interference", - "rnai", + "polyadenylated", + "mrna", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001224", - "lbl": "gene_silenced_by_RNA_interference", + "id": "http://purl.obolibrary.org/obo/SO_0000451", + "lbl": "gene_with_polyadenylated_mRNA", "meta": { "basicPropertyValues": [ { @@ -2493,7 +2491,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is silenced by RNA interference.", + "val": "A gene that encodes a polyadenylated mRNA.", "xrefs": [ "SO:xp", ], @@ -2501,15 +2499,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNA interference silenced gene", - }, - { - "pred": "hasExactSynonym", - "val": "RNAi silenced gene", - }, - { - "pred": "hasExactSynonym", - "val": "gene silenced by RNA interference", + "val": "gene with polyadenylated mRNA", + "xrefs": [], }, ], }, @@ -2517,14 +2508,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001225", + "so:0000548", "gene", - "silenced", - "histone", - "modification", + "edited", + "transcript", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001225", - "lbl": "gene_silenced_by_histone_modification", + "id": "http://purl.obolibrary.org/obo/SO_0000548", + "lbl": "gene_with_edited_transcript", "meta": { "basicPropertyValues": [ { @@ -2533,7 +2524,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is silenced by histone modification.", + "val": "A gene that encodes a transcript that is edited.", "xrefs": [ "SO:xp", ], @@ -2541,7 +2532,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene silenced by histone modification", + "val": "gene with edited transcript", + "xrefs": [], }, ], }, @@ -2549,13 +2541,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000281", - "engineered", - "foreign", + "so:1001196", + "cryptogene", + "maxicircle", "gene", + "extensively", + "edited", + "cannot", + "matched", + "mrna", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000281", - "lbl": "engineered_foreign_gene", + "id": "http://purl.obolibrary.org/obo/SO_1001196", + "lbl": "cryptogene", "meta": { "basicPropertyValues": [ { @@ -2564,46 +2562,67 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is engineered and foreign.", + "val": "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.", "xrefs": [ - "SO:xp", + "SO:ma", ], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "engineered foreign gene", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000288", - "engineered", - "fusion", + "so:0002127", + "lncrna", "gene", + "lnc", + "rna", + "long", + "non", + "coding", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000288", - "lbl": "engineered_fusion_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002127", + "lbl": "lncRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:03:33Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.", + ], "definition": { - "val": "A fusion gene that is engineered.", + "val": "A gene that encodes a long non-coding RNA.", "xrefs": [ - "SO:xp", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "engineered fusion gene", + "val": "lnc_RNA_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "long_non_coding_RNA_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "lnc RNA gene", + "xrefs": [], }, ], }, @@ -2611,32 +2630,50 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000373", - "recombinationally", - "inverted", + "so:0001637", + "rrna", "gene", - "rearranged", - "inversion", + "rdna", + "encodes", + "ribosomal", + "rna", ], - "id": "http://purl.obolibrary.org/obo/SO_0000373", - "lbl": "recombinationally_inverted_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001637", + "lbl": "rRNA_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-04-21T10:10:32Z", + }, + ], + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "A recombinationally rearranged gene by inversion.", + "val": "A gene that encodes for ribosomal RNA.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "recombinationally inverted gene", + "val": "rDNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "rRNA gene", + "xrefs": [], }, ], }, @@ -2644,16 +2681,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000941", - "recombinationally", - "rearranged", - "vertebrate", - "immune", - "system", + "so:0001269", + "srp", + "rna", "gene", + "encodes", + "signal", + "recognition", + "particle", ], - "id": "http://purl.obolibrary.org/obo/SO_0000941", - "lbl": "recombinationally_rearranged_vertebrate_immune_system_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001269", + "lbl": "SRP_RNA_gene", "meta": { "basicPropertyValues": [ { @@ -2662,15 +2700,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A recombinationally rearranged gene of the vertebrate immune system.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene that encodes a signal recognition particle (SRP) RNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "recombinationally rearranged vertebrate immune system gene", + "val": "SRP RNA gene", + "xrefs": [], }, ], }, @@ -2678,14 +2715,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000692", + "so:0001266", + "scrna", "gene", - "dicistronic", - "transcript", - "encodes", + "encoding", + "small", + "noncoding", + "rna", + "generally", + "found", + "cytoplasm", ], - "id": "http://purl.obolibrary.org/obo/SO_0000692", - "lbl": "gene_with_dicistronic_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001266", + "lbl": "scRNA_gene", "meta": { "basicPropertyValues": [ { @@ -2694,15 +2736,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that encodes a dicistronic transcript.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene encoding a small noncoding RNA that is generally found only in the cytoplasm.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with dicistronic transcript", + "val": "scRNA gene", + "xrefs": [], }, ], }, @@ -2710,32 +2751,51 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000818", - "wild", - "type", - "rescue", + "so:0002341", + "rna", + "7sk", "gene", - "rescues", + "encoding", + "so:0002340", ], - "id": "http://purl.obolibrary.org/obo/SO_0000818", - "lbl": "wild_type_rescue_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002341", + "lbl": "RNA_7SK_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-04-27T14:50:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Added as a request from FlyBase. See GitHub Issue #512", ], "definition": { - "val": "A gene that rescues.", + "val": "A gene encoding a 7SK RNA (SO:0002340).", "xrefs": [ - "SO:xp", + "PMID:19246988", + "PMID:21853533", + "PMID:27369380", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "wild type rescue gene", + "val": "RNA 7SK gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "7SK RNA gene", + "xrefs": [], }, ], }, @@ -2743,16 +2803,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000138", + "so:0001264", + "grna", "gene", - "rearranged", + "noncoding", + "rna", + "guides", + "insertion", + "deletion", + "uridine", + "residues", + "mitochondrial", + "mrnas", + "may", + "also", + "refer", + "synthetic", + "rnas", + "used", + "guide", "dna", - "level", - "epigenetically", - "modified", + "editing", + "using", + "cripsr", + "cas9", + "system", ], - "id": "http://purl.obolibrary.org/obo/SO_0000138", - "lbl": "gene_rearranged_at_DNA_level", + "id": "http://purl.obolibrary.org/obo/SO_0001264", + "lbl": "gRNA_gene", "meta": { "basicPropertyValues": [ { @@ -2761,15 +2839,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "An epigenetically modified gene, rearranged at the DNA level.", - "xrefs": [ - "SO:xp", - ], + "val": "A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene rearranged at DNA level", + "val": "gRNA gene", + "xrefs": [], }, ], }, @@ -2777,30 +2854,58 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000888", - "maternally", - "imprinted", + "so:0002342", + "sncrna", "gene", + "small", + "non", + "coding", + "rna", + "ncrna", + "encodes", + "less", + "200", + "nucleotides", + "length", ], - "id": "http://purl.obolibrary.org/obo/SO_0000888", - "lbl": "maternally_imprinted_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002342", + "lbl": "sncRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-04-27T14:50:30Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as a request from FlyBase to make the ncRNA_gene branch in SO mirror the ncRNA branch. See GitHub Issue #514", + ], "definition": { - "val": "A gene that is maternally_imprinted.", + "val": "A ncRNA_gene that encodes an ncRNA less than 200 nucleotides in length.", "xrefs": [ - "SO:xp", + "PMID:28449079", + "PMID:30069443", + "PMID:30937442", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "maternally imprinted gene", + "val": "sncRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "small non-coding RNA gene", + "xrefs": [], }, ], }, @@ -2808,30 +2913,51 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000889", - "paternally", - "imprinted", + "so:0002353", + "sbrna", "gene", + "stem", + "bulge", + "rna", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000889", - "lbl": "paternally_imprinted_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002353", + "lbl": "sbRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-09-30T21:25:37Z", + }, + ], + "comments": [ + "See GitHub Issue #516.", ], "definition": { - "val": "A gene that is paternally imprinted.", + "val": "A gene encoding a stem-bulge RNA.", "xrefs": [ - "SO:xp", + "PMID:25908866", + "PMID:30666901", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "paternally imprinted gene", + "val": "Stem-bulge RNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "stem_bulge_RNA_gene", + "xrefs": [], }, ], }, @@ -2839,30 +2965,59 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000897", - "allelically", - "excluded", + "so:0001643", + "telomerase", + "rna", "gene", + "terc", + "component", + "non", + "coding", + "product", ], - "id": "http://purl.obolibrary.org/obo/SO_0000897", - "lbl": "allelically_excluded_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001643", + "lbl": "telomerase_RNA_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-05-18T05:26:38Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "A gene that is allelically_excluded.", + "val": "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "allelically excluded gene", + "val": "TERC", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "telomerase RNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "Telomerase RNA component", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http:http://en.wikipedia.org/wiki/Telomerase_RNA_component", }, ], }, @@ -2870,30 +3025,38 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000363", - "floxed", + "so:0002180", + "enzymatic", + "rna", "gene", - "transgene", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000363", - "lbl": "floxed_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002180", + "lbl": "enzymatic_RNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2017-09-27T10:30:27Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A transgene that is floxed.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene that encodes an enzymatic RNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "floxed gene", + "val": "enzymatic RNA gene", + "xrefs": [], }, ], }, @@ -2901,95 +3064,130 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000451", + "so:0002359", + "y", + "rna", "gene", - "polyadenylated", - "mrna", "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000451", - "lbl": "gene_with_polyadenylated_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002359", + "lbl": "Y_RNA_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-11T23:52:21Z", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "comments": [ + "There are four genes from HGNC that are annotated this way. HGNC IDs: 10242, 10243, 10244, and 10248.", ], "definition": { - "val": "A gene that encodes a polyadenylated mRNA.", + "val": "A gene that encodes a Y RNA.", "xrefs": [ - "SO:xp", + "PMID:1698620", + "PMID:6187471", + "PMID:6816230", + "PMID:7520568", + "PMID:7539809", + "PMID:8836182", ], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "gene with polyadenylated mRNA", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000455", + "so:0002358", + "vault", + "rna", "gene", - "mrna", - "frameshift", "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000455", - "lbl": "gene_with_mRNA_with_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0002358", + "lbl": "vault_RNA_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-11T23:25:13Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + ], + "comments": [ + "As of 11 November 2021 the HNGC lists 4 genes as RNA, vault. These are HGNC IDs: 12654, 12655, 12656, 37054.", ], "definition": { - "val": "A gene that encodes an mRNA with a frameshift.", + "val": "A gene that encodes a vault RNA.", "xrefs": [ - "SO:xp", + "PMID:19298825", + "PMID:19491402", + "PMID:22058117", + "PMID:22926522", + "PMID:30773316", + "PMID:9535882", ], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "gene with mRNA with frameshift", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000548", + "so:0002355", + "hprna", "gene", - "edited", - "transcript", - "encodes", + "hairpin", + "rna", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000548", - "lbl": "gene_with_edited_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002355", + "lbl": "hpRNA_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-10-07T17:09:18Z", + }, + ], + "comments": [ + "See GitHub Issue #518.", ], "definition": { - "val": "A gene that encodes a transcript that is edited.", + "val": "A gene encoding a hpRNA.", "xrefs": [ - "SO:xp", + "PMID:18463630", + "PMID:18719707", + "PMID:25544562", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with edited transcript", + "val": "Hairpin RNA gene", + "xrefs": [], }, ], }, @@ -2997,14 +3195,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000693", + "so:0000281", + "engineered", + "foreign", "gene", - "recoded", - "mrna", - "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000693", - "lbl": "gene_with_recoded_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000281", + "lbl": "engineered_foreign_gene", "meta": { "basicPropertyValues": [ { @@ -3013,7 +3210,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that encodes an mRNA that is recoded.", + "val": "A gene that is engineered and foreign.", "xrefs": [ "SO:xp", ], @@ -3021,7 +3218,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with recoded mRNA", + "val": "engineered foreign gene", + "xrefs": [], }, ], }, @@ -3029,12 +3227,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001264", - "grna", + "so:0000288", + "engineered", + "fusion", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0001264", - "lbl": "gRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000288", + "lbl": "engineered_fusion_gene", "meta": { "basicPropertyValues": [ { @@ -3042,10 +3241,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "val": "sequence", }, ], + "definition": { + "val": "A fusion gene that is engineered.", + "xrefs": [ + "SO:xp", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gRNA gene", + "val": "engineered fusion gene", + "xrefs": [], }, ], }, @@ -3053,36 +3259,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001265", - "mirna", + "so:0002363", + "mt", + "rrna", "gene", - "strna", + "mitochondrial", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001265", - "lbl": "miRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002363", + "lbl": "mt_rRNA_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "SO:0001270", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "miRNA gene", - }, { - "pred": "hasExactSynonym", - "val": "stRNA gene", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T04:55:58Z", }, + ], + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], + "definition": { + "val": "A gene that codes for mitochondrial rRNA.", + "xrefs": [], + }, + "synonyms": [ { "pred": "hasExactSynonym", - "val": "stRNA_gene", + "val": "mitochondrial rRNA gene", + "xrefs": [], }, ], }, @@ -3090,12 +3302,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001266", - "scrna", + "so:0000089", + "kinetoplast", "gene", + "located", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0001266", - "lbl": "scRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000089", + "lbl": "kinetoplast_gene", "meta": { "basicPropertyValues": [ { @@ -3103,10 +3317,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "val": "sequence", }, ], + "definition": { + "val": "A gene located in kinetoplast sequence.", + "xrefs": [ + "SO:xp", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "scRNA gene", + "val": "kinetoplast gene", + "xrefs": [], }, ], }, @@ -3114,23 +3335,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001267", - "snorna", + "so:0002133", + "cell", + "receptor", "gene", + "tr", + "germline", ], - "id": "http://purl.obolibrary.org/obo/SO_0001267", - "lbl": "snoRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002133", + "lbl": "T_cell_receptor_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:17:12Z", + }, + ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], + "definition": { + "val": "A T-cell receptor germline gene.", + "xrefs": [], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "snoRNA gene", + "val": "TR_gene", + "xrefs": [], }, ], }, @@ -3138,37 +3378,49 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001268", - "snrna", + "so:0002122", + "immunoglobulin", "gene", - "small", - "nuclear", - "rna", - "encodes", + "ig", + "genes", + "germline", ], - "id": "http://purl.obolibrary.org/obo/SO_0001268", - "lbl": "snRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002122", + "lbl": "immunoglobulin_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T15:56:09Z", + }, + ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "A gene that encodes a small nuclear RNA.", + "val": "A germline immunoglobulin gene.", "xrefs": [ - "http://en.wikipedia.org/wiki/Small_nuclear_RNA", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "small nuclear RNA gene", + "val": "IG_genes", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snRNA gene", + "val": "All_IG_genes", + "xrefs": [], }, ], }, @@ -3176,13 +3428,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001269", - "srp", - "rna", + "so:0000941", + "recombinationally", + "rearranged", + "vertebrate", + "immune", + "system", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0001269", - "lbl": "SRP_RNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000941", + "lbl": "recombinationally_rearranged_vertebrate_immune_system_gene", "meta": { "basicPropertyValues": [ { @@ -3190,10 +3445,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "val": "sequence", }, ], + "definition": { + "val": "A recombinationally rearranged gene of the vertebrate immune system.", + "xrefs": [ + "SO:xp", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "SRP RNA gene", + "val": "recombinationally rearranged vertebrate immune system gene", + "xrefs": [], }, ], }, @@ -3201,12 +3463,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001271", - "tmrna", + "so:0000373", + "recombinationally", + "inverted", "gene", + "rearranged", + "inversion", ], - "id": "http://purl.obolibrary.org/obo/SO_0001271", - "lbl": "tmRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000373", + "lbl": "recombinationally_inverted_gene", "meta": { "basicPropertyValues": [ { @@ -3214,10 +3479,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "val": "sequence", }, ], + "definition": { + "val": "A recombinationally rearranged gene by inversion.", + "xrefs": [ + "SO:xp", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "tmRNA gene", + "val": "recombinationally inverted gene", + "xrefs": [], }, ], }, @@ -3225,12 +3497,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001272", - "trna", + "so:0000897", + "allelically", + "excluded", "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0001272", - "lbl": "tRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000897", + "lbl": "allelically_excluded_gene", "meta": { "basicPropertyValues": [ { @@ -3238,10 +3511,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "val": "sequence", }, ], + "definition": { + "val": "A gene that is allelically_excluded.", + "xrefs": [ + "SO:xp", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "tRNA gene", + "val": "allelically excluded gene", + "xrefs": [], }, ], }, @@ -3249,45 +3529,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001637", - "rrna", + "so:0000888", + "maternally", + "imprinted", "gene", - "rdna", - "encodes", - "ribosomal", - "rna", ], - "id": "http://purl.obolibrary.org/obo/SO_0001637", - "lbl": "rRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000888", + "lbl": "maternally_imprinted_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-04-21T10:10:32Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A gene that encodes for ribosomal RNA.", + "val": "A gene that is maternally_imprinted.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "rDNA", - }, - { - "pred": "hasExactSynonym", - "val": "rRNA gene", + "val": "maternally imprinted gene", + "xrefs": [], }, ], }, @@ -3295,41 +3561,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001638", - "pirna", + "so:0000138", "gene", - "encodes", - "piwi", - "associated", - "rna", + "rearranged", + "dna", + "level", + "epigenetically", + "modified", ], - "id": "http://purl.obolibrary.org/obo/SO_0001638", - "lbl": "piRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000138", + "lbl": "gene_rearranged_at_DNA_level", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-04-21T10:11:36Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A gene that encodes for an piwi associated RNA.", + "val": "An epigenetically modified gene, rearranged at the DNA level.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "piRNA gene", + "val": "gene rearranged at DNA level", + "xrefs": [], }, ], }, @@ -3337,40 +3596,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001639", - "rnase", - "p", - "rna", + "so:0000889", + "paternally", + "imprinted", "gene", - "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001639", - "lbl": "RNase_P_RNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000889", + "lbl": "paternally_imprinted_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-04-21T10:13:23Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A gene that encodes an RNase P RNA.", + "val": "A gene that is paternally imprinted.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNase P RNA gene", + "val": "paternally imprinted gene", + "xrefs": [], }, ], }, @@ -3378,40 +3628,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001640", - "rnase", - "mrp", - "rna", + "so:0000363", + "floxed", "gene", - "encodes", + "transgene", ], - "id": "http://purl.obolibrary.org/obo/SO_0001640", - "lbl": "RNase_MRP_RNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000363", + "lbl": "floxed_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-04-21T10:13:58Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A gene that encodes a RNase_MRP_RNA.", + "val": "A transgene that is floxed.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { - "pred": "hasRelatedSynonym", - "val": "RNase MRP RNA gene", + "pred": "hasExactSynonym", + "val": "floxed gene", + "xrefs": [], }, ], }, @@ -3419,56 +3660,77 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001643", - "telomerase", - "rna", + "so:0001740", "gene", - "terc", - "component", - "non", - "coding", - "product", + "start", + "codon", + "cug", + "translational", ], - "id": "http://purl.obolibrary.org/obo/SO_0001643", - "lbl": "telomerase_RNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001740", + "lbl": "gene_with_start_codon_CUG", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "kareneilbeck", }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-05-18T05:26:38Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2011-01-10T01:32:35Z", + }, + ], + "comments": [ + "Requested by flybase, Dec 2010.", ], "definition": { - "val": "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.", + "val": "A gene with a translational start codon of CUG.", "xrefs": [ - "SO:ke", + "SO:mc", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "TERC", - }, - { - "pred": "hasExactSynonym", - "val": "Telomerase RNA component", + "val": "gene with start codon CUG", + "xrefs": [], }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000128", + "gene", + "silenced", + "dna", + "modification", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000128", + "lbl": "gene_silenced_by_DNA_modification", + "meta": { + "basicPropertyValues": [ { - "pred": "hasExactSynonym", - "val": "telomerase RNA gene", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, ], - "xrefs": [ + "definition": { + "val": "A gene that is silenced by DNA modification.", + "xrefs": [ + "SO:xp", + ], + }, + "synonyms": [ { - "val": "http:http://en.wikipedia.org/wiki/Telomerase_RNA_component", + "pred": "hasExactSynonym", + "val": "gene silenced by DNA modification", + "xrefs": [], }, ], }, @@ -3476,54 +3738,43 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002127", - "lncrna", + "so:0001224", "gene", - "lnc", + "silenced", "rna", - "long", - "non", - "coding", - "encodes", + "interference", + "rnai", ], - "id": "http://purl.obolibrary.org/obo/SO_0002127", - "lbl": "lncRNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001224", + "lbl": "gene_silenced_by_RNA_interference", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:03:33Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.", - ], "definition": { - "val": "A gene that encodes a long non-coding RNA.", + "val": "A gene that is silenced by RNA interference.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "lnc RNA gene", + "val": "RNAi silenced gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "lnc_RNA_gene", + "val": "gene silenced by RNA interference", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "long_non_coding_RNA_gene", + "val": "RNA interference silenced gene", + "xrefs": [], }, ], }, @@ -3531,36 +3782,32 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002180", - "enzymatic", - "rna", + "so:0001225", "gene", - "encodes", + "silenced", + "histone", + "modification", ], - "id": "http://purl.obolibrary.org/obo/SO_0002180", - "lbl": "enzymatic_RNA_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001225", + "lbl": "gene_silenced_by_histone_modification", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-09-27T10:30:27Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A gene that encodes an enzymatic RNA.", + "val": "A gene that is silenced by histone modification.", + "xrefs": [ + "SO:xp", + ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "enzymatic RNA gene", + "val": "gene silenced by histone modification", + "xrefs": [], }, ], }, @@ -3568,74 +3815,72 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:1001196", - "cryptogene", - "maxicircle", + "so:0002366", + "plastid", + "rrna", "gene", - "extensively", - "edited", - "cannot", - "matched", - "mrna", - "sequence", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_1001196", - "lbl": "cryptogene", + "id": "http://purl.obolibrary.org/obo/SO_0002366", + "lbl": "plastid_rRNA_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:00:08Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + ], + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.", - "xrefs": [ - "SO:ma", - ], + "val": "A gene that codes for plastid rRNA.", + "xrefs": [], }, }, "type": "CLASS", }, { "fullTextWords": [ - "so:0001740", + "so:0000092", + "ct", "gene", - "start", - "codon", - "cug", - "translational", + "chloroplast", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0001740", - "lbl": "gene_with_start_codon_CUG", + "id": "http://purl.obolibrary.org/obo/SO_0000092", + "lbl": "ct_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2011-01-10T01:32:35Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Requested by flybase, Dec 2010.", - ], "definition": { - "val": "A gene with a translational start codon of CUG.", + "val": "A gene from chloroplast sequence.", "xrefs": [ - "SO:mc", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with start codon CUG", + "val": "chloroplast gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "ct gene", + "xrefs": [], }, ], }, @@ -3643,52 +3888,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001868", - "positional", - "candidate", + "so:0000091", + "apicoplast", "gene", - "target", - "whose", - "association", - "trait", - "based", - "location", - "chromosome", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0001868", - "lbl": "positional_candidate_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000091", + "lbl": "apicoplast_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-01-17T02:54:42Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Requested by Bayer Cropscience December, 2011.", - ], "definition": { - "val": "A candidate gene whose association with a trait is based on the gene's location on a chromosome.", + "val": "A gene from apicoplast sequence.", "xrefs": [ - "GMOD:ea", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "positional candidate gene", - }, - { - "pred": "hasRelatedSynonym", - "val": "positional target gene", + "val": "apicoplast gene", + "xrefs": [], }, ], }, @@ -3696,53 +3920,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001869", - "functional", - "candidate", + "so:0000094", + "cyanelle", "gene", - "target", - "whose", - "function", - "something", - "common", - "biologically", - "trait", - "investigation", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0001869", - "lbl": "functional_candidate_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000094", + "lbl": "cyanelle_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-01-17T02:57:30Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Requested by Bayer Cropscience December, 2011.", - ], "definition": { - "val": "A candidate gene whose function has something in common biologically with the trait under investigation.", + "val": "A gene from cyanelle sequence.", "xrefs": [ - "GMOD:ea", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "functional candidate gene", - }, - { - "pred": "hasExactSynonym", - "val": "functional target gene", + "val": "cyanelle gene", + "xrefs": [], }, ], }, @@ -3750,47 +3952,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002122", - "immunoglobulin", + "so:0000093", + "chromoplast", "gene", - "ig", - "genes", - "germline", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0002122", - "lbl": "immunoglobulin_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000093", + "lbl": "chromoplast_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T15:56:09Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", - ], "definition": { - "val": "A germline immunoglobulin gene.", + "val": "A gene from chromoplast_sequence.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "All_IG_genes", - }, - { - "pred": "hasExactSynonym", - "val": "IG_genes", + "val": "chromoplast gene", + "xrefs": [], }, ], }, @@ -3798,40 +3984,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002133", - "cell", - "receptor", + "so:0000096", + "proplastid", "gene", - "tr", - "germline", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0002133", - "lbl": "T_cell_receptor_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000096", + "lbl": "proplastid_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:17:12Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", - ], "definition": { - "val": "A T-cell receptor germline gene.", + "val": "A gene from proplastid sequence.", + "xrefs": [ + "SO:ke", + ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "TR_gene", + "val": "proplastid gene", + "xrefs": [], }, ], }, @@ -3839,16 +4016,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000654", - "maxicircle", + "so:0000095", + "leucoplast", "gene", - "maxi", - "circle", - "mitochondrial", - "located", + "plastid", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000654", - "lbl": "maxicircle_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000095", + "lbl": "leucoplast_gene", "meta": { "basicPropertyValues": [ { @@ -3857,7 +4032,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A mitochondrial gene located in a maxicircle.", + "val": "A plastid gene from leucoplast sequence.", "xrefs": [ "SO:xp", ], @@ -3865,11 +4040,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "maxi-circle gene", - }, - { - "pred": "hasExactSynonym", - "val": "maxicircle gene", + "val": "leucoplast gene", + "xrefs": [], }, ], }, @@ -3877,12 +4049,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000975", - "minicircle", + "so:0000818", + "wild", + "type", + "rescue", "gene", + "rescues", ], - "id": "http://purl.obolibrary.org/obo/SO_0000975", - "lbl": "minicircle_gene", + "id": "http://purl.obolibrary.org/obo/SO_0000818", + "lbl": "wild_type_rescue_gene", "meta": { "basicPropertyValues": [ { @@ -3890,10 +4065,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "val": "sequence", }, ], + "definition": { + "val": "A gene that rescues.", + "xrefs": [ + "SO:xp", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "minicircle gene", + "val": "wild type rescue gene", + "xrefs": [], }, ], }, @@ -3901,14 +4083,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000129", + "so:0000100", + "endogenous", + "retroviral", "gene", - "silenced", - "dna", - "methylation", + "proviral", + "origin", + "retrovirus", ], - "id": "http://purl.obolibrary.org/obo/SO_0000129", - "lbl": "gene_silenced_by_DNA_methylation", + "id": "http://purl.obolibrary.org/obo/SO_0000100", + "lbl": "endogenous_retroviral_gene", "meta": { "basicPropertyValues": [ { @@ -3917,7 +4101,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene that is silenced by DNA methylation.", + "val": "A proviral gene with origin endogenous retrovirus.", "xrefs": [ "SO:xp", ], @@ -3925,11 +4109,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene silenced by DNA methylation", - }, - { - "pred": "hasExactSynonym", - "val": "methylation-silenced gene", + "val": "endogenous retroviral gene", + "xrefs": [], }, ], }, @@ -3937,71 +4118,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0001226", - "gene", - "silenced", - "histone", - "methylation", - ], - "id": "http://purl.obolibrary.org/obo/SO_0001226", - "lbl": "gene_silenced_by_histone_methylation", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], - "definition": { - "val": "A gene that is silenced by histone methylation.", - "xrefs": [ - "SO:xp", - ], - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "gene silenced by histone methylation", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0001227", - "gene", - "silenced", - "histone", - "deacetylation", - ], - "id": "http://purl.obolibrary.org/obo/SO_0001227", - "lbl": "gene_silenced_by_histone_deacetylation", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], - "definition": { - "val": "A gene that is silenced by histone deacetylation.", - "xrefs": [ - "SO:xp", - ], - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "gene silenced by histone deacetylation", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0000721", + "so:0000721", "gene", "dicistronic", "primary", @@ -4030,6 +4147,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` { "pred": "hasExactSynonym", "val": "gene with dicistronic primary transcript", + "xrefs": [], }, ], }, @@ -4068,10 +4186,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` { "pred": "hasExactSynonym", "val": "gene with dicistronic mRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", "val": "gene with dicistronic processed transcript", + "xrefs": [], }, ], }, @@ -4107,6 +4227,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` { "pred": "hasExactSynonym", "val": "gene with stop codon read through", + "xrefs": [], }, ], }, @@ -4114,15 +4235,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000711", + "so:0000712", "gene", - "mrna", - "recoded", + "transcript", "translational", - "bypass", + "frameshift", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000711", - "lbl": "gene_with_mRNA_recoded_by_translational_bypass", + "id": "http://purl.obolibrary.org/obo/SO_0000712", + "lbl": "gene_with_transcript_with_translational_frameshift", "meta": { "basicPropertyValues": [ { @@ -4131,7 +4252,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene with mRNA recoded by translational bypass.", + "val": "A gene encoding a transcript that has a translational frameshift.", "xrefs": [ "SO:xp", ], @@ -4139,7 +4260,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with mRNA recoded by translational bypass", + "val": "gene with transcript with translational frameshift", + "xrefs": [], }, ], }, @@ -4147,15 +4269,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000712", + "so:0000711", "gene", - "transcript", + "mrna", + "recoded", "translational", - "frameshift", - "encoding", + "bypass", ], - "id": "http://purl.obolibrary.org/obo/SO_0000712", - "lbl": "gene_with_transcript_with_translational_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0000711", + "lbl": "gene_with_mRNA_recoded_by_translational_bypass", "meta": { "basicPropertyValues": [ { @@ -4164,7 +4286,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "definition": { - "val": "A gene encoding a transcript that has a translational frameshift.", + "val": "A gene with mRNA recoded by translational bypass.", "xrefs": [ "SO:xp", ], @@ -4172,7 +4294,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with transcript with translational frameshift", + "val": "gene with mRNA recoded by translational bypass", + "xrefs": [], }, ], }, @@ -4194,10 +4317,6 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "lbl": "lincRNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2010-04-21T10:14:24Z", @@ -4206,6 +4325,10 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { "val": "A gene that encodes a long, intervening non-coding RNA.", @@ -4219,6 +4342,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` { "pred": "hasExactSynonym", "val": "lincRNA gene", + "xrefs": [], }, ], }, @@ -4244,22 +4368,24 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "nicole", }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-09-27T10:44:00Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2017-09-27T10:44:00Z", + }, ], "definition": { "val": "A gene that encodes an antisense long, non-coding RNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", "val": "antisense lncRNA gene", + "xrefs": [], }, ], }, @@ -4270,9 +4396,9 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "so:0002183", "sense", "overlap", - "ncrna", - "gene", "lncrna", + "gene", + "ncrna", "encodes", "long", "non", @@ -4280,13 +4406,9 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "rna", ], "id": "http://purl.obolibrary.org/obo/SO_0002183", - "lbl": "sense_overlap_ncRNA_gene", + "lbl": "sense_overlap_lncRNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-09-27T10:48:05Z", @@ -4295,22 +4417,33 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + ], + "comments": [ + "Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579.", ], "definition": { "val": "A gene that encodes a sense overlap long non-coding RNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "sense overlap lncRNA gene", + "val": "sense_overlap_lncRNA_gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense overlap ncRNA gene", + "val": "sense overlap lncRNA gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense_overlap_lncRNA_gene", + "val": "sense overlap ncRNA gene", + "xrefs": [], }, ], }, @@ -4321,9 +4454,9 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "so:0002184", "sense", "intronic", - "ncrna", - "gene", "lncrna", + "gene", + "ncrna", "encodes", "long", "non", @@ -4331,9 +4464,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "rna", ], "id": "http://purl.obolibrary.org/obo/SO_0002184", - "lbl": "sense_intronic_ncRNA_gene", + "lbl": "sense_intronic_lncRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "nicole", @@ -4342,26 +4479,29 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-09-27T11:03:50Z", }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, + ], + "comments": [ + "Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579.", ], "definition": { "val": "A gene that encodes a sense intronic long non-coding RNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", "val": "sense intronic lncRNA gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense intronic ncRNA gene", + "val": "sense_intronic_lncRNA_gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense_intronic_lncRNA_gene", + "val": "sense intronic ncRNA gene", + "xrefs": [], }, ], }, @@ -4373,6 +4513,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "bidirectional", "promoter", "lncrna", + "gene", "non", "coding", "locus", @@ -4380,7 +4521,6 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "within", "region", "protein", - "gene", "transcription", "proceeding", "opposite", @@ -4388,13 +4528,9 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "strand", ], "id": "http://purl.obolibrary.org/obo/SO_0002185", - "lbl": "bidirectional_promoter_lncRNA", + "lbl": "bidirectional_promoter_lncRNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-10-03T11:43:48Z", @@ -4403,17 +4539,35 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + ], + "comments": [ + "This is a gencode term. See GitHub Issue #408. Synonyms "bidirectional promoter lncRNA gene" and "bidirectional_promoter_lncRNA_gene" added 23 April 2021 by David Sant. See GitHub Issue #506.", ], "definition": { "val": "A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand.", "xrefs": [ - "https://www.gencodegenes.org/gencode_biotypes.html", + "https://www.gencodegenes.org/pages/biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", "val": "bidirectional promoter lncRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "bidirectional promoter lncRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "bidirectional_promoter_lncRNA_gene", + "xrefs": [], }, ], }, @@ -4421,93 +4575,72 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002181", - "ribozyme", + "so:0002360", + "cytosolic", + "rrna", "gene", - "encodes", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002181", - "lbl": "ribozyme_gene", + "id": "http://purl.obolibrary.org/obo/SO_0002360", + "lbl": "cytosolic_rRNA_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T04:30:40Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-09-27T10:31:09Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], "definition": { - "val": "A gene that encodes a ribozyme.", + "val": "A gene that codes for cytosolic rRNA.", + "xrefs": [], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "ribozyme gene", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0002123", - "ig", - "c", + "so:0001271", + "tmrna", "gene", - "igc", - "immunoglobulin", - "constant", - "germline", - "codes", - "region", - "chain", + "bacterial", + "rna", + "trna", + "mrna", + "like", + "properties", ], - "id": "http://purl.obolibrary.org/obo/SO_0002123", - "lbl": "IG_C_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001271", + "lbl": "tmRNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T15:57:29Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", + "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.", ], "definition": { - "val": "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain.", - "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", - ], + "val": "A bacterial RNA with both tRNA and mRNA like properties.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "IGC_gene", - }, - { - "pred": "hasExactSynonym", - "val": "Immunoglobulin_Constant_germline_Gene", - }, - { - "pred": "hasExactSynonym", - "val": "immunoglobulin_C_gene", + "val": "tmRNA gene", + "xrefs": [], }, ], }, @@ -4515,61 +4648,41 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002124", - "ig", - "d", + "so:0001272", + "trna", "gene", - "igd", - "immunoglobulin", - "diversity", - "rearranges", - "dna", - "level", - "codes", - "region", - "variable", - "domain", - "immunoglobuin", - ], - "id": "http://purl.obolibrary.org/obo/SO_0002124", - "lbl": "IG_D_gene", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T15:59:10Z", - }, + "noncoding", + "rna", + "binds", + "specific", + "amino", + "acid", + "allow", + "used", + "ribosome", + "translation", + ], + "id": "http://purl.obolibrary.org/obo/SO_0001272", + "lbl": "tRNA_gene", + "meta": { + "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", + "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.", ], "definition": { - "val": "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene.", - "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", - ], + "val": "A noncoding RNA that binds to a specific amino acid to allow that amino acid to be used by the ribosome during translation of RNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "IGD_gene", - }, - { - "pred": "hasExactSynonym", - "val": "Immunoglobulin_Diversity_ gene", - }, - { - "pred": "hasExactSynonym", - "val": "immunoglobulin_D_gene", + "val": "tRNA gene", + "xrefs": [], }, ], }, @@ -4577,32 +4690,25 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002125", - "ig", - "j", + "so:0001638", + "pirna", "gene", - "joining", - "immunoglobulin", - "rearranges", - "dna", - "level", - "codes", - "region", - "variable", - "domain", - "chain", + "encodes", + "piwi", + "associated", + "rna", ], - "id": "http://purl.obolibrary.org/obo/SO_0002125", - "lbl": "IG_J_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001638", + "lbl": "piRNA_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", + "val": "kareneilbeck", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:00:36Z", + "val": "2010-04-21T10:11:36Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -4610,27 +4716,64 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", + "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.", ], "definition": { - "val": "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.", + "val": "A gene that encodes for an piwi associated RNA.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "IG_joining_gene", + "val": "piRNA gene", + "xrefs": [], }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0001267", + "snorna", + "gene", + "encoding", + "small", + "noncoding", + "rna", + "participates", + "processing", + "chemical", + "modifications", + "many", + "rnas", + "including", + "ribosomal", + "spliceosomal", + ], + "id": "http://purl.obolibrary.org/obo/SO_0001267", + "lbl": "snoRNA_gene", + "meta": { + "basicPropertyValues": [ { - "pred": "hasExactSynonym", - "val": "Immunoglobulin_Joining_Gene", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, + ], + "comments": [ + "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. Added additional children of snoRNA on 18 Nov 2021 at the request of Steven Marygold. See GitHub Issue #519.", + ], + "definition": { + "val": "A gene encoding a small noncoding RNA that participates in the processing or chemical modifications of many RNAs, including ribosomal RNAs and spliceosomal RNAs.", + "xrefs": [], + }, + "synonyms": [ { "pred": "hasExactSynonym", - "val": "immunoglobulin_J_gene", + "val": "snoRNA gene", + "xrefs": [], }, ], }, @@ -4638,60 +4781,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002126", - "ig", - "v", + "so:0001268", + "snrna", "gene", - "igv", - "variable", - "immunoglobulin", - "rearranges", - "dna", - "level", - "codes", - "region", - "domain", - "chain", + "small", + "nuclear", + "rna", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002126", - "lbl": "IG_V_gene", + "id": "http://purl.obolibrary.org/obo/SO_0001268", + "lbl": "snRNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:02:09Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", + "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.", ], "definition": { - "val": "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain.", + "val": "A gene that encodes a small nuclear RNA.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", + "http://en.wikipedia.org/wiki/Small_nuclear_RNA", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "IGV_gene", - }, - { - "pred": "hasExactSynonym", - "val": "IG_variable_gene", + "val": "snRNA gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "Immunoglobulin_variable_gene", + "val": "small nuclear RNA gene", + "xrefs": [], }, ], }, @@ -4699,48 +4824,57 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002134", - "tr", - "c", + "so:0001265", + "mirna", "gene", - "cell", - "receptor", - "constant", - "codes", - "region", - "chain", + "strna", + "small", + "noncoding", + "rna", + "approximately", + "22", + "nucleotides", + "length", + "may", + "involved", + "regulation", + "expression", ], - "id": "http://purl.obolibrary.org/obo/SO_0002134", - "lbl": "TR_C_Gene", + "id": "http://purl.obolibrary.org/obo/SO_0001265", + "lbl": "miRNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:19:20Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val": "SO:0001270", + }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", + "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.", ], "definition": { - "val": "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain.", - "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", - ], + "val": "A small noncoding RNA of approximately 22 nucleotides in length which may be involved in regulation of gene expression.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "T_cell_receptor_C_gene", + "val": "miRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "stRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "stRNA_gene", + "xrefs": [], }, ], }, @@ -4748,52 +4882,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002135", - "tr", - "d", + "so:0001639", + "rnase", + "p", + "rna", "gene", - "cell", - "receptor", - "rearranges", - "dna", - "level", - "codes", - "diversity", - "region", - "variable", - "domain", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002135", - "lbl": "TR_D_Gene", + "id": "http://purl.obolibrary.org/obo/SO_0001639", + "lbl": "RNase_P_RNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:20:06Z", + "val": "2010-04-21T10:13:23Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", + "Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533.", ], "definition": { - "val": "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene.", + "val": "A gene that encodes an RNase P RNA.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "T_cell_receptor_D_gene", + "val": "RNase P RNA gene", + "xrefs": [], }, ], }, @@ -4801,53 +4927,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002136", - "tr", - "j", + "so:0001640", + "rnase", + "mrp", + "rna", "gene", - "cell", - "receptor", - "joining", - "rearranges", - "dna", - "level", - "codes", - "region", - "variable", - "domain", - "chain", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002136", - "lbl": "TR_J_Gene", + "id": "http://purl.obolibrary.org/obo/SO_0001640", + "lbl": "RNase_MRP_RNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:20:36Z", + "val": "2010-04-21T10:13:58Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", + "Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533.", ], "definition": { - "val": "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain.", + "val": "A gene that encodes a RNase_MRP_RNA.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", + "SO:ke", ], }, "synonyms": [ { - "pred": "hasExactSynonym", - "val": "T_cell_receptor_J_gene", + "pred": "hasRelatedSynonym", + "val": "RNase MRP RNA gene", + "xrefs": [], }, ], }, @@ -4855,23 +4972,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0002137", - "tr", - "v", + "so:0002181", + "ribozyme", "gene", - "cell", - "receptor", - "variable", - "rearranges", - "dna", - "level", - "codes", - "region", - "domain", - "chain", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002137", - "lbl": "TR_V_Gene", + "id": "http://purl.obolibrary.org/obo/SO_0002181", + "lbl": "ribozyme_gene", "meta": { "basicPropertyValues": [ { @@ -4880,27 +4987,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:21:04Z", + "val": "2017-09-27T10:31:09Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", - ], "definition": { - "val": "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain.", - "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", - ], + "val": "A gene that encodes a ribozyme.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "T_cell_receptor_V_gene", + "val": "ribozyme gene", + "xrefs": [], }, ], }, @@ -4908,34 +5010,56 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000698", + "so:0002364", + "mt", + "lsu", + "rrna", "gene", - "stop", - "codon", - "redefined", - "pyrrolysine", - "encoding", - "mrna", + "mitochondrial", + "large", + "subunit", + "21s", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000698", - "lbl": "gene_with_stop_codon_redefined_as_pyrrolysine", + "id": "http://purl.obolibrary.org/obo/SO_0002364", + "lbl": "mt_LSU_rRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T04:57:49Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + ], + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). Obsoleted term rRNA_21S_gene (SO:0002241) merged into this term on 12 Sept 2022, see GitHub Issue #513.", ], "definition": { - "val": "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene that codes for mitochondrial LSU rRNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with stop codon redefined as pyrrolysine", + "val": "mitochondrial large subunit rRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "rRNA_21S_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "rRNA 21S gene", + "xrefs": [], }, ], }, @@ -4943,53 +5067,62 @@ exports[`OntologyStore can query SO gene terms and parts of genes 1`] = ` }, { "fullTextWords": [ - "so:0000710", + "so:0002365", + "mt", + "ssu", + "rrna", "gene", - "stop", - "codon", - "redefined", - "selenocysteine", - "encoding", - "mrna", + "mitochondrial", + "small", + "subunit", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000710", - "lbl": "gene_with_stop_codon_redefined_as_selenocysteine", + "id": "http://purl.obolibrary.org/obo/SO_0002365", + "lbl": "mt_SSU_rRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T04:58:07Z", + }, + ], + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "A gene encoding an mRNA that has the stop codon redefined as selenocysteine.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene that codes for mitochondrial SSU rRNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene with stop codon redefined as selenocysteine", + "val": "mitochondrial small subunit rRNA gene", + "xrefs": [], }, ], }, "type": "CLASS", }, -] -`; - -exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` -[ { "fullTextWords": [ - "so:0000831", + "so:0000654", + "maxicircle", "gene", - "member", - "region", + "maxi", + "circle", + "mitochondrial", + "located", ], - "id": "http://purl.obolibrary.org/obo/SO_0000831", - "lbl": "gene_member_region", + "id": "http://purl.obolibrary.org/obo/SO_0000654", + "lbl": "maxicircle_gene", "meta": { "basicPropertyValues": [ { @@ -4997,22 +5130,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], - "comments": [ - "A manufactured term used to allow the parts of a gene to have an is_a path to the root.", - ], "definition": { - "val": "A region of a gene.", + "val": "A mitochondrial gene located in a maxicircle.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene member region", + "val": "maxi-circle gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "maxicircle gene", + "xrefs": [], }, ], }, @@ -5020,13 +5153,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000842", + "so:0000975", + "minicircle", "gene", - "component", - "region", + "found", + "within", ], - "id": "http://purl.obolibrary.org/obo/SO_0000842", - "lbl": "gene_component_region", + "id": "http://purl.obolibrary.org/obo/SO_0000975", + "lbl": "minicircle_gene", "meta": { "basicPropertyValues": [ { @@ -5034,13 +5168,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], + "definition": { + "val": "A gene found within a minicircle.", + "xrefs": [], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene component region", + "val": "minicircle gene", + "xrefs": [], }, ], }, @@ -5048,43 +5184,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000673", - "transcript", - "insdc", - "feature:misc", - "rna", - "synthesized", + "so:0002137", + "tr", + "v", + "gene", + "cell", + "receptor", + "variable", + "rearranges", "dna", - "template", - "polymerase", + "level", + "codes", + "region", + "domain", + "chain", ], - "id": "http://purl.obolibrary.org/obo/SO_0000673", - "lbl": "transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002137", + "lbl": "TR_V_Gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:21:04Z", + }, + ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", + "val": "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain.", "xrefs": [ - "SO:ma", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:misc_RNA", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/RNA", + "pred": "hasExactSynonym", + "val": "T_cell_receptor_V_gene", + "xrefs": [], }, ], }, @@ -5092,49 +5238,49 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002188", - "functional", + "so:0002134", + "tr", + "c", "gene", + "cell", + "receptor", + "constant", + "codes", "region", - "member", - "encodes", - "sequence", - "directly", - "contributes", - "molecular", - "function", - "product", + "chain", ], - "id": "http://purl.obolibrary.org/obo/SO_0002188", - "lbl": "functional_gene_region", + "id": "http://purl.obolibrary.org/obo/SO_0002134", + "lbl": "TR_C_Gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "nicole", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-12-15T11:08:43Z", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "val": "2016-08-23T16:19:20Z", }, ], "comments": [ - "A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors.", + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product.", + "val": "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain.", "xrefs": [ - "Clingen:mb", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "functional gene region", + "val": "T_cell_receptor_C_gene", + "xrefs": [], }, ], }, @@ -5142,53 +5288,54 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0005836", - "regulatory", + "so:0002136", + "tr", + "j", + "gene", + "cell", + "receptor", + "joining", + "rearranges", + "dna", + "level", + "codes", "region", - "insdc", - "feature:regulatory", - "qualifier:other", - "sequence", - "involved", - "control", - "biological", - "process", + "variable", + "domain", + "chain", ], - "id": "http://purl.obolibrary.org/obo/SO_0005836", - "lbl": "regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002136", + "lbl": "TR_J_Gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:20:36Z", + }, + ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "A region of sequence that is involved in the control of a biological process.", + "val": "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain.", "xrefs": [ - "SO:ke", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:other", - }, { "pred": "hasExactSynonym", - "val": "regulatory region", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Regulatory_region", + "val": "T_cell_receptor_J_gene", + "xrefs": [], }, ], }, @@ -5196,48 +5343,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000183", - "non", - "transcribed", - "region", - "sequence", - "nontranscribed", + "so:0002135", + "tr", + "d", "gene", + "cell", + "receptor", + "rearranges", + "dna", + "level", + "codes", + "diversity", + "region", + "variable", + "domain", ], - "id": "http://purl.obolibrary.org/obo/SO_0000183", - "lbl": "non_transcribed_region", + "id": "http://purl.obolibrary.org/obo/SO_0002135", + "lbl": "TR_D_Gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:20:06Z", + }, + ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "A region of the gene which is not transcribed.", + "val": "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene.", "xrefs": [ - "SO:ke", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "non transcribed region", - }, - { - "pred": "hasExactSynonym", - "val": "non-transcribed sequence", - }, - { - "pred": "hasExactSynonym", - "val": "nontranscribed region", - }, - { - "pred": "hasExactSynonym", - "val": "nontranscribed sequence", + "val": "T_cell_receptor_D_gene", + "xrefs": [], }, ], }, @@ -5245,26 +5397,63 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000997", + "so:0002125", + "ig", + "j", "gene", - "fragment", + "immunoglobulin", + "joining", + "rearranges", + "dna", + "level", + "codes", + "region", + "variable", + "domain", + "chain", ], - "id": "http://purl.obolibrary.org/obo/SO_0000997", - "lbl": "gene_fragment", + "id": "http://purl.obolibrary.org/obo/SO_0002125", + "lbl": "IG_J_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:00:36Z", + }, ], "comments": [ - "This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], + "definition": { + "val": "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.", + "xrefs": [ + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene fragment", + "val": "immunoglobulin_J_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "Immunoglobulin_Joining_Gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "IG_joining_gene", + "xrefs": [], }, ], }, @@ -5272,30 +5461,64 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001240", - "tss", - "region", + "so:0002124", + "ig", + "d", "gene", + "immunoglobulin", + "igd", + "diversity", + "rearranges", + "dna", + "level", + "codes", + "region", + "variable", + "domain", + "immunoglobuin", ], - "id": "http://purl.obolibrary.org/obo/SO_0001240", - "lbl": "TSS_region", + "id": "http://purl.obolibrary.org/obo/SO_0002124", + "lbl": "IG_D_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T15:59:10Z", + }, + ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "The region of a gene from the 5' most TSS to the 3' TSS.", + "val": "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene.", "xrefs": [ - "BBOP:nw", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "TSS region", + "val": "immunoglobulin_D_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "IGD_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "Immunoglobulin_Diversity_ gene", + "xrefs": [], }, ], }, @@ -5303,85 +5526,124 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002026", - "intein", - "encoding", - "region", - "nucleotide", - "sequence", - "encodes", - "portion", - "precursor", + "so:0002126", + "ig", + "v", "gene", + "igv", + "variable", + "immunoglobulin", + "rearranges", + "dna", + "level", + "codes", + "region", + "domain", + "chain", ], - "id": "http://purl.obolibrary.org/obo/SO_0002026", - "lbl": "intein_encoding_region", + "id": "http://purl.obolibrary.org/obo/SO_0002126", + "lbl": "IG_V_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-07-14T11:53:21Z", + "val": "2016-08-23T16:02:09Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, ], "comments": [ - "Requested by Janos Demeter 2014.", + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "The nucleotide sequence which encodes the intein portion of the precursor gene.", + "val": "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain.", "xrefs": [ - "PMID:8165123", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "IGV_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "IG_variable_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "Immunoglobulin_variable_gene", + "xrefs": [], + }, + ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:3000000", + "so:0002123", + "ig", + "c", "gene", - "segment", - "component", + "immunoglobulin", + "constant", + "germline", + "igc", + "codes", "region", - "acts", - "recombinational", - "unit", - "whose", - "functional", - "form", - "generated", - "somatic", - "recombination", + "chain", ], - "id": "http://purl.obolibrary.org/obo/SO_3000000", - "lbl": "gene_segment", + "id": "http://purl.obolibrary.org/obo/SO_0002123", + "lbl": "IG_C_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T15:57:29Z", + }, ], "comments": [ - "Requested by tracker 2021594, July 2008, by Alex.", + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.", ], "definition": { - "val": "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.", + "val": "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain.", "xrefs": [ - "GOC:add", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene segment", + "val": "Immunoglobulin_Constant_germline_Gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "IGC_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "immunoglobulin_C_gene", + "xrefs": [], }, ], }, @@ -5389,12 +5651,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000078", - "polycistronic", - "transcript", + "so:0000129", + "gene", + "silenced", + "dna", + "methylation", ], - "id": "http://purl.obolibrary.org/obo/SO_0000078", - "lbl": "polycistronic_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000129", + "lbl": "gene_silenced_by_DNA_methylation", "meta": { "basicPropertyValues": [ { @@ -5403,7 +5667,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A transcript that is polycistronic.", + "val": "A gene that is silenced by DNA methylation.", "xrefs": [ "SO:xp", ], @@ -5411,7 +5675,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "polycistronic transcript", + "val": "gene silenced by DNA methylation", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "methylation-silenced gene", + "xrefs": [], }, ], }, @@ -5419,13 +5689,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000118", - "transcript", - "translational", - "frameshift", + "so:0001226", + "gene", + "silenced", + "histone", + "methylation", ], - "id": "http://purl.obolibrary.org/obo/SO_0000118", - "lbl": "transcript_with_translational_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0001226", + "lbl": "gene_silenced_by_histone_methylation", "meta": { "basicPropertyValues": [ { @@ -5434,7 +5705,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A transcript with a translational frameshift.", + "val": "A gene that is silenced by histone methylation.", "xrefs": [ "SO:xp", ], @@ -5442,7 +5713,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "transcript with translational frameshift", + "val": "gene silenced by histone methylation", + "xrefs": [], }, ], }, @@ -5450,22 +5722,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000185", - "primary", - "transcript", - "insdc", - "feature:precursor", - "rna", - "feature:prim", - "precursor", - "initial", - "state", - "requires", - "modification", - "functional", + "so:0001227", + "gene", + "silenced", + "histone", + "deacetylation", ], - "id": "http://purl.obolibrary.org/obo/SO_0000185", - "lbl": "primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001227", + "lbl": "gene_silenced_by_histone_deacetylation", "meta": { "basicPropertyValues": [ { @@ -5474,35 +5738,61 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A transcript that in its initial state requires modification to be functional.", + "val": "A gene that is silenced by histone deacetylation.", "xrefs": [ - "SO:ma", + "SO:xp", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "INSDC_feature:precursor_RNA", + "val": "gene silenced by histone deacetylation", + "xrefs": [], }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0002368", + "plastid", + "ssu", + "rrna", + "gene", + "small", + "subunit", + "codes", + ], + "id": "http://purl.obolibrary.org/obo/SO_0002368", + "lbl": "plastid_SSU_rRNA_gene", + "meta": { + "basicPropertyValues": [ { - "pred": "hasExactSynonym", - "val": "INSDC_feature:prim_transcript", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, { - "pred": "hasExactSynonym", - "val": "precursor RNA", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:01:03Z", }, { - "pred": "hasExactSynonym", - "val": "primary transcript", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", }, ], - "xrefs": [ + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], + "definition": { + "val": "A gene that codes for plastid SSU rRNA.", + "xrefs": [], + }, + "synonyms": [ { - "val": "http://en.wikipedia.org/wiki/Primary_transcript", + "pred": "hasExactSynonym", + "val": "plastid small subunit rRNA gene", + "xrefs": [], }, ], }, @@ -5510,60 +5800,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000233", - "mature", - "transcript", - "undergone", - "necessary", - "modifications", - "function", - "eukaryotes", - "includes", - "example", - "processing", - "introns", - "cleavage", - "base", - "modification", - "ends", - "addition", - "bases", - "bacteria", - "functional", - "mrnas", - "usually", - "modified", + "so:0002367", + "plastid", + "lsu", + "rrna", + "gene", + "large", + "subunit", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000233", - "lbl": "mature_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002367", + "lbl": "plastid_LSU_rRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:00:49Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, ], "comments": [ - "A processed transcript cannot contain introns.", + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene that codes for plastid LSU rRNA.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "mature transcript", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Mature_transcript", + "val": "plastid large subunit rRNA gene", + "xrefs": [], }, ], }, @@ -5571,14 +5845,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000278", - "transcript", - "bound", - "nucleic", - "acid", + "so:0000698", + "gene", + "stop", + "codon", + "redefined", + "pyrrolysine", + "encoding", + "mrna", ], - "id": "http://purl.obolibrary.org/obo/SO_0000278", - "lbl": "transcript_bound_by_nucleic_acid", + "id": "http://purl.obolibrary.org/obo/SO_0000698", + "lbl": "gene_with_stop_codon_redefined_as_pyrrolysine", "meta": { "basicPropertyValues": [ { @@ -5586,11 +5863,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], - "comments": [ - "Formerly called transcript_by_bound_nucleic_acid.", - ], "definition": { - "val": "A transcript that is bound by a nucleic acid.", + "val": "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.", "xrefs": [ "SO:xp", ], @@ -5598,7 +5872,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "transcript bound by nucleic acid", + "val": "gene with stop codon redefined as pyrrolysine", + "xrefs": [], }, ], }, @@ -5606,13 +5881,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000279", - "transcript", - "bound", - "protein", + "so:0000710", + "gene", + "stop", + "codon", + "redefined", + "selenocysteine", + "encoding", + "mrna", ], - "id": "http://purl.obolibrary.org/obo/SO_0000279", - "lbl": "transcript_bound_by_protein", + "id": "http://purl.obolibrary.org/obo/SO_0000710", + "lbl": "gene_with_stop_codon_redefined_as_selenocysteine", "meta": { "basicPropertyValues": [ { @@ -5620,11 +5899,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], - "comments": [ - "Formerly called transcript_by_bound_protein.", - ], "definition": { - "val": "A transcript that is bound by a protein.", + "val": "A gene encoding an mRNA that has the stop codon redefined as selenocysteine.", "xrefs": [ "SO:xp", ], @@ -5632,7 +5908,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "transcript bound by protein", + "val": "gene with stop codon redefined as selenocysteine", + "xrefs": [], }, ], }, @@ -5640,41 +5917,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000372", - "enzymatic", - "rna", - "sequence", - "catalytic", - "activity", - "without", - "associated", - "ribonucleoprotein", + "so:0002362", + "cytosolic", + "ssu", + "rrna", + "gene", + "small", + "subunit", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000372", - "lbl": "enzymatic_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0002362", + "lbl": "cytosolic_SSU_rRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T04:37:02Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "comments": [ - "This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.", + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.", - "xrefs": [ - "RSC:cb", - ], + "val": "A gene that codes for cytosolic SSU rRNA.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "enzymatic RNA", + "val": "cytosolic small subunit rRNA gene", + "xrefs": [], }, ], }, @@ -5682,76 +5962,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000479", - "trans", - "spliced", - "transcript", - "insdc", - "feature:trna", - "qualifier:trans", - "splicing", + "so:0002361", + "cytosolic", + "lsu", + "rrna", + "gene", + "large", + "subunit", + "codes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000479", - "lbl": "trans_spliced_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002361", + "lbl": "cytosolic_LSU_rRNA_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], - "definition": { - "val": "A transcript that is trans-spliced.", - "xrefs": [ - "SO:xp", - ], - }, - "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:trans_splicing", - }, - { - "pred": "hasExactSynonym", - "val": "trans spliced transcript", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", }, { - "pred": "hasExactSynonym", - "val": "trans-spliced transcript", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T04:32:20Z", }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0000665", - "monocistronic", - "transcript", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000665", - "lbl": "monocistronic_transcript", - "meta": { - "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], "definition": { - "val": "A transcript that is monocistronic.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene that codes for cytosolic LSU rRNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "monocistronic transcript", + "val": "cytosolic large subunit rRNA gene", + "xrefs": [], }, ], }, @@ -5759,66 +6007,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000681", - "aberrant", - "processed", - "transcript", - "incorrectly", - "example", - "failure", - "splicing", - "one", - "exons", + "so:0002339", + "scarna", + "gene", + "small", + "cajal", + "body", + "specific", + "rna", + "encodes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000681", - "lbl": "aberrant_processed_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002339", + "lbl": "scaRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "definition": { - "val": "A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.", - "xrefs": [ - "SO:ke", - ], - }, - "synonyms": [ { - "pred": "hasExactSynonym", - "val": "aberrant processed transcript", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-04-24T16:59:30Z", }, ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0000873", - "edited", - "transcript", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000873", - "lbl": "edited_transcript", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, + "comments": [ + "Added as a request from FlyBase. See GitHub Issue #510", ], "definition": { - "val": "A transcript that is edited.", + "val": "A gene that encodes for a scaRNA (small Cajal body-specific RNA).", "xrefs": [ - "SO:ke", + "PMID:27775477", + "PMID:28869095", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "edited transcript", + "val": "Small Cajal body-specific RNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "scaRNA gene", + "xrefs": [], }, ], }, @@ -5826,46 +6061,87 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001503", - "processed", - "transcript", - "open", - "reading", - "frame", - "identified", + "so:0002376", + "h", + "aca", + "box", + "snorna", + "gene", + "codes", + "members", + "family", + "contain", + "triplet", + "exactly", + "nt", + "upstream", + "end", + "hinge", + "region", + "links", + "two", + "structurally", + "similar", + "functional", + "domains", + "molecule", + "boxes", + "important", + "biosynthesis", "function", - "determined", + "snornas", + "involved", + "rrna", + "processing", + "others", + "known", + "predicted", + "participate", + "selection", + "uridine", + "nucleosides", + "converted", + "pseudouridines", + "site", + "mediated", + "direct", + "base", + "pairing", + "one", + "targeting", ], - "id": "http://purl.obolibrary.org/obo/SO_0001503", - "lbl": "processed_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002376", + "lbl": "H_ACA_box_snoRNA_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2009-12-21T05:37:14Z", + "val": "2021-11-19T05:50:14Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, ], "comments": [ - "Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.", + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565.", ], "definition": { - "val": "A transcript for which no open reading frame has been identified and for which no other function has been determined.", + "val": "A gene that codes for H_ACA_box_snoRNA. Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.", "xrefs": [ - "MGI:hdeen", + "PMID:12457565", + "PMID:22065625", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "processed transcript", + "val": "box H/ACA snoRNA gene, H ACA box snoRNA gene, H/ACA box snoRNA gene", + "xrefs": [], }, ], }, @@ -5873,40 +6149,91 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002138", - "predicted", - "transcript", - "feature", - "yet", - "validated", - ], - "id": "http://purl.obolibrary.org/obo/SO_0002138", - "lbl": "predicted_transcript", - "meta": { - "basicPropertyValues": [ + "so:0002375", + "c", + "d", + "box", + "snorna", + "gene", + "codes", + "snornas", + "also", + "contain", + "long", + "10", + "nt", + "sequences", + "complementary", + "rrna", + "boxes", + "well", + "usually", + "located", + "close", + "proximity", + "form", + "structure", + "known", + "motif", + "important", + "stability", + "processing", + "nucleolar", + "targeting", + "function", + "small", + "number", + "involved", + "however", + "predicted", + "serve", + "guide", + "rnas", + "ribose", + "methylation", + "involves", + "direct", + "base", + "pairing", + "site", + "modified", + "selection", + "nucleotide", + "fixed", + "distance", + ], + "id": "http://purl.obolibrary.org/obo/SO_0002375", + "lbl": "C_D_box_snoRNA_gene", + "meta": { + "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:27:38Z", + "val": "evan", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:49:55Z", + }, + ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565.", ], "definition": { - "val": "A transcript feature that has been predicted but is not yet validated.", + "val": "A gene that codes a C_D_box_snoRNA. Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.", "xrefs": [ - "SO:ke", + "PMID:12457565", + "PMID:22065625", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "predicted transcript", + "val": "box C/D snoRNA gene, C D box snoRNA gene, C/D box snoRNA gene", + "xrefs": [], }, ], }, @@ -5914,30 +6241,52 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:1001187", - "alternatively", - "spliced", - "transcript", + "so:0002236", + "cytosolic", + "rrna", + "18s", + "gene", + "codes", + "functions", + "small", + "subunit", + "ribosome", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_1001187", - "lbl": "alternatively_spliced_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002236", + "lbl": "cytosolic_rRNA_18S_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-05-07T16:12:30Z", + }, + ], + "comments": [ + "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "A transcript that is alternatively spliced.", - "xrefs": [ - "SO:xp", - ], + "val": "A gene which codes for 18S_rRNA, which functions as the small subunit of the ribosome in eukaryotes.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "alternatively spliced transcript", + "val": "18S_rRNA_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "18S rRNA gene", + "xrefs": [], }, ], }, @@ -5945,44 +6294,52 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001679", - "transcription", - "regulatory", - "region", - "involved", - "control", - "process", + "so:0002237", + "cytosolic", + "rrna", + "16s", + "gene", + "codes", + "functions", + "small", + "subunit", + "ribosome", + "prokaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001679", - "lbl": "transcription_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002237", + "lbl": "cytosolic_rRNA_16S_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-10-12T03:49:35Z", + "val": "david", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-05-07T16:12:30Z", + }, + ], + "comments": [ + "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "A regulatory region that is involved in the control of the process of transcription.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene which codes for 16S_rRNA, which functions as the small subunit of the ribosome in prokaryotes.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "transcription regulatory region", + "val": "16S rRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "16S_rRNA_gene", + "xrefs": [], }, ], }, @@ -5990,41 +6347,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001680", - "translation", - "regulatory", - "region", - "involved", - "control", - "process", + "so:0002238", + "cytosolic", + "rrna", + "5s", + "gene", + "codes", + "portion", + "large", + "subunit", + "ribosome", + "eukaryotes", + "prokaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001680", - "lbl": "translation_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002238", + "lbl": "cytosolic_rRNA_5S_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-10-12T03:52:45Z", + "val": "2020-05-07T16:12:30Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", }, ], + "comments": [ + "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], "definition": { - "val": "A regulatory region that is involved in the control of the process of translation.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene which codes for 5S_rRNA, which is a portion of the large subunit of the ribosome in both eukaryotes and prokaryotes.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "translation regulatory region", + "val": "5S rRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "5S_rRNA_gene", + "xrefs": [], }, ], }, @@ -6032,41 +6401,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001681", - "recombination", - "regulatory", - "region", - "involved", - "control", - "process", + "so:0002239", + "cytosolic", + "rrna", + "28s", + "gene", + "codes", + "functions", + "component", + "large", + "subunit", + "ribosome", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001681", - "lbl": "recombination_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002239", + "lbl": "cytosolic_rRNA_28S_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-05-07T16:12:30Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-10-12T03:53:35Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], "definition": { - "val": "A regulatory region that is involved in the control of the process of recombination.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene which codes for 28S_rRNA, which functions as a component of the large subunit of the ribosome in eukaryotes.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "recombination regulatory region", + "val": "28S rRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "28S_rRNA_gene", + "xrefs": [], }, ], }, @@ -6074,53 +6455,65 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001682", - "replication", - "regulatory", - "region", - "insdc", - "feature:regulatory", - "qualifier:replication", - "involved", - "control", - "process", - "nucleotide", + "so:0002336", + "cytosolic", + "rrna", + "2s", + "gene", + "encodes", + "ribosomal", + "rna", + "functions", + "component", + "large", + "subunit", + "ribosome", + "drosophila", + "least", + "diptera", ], - "id": "http://purl.obolibrary.org/obo/SO_0001682", - "lbl": "replication_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002336", + "lbl": "cytosolic_rRNA_2S_gene", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-10-12T03:54:09Z", + "val": "2021-04-23T22:59:30Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Added as a request from FlyBase. See GitHub Issue #507. Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", ], "definition": { - "val": "A regulatory region that is involved in the control of the process of nucleotide replication.", + "val": "A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera.", "xrefs": [ - "SO:ke", + "PMID: 118436", + "PMID: 29474379", + "PMID: 3136294", + "PMID:10788608", + "PMID:407103", + "PMID:4847940", + "PMID:768488", ], }, "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:replication_regulatory_region", + "val": "2S rRNA gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "replication regulatory region", + "val": "rRNA 2S gene", + "xrefs": [], }, ], }, @@ -6128,68 +6521,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002191", - "imprinting", - "control", - "region", - "insdc", - "feature:regulatory", - "qualifier:imprinting", - "regulatory", - "controls", - "epigenetic", - "affects", - "expression", - "target", - "genes", - "allele", - "parent", - "origin", - "specific", - "manner", - "associated", - "elements", - "may", - "include", - "differentially", - "methylated", - "regions", - "non", - "coding", - "rnas", + "so:0002242", + "cytosolic", + "rrna", + "25s", + "gene", + "codes", + "functions", + "component", + "large", + "subunit", + "ribosome", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002191", - "lbl": "imprinting_control_region", + "id": "http://purl.obolibrary.org/obo/SO_0002242", + "lbl": "cytosolic_rRNA_25S_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-05-07T16:12:30Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2018-01-04T17:35:34Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], "definition": { - "val": "A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs.", + "val": "A gene which codes for 25S_rRNA, which functions as a component of the large subunit of the ribosome in some eukaryotes.", + "xrefs": [], }, "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:imprinting_control_region", + "val": "25S_rRNA_gene", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "imprinting control region", + "val": "25S rRNA gene", + "xrefs": [], }, ], }, @@ -6197,46 +6575,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001741", - "pseudogenic", + "so:0002243", + "cytosolic", + "rrna", + "23s", "gene", - "segment", - "incorporated", - "somatic", - "recombination", - "final", - "transcript", - "results", - "nonfunctional", - "product", + "codes", + "functions", + "component", + "large", + "subunit", + "ribosome", + "prokaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001741", - "lbl": "pseudogenic_gene_segment", + "id": "http://purl.obolibrary.org/obo/SO_0002243", + "lbl": "cytosolic_rRNA_23S_gene", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "batchelorc", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2011-02-15T05:07:52Z", + "val": "2020-05-07T16:12:30Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", }, ], + "comments": [ + "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], "definition": { - "val": "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.", - "xrefs": [ - "SO:hd", - ], + "val": "A gene which codes for 23S_rRNA, which functions as a component of the large subunit of the ribosome in prokaryotes.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "pseudogenic gene segment", + "val": "23S_rRNA_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "23S rRNA gene", + "xrefs": [], }, ], }, @@ -6244,29 +6629,58 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000079", - "dicistronic", - "transcript", + "so:0002240", + "cytosolic", + "rrna", + "8s", + "gene", + "codes", + "functions", + "component", + "large", + "subunit", + "ribosome", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000079", - "lbl": "dicistronic_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002240", + "lbl": "cytosolic_rRNA_5_8S_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-05-07T16:12:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).", + ], "definition": { - "val": "A transcript that is dicistronic.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene which codes for 5_8S_rRNA (5.8S rRNA), which functions as a component of the large subunit of the ribosome in eukaryotes.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "dicistronic transcript", + "val": "5_8S rRNA gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "5_8S_rRNA_gene", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "5.8S rRNA gene", + "xrefs": [], }, ], }, @@ -6274,34 +6688,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000631", - "polycistronic", - "primary", - "transcript", - "encoding", - "one", + "so:0002374", + "c", + "d", + "h", + "aca", + "box", + "scarna", "gene", - "product", + "codes", + "possessing", + "sequence", + "motifs", + "guiding", + "methylation", + "pseudouridylation", + "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0000631", - "lbl": "polycistronic_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002374", + "lbl": "C-D_H_ACA_box_scaRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:41:06Z", + }, + ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", ], "definition": { - "val": "A primary transcript encoding for more than one gene product.", + "val": "A gene that codes for scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs.", "xrefs": [ - "SO:ke", + "PMID:17099227", + "PMID:24659245", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "polycistronic primary transcript", + "val": "C/D-H/ACA scaRNA gene", + "xrefs": [], }, ], }, @@ -6309,48 +6744,52 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000634", - "polycistronic", - "mrna", - "processed", - "transcript", - "encodes", - "multiple", - "proteins", - "least", - "two", - "non", - "overlapping", - "regions", + "so:0002372", + "c", + "d", + "box", + "scarna", + "gene", + "codes", + "possessing", + "sequence", + "motif", + "guiding", + "methylation", + "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0000634", - "lbl": "polycistronic_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002372", + "lbl": "C_D_box_scaRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:40:46Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", + ], "definition": { - "val": "An mRNA that encodes multiple proteins from at least two non-overlapping regions.", + "val": "A gene that codes for scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs.", "xrefs": [ - "SO:rd", + "PMID:17099227", + "PMID:24659245", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "polycistronic mRNA", - }, - { - "pred": "hasRelatedSynonym", - "val": "polycistronic processed transcript", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Polycistronic_mRNA", + "val": "C/D scaRNA gene", + "xrefs": [], }, ], }, @@ -6358,48 +6797,52 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000120", - "protein", - "coding", - "primary", - "transcript", - "pre", - "mrna", - "least", - "part", - "encodes", - "one", - "proteins", + "so:0002373", + "h", + "aca", + "box", + "scarna", + "gene", + "codes", + "possessing", + "sequence", + "motif", + "guiding", + "pseudouridylation", + "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0000120", - "lbl": "protein_coding_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002373", + "lbl": "H_ACA_box_scaRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:40:58Z", + }, ], "comments": [ - "May contain introns.", + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", ], "definition": { - "val": "A primary transcript that, at least in part, encodes one or more proteins.", + "val": "A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs.", "xrefs": [ - "SO:ke", + "PMID:17099227", + "PMID:24659245", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "protein coding primary transcript", - }, - { - "pred": "hasRelatedSynonym", - "val": "pre mRNA", + "val": "H/ACA scaRNA gene", + "xrefs": [], }, ], }, @@ -6407,41 +6850,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000483", - "nc", - "primary", - "transcript", - "noncoding", - "never", - "translated", - "protein", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000483", - "lbl": "nc_primary_transcript", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], + "so:0002380", + "pseudouridylation", + "guide", + "snorna", + "gene", + "codes", + "specifies", + "site", + "rna", + "molecule", + "base", + "pairing", + "short", + "sequence", + "around", + "target", + "residue", + ], + "id": "http://purl.obolibrary.org/obo/SO_0002380", + "lbl": "pseudouridylation_guide_snoRNA_gene", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:51:40Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", + ], "definition": { - "val": "A primary transcript that is never translated into a protein.", + "val": "A gene that codes for pseudouridylation_guide_snoRNA. A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.", "xrefs": [ - "SO:ke", + "PMID:12457565", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "nc primary transcript", - }, - { - "pred": "hasExactSynonym", - "val": "noncoding primary transcript", + "val": "pseudouridylation guide snoRNA gene", + "xrefs": [], }, ], }, @@ -6449,34 +6906,57 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000632", - "monocistronic", - "primary", - "transcript", - "encoding", - "one", + "so:0002379", + "methylation", + "guide", + "snorna", "gene", - "product", + "codes", + "specifies", + "site", + "o", + "ribose", + "rna", + "molecule", + "base", + "pairing", + "short", + "sequence", + "around", + "target", + "residue", ], - "id": "http://purl.obolibrary.org/obo/SO_0000632", - "lbl": "monocistronic_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002379", + "lbl": "methylation_guide_snoRNA_gene", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:51:12Z", + }, + ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", ], "definition": { - "val": "A primary transcript encoding for one gene product.", + "val": "A gene that codes for methylation_guide_snoRNA. A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.", "xrefs": [ - "SO:ke", + "PMID:12457565", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "monocistronic primary transcript", + "val": "methylation guide snoRNA gene", + "xrefs": [], }, ], }, @@ -6484,41 +6964,94 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000635", - "mini", - "exon", - "donor", + "so:0002378", + "u3", + "snorna", + "gene", + "small", + "nucleolar", "rna", - "primary", - "transcript", - "donates", - "spliced", - "leader", - "mrna", + "codes", + "member", + "box", + "c", + "d", + "class", + "rnas", + "secondary", + "structure", + "characterised", + "domain", + "boxes", + "larger", + "b", + "two", + "domains", + "linked", + "single", + "stranded", + "hinge", + "form", + "motif", + "appears", + "exclusive", + "snornas", + "latter", + "functionally", + "similar", + "motifs", + "found", + "region", + "act", + "pre", + "rrna", + "binding", + "conserved", + "protein", + "sites", + "sufficient", + "nuclear", + "retention", + "also", + "necessary", + "localization", + "stability", + "hypermethylation", + "involved", + "specific", + "interactions", + "processing", + "functions", ], - "id": "http://purl.obolibrary.org/obo/SO_0000635", - "lbl": "mini_exon_donor_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0002378", + "lbl": "U3_snoRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:50:57Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", ], "definition": { - "val": "A primary transcript that donates the spliced leader to other mRNA.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene that codes for U3_snoRNA. U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "mini exon donor RNA", - }, - { - "pred": "hasExactSynonym", - "val": "mini-exon donor RNA", + "val": "small nucleolar RNA U3 gene, snoRNA U3 gene, U3 small nucleolar RNA gene, U3 snoRNA gene", + "xrefs": [], }, ], }, @@ -6526,49 +7059,91 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000645", - "antisense", - "primary", - "transcript", - "reverse", - "complement", + "so:0002377", + "u14", + "snorna", + "gene", + "small", + "nucleolar", + "rna", + "codes", + "required", + "early", + "cleavages", + "eukaryotic", + "precursor", + "rrnas", + "yeasts", + "molecule", + "possess", + "stem", + "loop", + "region", + "known", + "y", + "domain", + "essential", + "function", + "similar", + "structure", + "different", + "consensus", + "sequence", + "found", + "plants", + "absent", + "vertebrates", ], - "id": "http://purl.obolibrary.org/obo/SO_0000645", - "lbl": "antisense_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002377", + "lbl": "U14_snoRNA_gene", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:50:43Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", + ], "definition": { - "val": "The reverse complement of the primary transcript.", - "xrefs": [ - "SO:ke", - ], + "val": "A gene that codes for U14_snoRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "antisense primary transcript", + "val": "small nucleolar RNA U14 gene, snoRNA U14 gene, U14 small nucleolar RNA gene, U14 snoRNA gene", + "xrefs": [], }, ], }, "type": "CLASS", }, +] +`; + +exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` +[ { "fullTextWords": [ - "so:0000861", - "capped", - "primary", - "transcript", + "so:0000842", + "gene", + "component", + "region", + "specific", + "function", ], - "id": "http://purl.obolibrary.org/obo/SO_0000861", - "lbl": "capped_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000842", + "lbl": "gene_component_region", "meta": { "basicPropertyValues": [ { @@ -6577,15 +7152,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript that is capped.", - "xrefs": [ - "SO:xp", - ], + "val": "A region of a gene that has a specific function.", + "xrefs": [], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "capped primary transcript", + "val": "gene component region", + "xrefs": [], }, ], }, @@ -6593,50 +7170,37 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001905", - "regional", - "centromere", - "outer", - "repeat", - "transcript", + "so:0000831", + "gene", + "member", "region", - "transcribed", ], - "id": "http://purl.obolibrary.org/obo/SO_0001905", - "lbl": "regional_centromere_outer_repeat_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000831", + "lbl": "gene_member_region", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-04-11T04:54:22Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "A manufactured term used to allow the parts of a gene to have an is_a path to the root.", + ], "definition": { - "val": "A transcript that is transcribed from the outer repeat region of a regional centromere.", + "val": "A region of a gene.", "xrefs": [ - "PomBase:mah", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "centromere outer repeat transcript", - }, - { - "pred": "hasExactSynonym", - "val": "regional centromere outer repeat region transcript", - }, - { - "pred": "hasExactSynonym", - "val": "regional_centromere_outer_repeat_region_transcript", + "val": "gene member region", + "xrefs": [], }, ], }, @@ -6644,54 +7208,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002115", - "pseudogenic", - "transcript", - "retained", - "intron", - "pseudogene", - "supported", - "est", - "mrna", - "evidence", - "aligns", - "unambiguously", - "locus", - "intronic", - "sequence", - "compared", - "reference", + "so:0002310", + "cryptic", + "promoter", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0002115", - "lbl": "pseudogenic_transcript_with_retained_intron", + "id": "http://purl.obolibrary.org/obo/SO_0002310", + "lbl": "cryptic_promoter", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-07-18T14:19:04Z", + "val": "david", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-08-12T14:01:30Z", + }, ], "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.", + "Added by Dave to be consistent with other ontologies updated with GREEKC initiative.", ], "definition": { - "val": "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence.", + "val": "The promoter of a cryptic gene.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "GREEKC:cl", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "pseudogene retained intron", + "val": "cryptic promoter", + "xrefs": [], }, ], }, @@ -6699,26 +7251,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000234", - "mrna", + "so:0000167", + "promoter", "insdc", - "feature:mrna", - "messenger", - "rna", - "protein", - "coding", - "transcript", - "intermediate", - "molecule", + "feature:regulatory", + "sequence", + "qualifier:promoter", + "regulatory", + "region", + "composed", + "tss", + "binding", + "sites", + "tf", + "complexes", + "core", + "transcription", + "machinery", "dna", - "includes", - "utr", - "sequences", - "contain", - "introns", + "rna", + "polymerase", + "binds", + "begin", ], - "id": "http://purl.obolibrary.org/obo/SO_0000234", - "lbl": "mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000167", + "lbl": "promoter", "meta": { "basicPropertyValues": [ { @@ -6727,12 +7284,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "comments": [ - "An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", + "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter.", ], "definition": { - "val": "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.", + "val": "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.", "xrefs": [ - "SO:ma", + "SO:regcreative", ], }, "subsets": [ @@ -6740,24 +7297,24 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` ], "synonyms": [ { - "pred": "hasExactSynonym", - "val": "INSDC_feature:mRNA", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "messenger RNA", + "val": "promoter sequence", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "protein_coding_transcript", + "val": "INSDC_qualifier:promoter", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/MRNA", - }, - { - "val": "http://www.gencodegenes.org/gencode_biotypes.html", + "val": "http://en.wikipedia.org/wiki/Promoter", }, ], }, @@ -6765,23 +7322,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000655", - "ncrna", - "insdc", - "qualifier:other", - "known", - "noncoding", - "rna", - "transcript", - "encode", - "protein", - "rather", - "molecule", + "so:0000997", "gene", - "product", + "fragment", + "portion", + "complete", ], - "id": "http://purl.obolibrary.org/obo/SO_0000655", - "lbl": "ncRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000997", + "lbl": "gene_fragment", "meta": { "basicPropertyValues": [ { @@ -6790,37 +7338,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "comments": [ - "A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.", + "This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", ], "definition": { - "val": "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.", - "xrefs": [ - "SO:ke", - ], + "val": "A portion of a gene that is not the complete gene.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_qualifier:other", - }, { "pred": "hasExactSynonym", - "val": "known_ncrna", - }, - { - "pred": "hasExactSynonym", - "val": "noncoding RNA", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/NcRNA", - }, - { - "val": "http://www.gencodegenes.org/gencode_biotypes.html", + "val": "gene fragment", + "xrefs": [], }, ], }, @@ -6828,17 +7356,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000374", - "ribozyme", - "insdc", - "feature:ncrna", - "qualifier:ribozyme", - "rna", - "catalytic", - "activity", + "so:3000000", + "gene", + "segment", + "component", + "region", + "acts", + "recombinational", + "unit", + "whose", + "functional", + "form", + "generated", + "somatic", + "recombination", ], - "id": "http://purl.obolibrary.org/obo/SO_0000374", - "lbl": "ribozyme", + "id": "http://purl.obolibrary.org/obo/SO_3000000", + "lbl": "gene_segment", "meta": { "basicPropertyValues": [ { @@ -6846,28 +7380,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Requested by tracker 2021594, July 2008, by Alex.", + ], "definition": { - "val": "An RNA with catalytic activity.", + "val": "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.", "xrefs": [ - "SO:ma", + "GOC:add", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:ribozyme", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Ribozyme", + "val": "gene segment", + "xrefs": [], }, ], }, @@ -6875,53 +7401,58 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000872", - "trans", - "spliced", - "mrna", + "so:0002026", + "intein", + "encoding", + "region", + "nucleotide", + "sequence", + "encodes", + "portion", + "precursor", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000872", - "lbl": "trans_spliced_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002026", + "lbl": "intein_encoding_region", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2014-07-14T11:53:21Z", + }, + ], + "comments": [ + "Requested by Janos Demeter 2014.", ], "definition": { - "val": "An mRNA that is trans-spliced.", + "val": "The nucleotide sequence which encodes the intein portion of the precursor gene.", "xrefs": [ - "SO:xp", + "PMID:8165123", ], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "trans-spliced mRNA", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000633", - "monocistronic", - "mrna", - "processed", - "transcript", - "either", - "single", - "protein", - "product", - "regions", - "encoding", - "products", - "overlap", + "so:0000183", + "non", + "transcribed", + "region", + "nontranscribed", + "sequence", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000633", - "lbl": "monocistronic_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000183", + "lbl": "non_transcribed_region", "meta": { "basicPropertyValues": [ { @@ -6930,24 +7461,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.", + "val": "A region of the gene which is not transcribed.", "xrefs": [ - "SO:rd", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "monocistronic mRNA", + "val": "non transcribed region", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "monocistronic processed transcript", + "val": "nontranscribed sequence", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Monocistronic_mRNA", + "pred": "hasExactSynonym", + "val": "nontranscribed region", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "non-transcribed sequence", + "xrefs": [], }, ], }, @@ -6955,30 +7496,50 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000874", - "edited", - "transcript", - "substitution", + "so:0002188", + "functional", + "gene", + "region", + "member", + "encodes", + "sequence", + "directly", + "contributes", + "molecular", + "function", + "product", ], - "id": "http://purl.obolibrary.org/obo/SO_0000874", - "lbl": "edited_transcript_by_A_to_I_substitution", + "id": "http://purl.obolibrary.org/obo/SO_0002188", + "lbl": "functional_gene_region", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2017-12-15T11:08:43Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors.", + ], "definition": { - "val": "A transcript that has been edited by A to I substitution.", + "val": "A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product.", "xrefs": [ - "SO:ke", + "Clingen:mb", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "edited transcript by A to I substitution", + "val": "functional gene region", + "xrefs": [], }, ], }, @@ -6986,12 +7547,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000929", - "edited", - "mrna", + "so:0005836", + "regulatory", + "region", + "insdc", + "qualifier:other", + "feature:regulatory", + "sequence", + "involved", + "control", + "biological", + "process", ], - "id": "http://purl.obolibrary.org/obo/SO_0000929", - "lbl": "edited_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0005836", + "lbl": "regulatory_region", "meta": { "basicPropertyValues": [ { @@ -7000,15 +7569,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "An mRNA that is edited.", + "val": "A region of sequence that is involved in the control of a biological process.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "edited mRNA", + "val": "INSDC_qualifier:other", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "regulatory region", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Regulatory_region", }, ], }, @@ -7016,53 +7604,47 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002111", - "pseudogene", - "processed", + "so:0000673", "transcript", - "supported", - "est", - "mrna", - "evidence", - "aligns", - "unambiguously", - "locus", - "e", - "alignment", - "clearly", - "better", - "parent", + "insdc", + "feature:misc", + "rna", + "synthesized", + "dna", + "template", + "polymerase", ], - "id": "http://purl.obolibrary.org/obo/SO_0002111", - "lbl": "pseudogene_processed_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000673", + "lbl": "transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-07-18T14:07:00Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "comments": [ - "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", + "Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020.", ], "definition": { - "val": "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus).", + "val": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ma", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { - "pred": "hasExactSynonym", - "val": "pseudogene processed transcript", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:misc_RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/RNA", }, ], }, @@ -7070,80 +7652,46 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002139", - "unconfirmed", - "transcript", - "tec", - "experimentally", - "confirmed", - "used", - "non", - "spliced", - "est", - "clusters", - "polya", - "features", - "category", - "specifically", - "created", - "encode", - "project", - "highlight", - "regions", - "could", - "indicate", + "so:0002051", + "inducible", + "promoter", + "whereby", + "activity", + "induced", "presence", - "protein", - "coding", - "genes", - "require", - "experimental", - "validation", - "either", - "race", - "rt", - "pcr", - "extend", - "transcripts", - "confirming", - "expression", - "putatively", - "encoded", - "peptide", - "specific", - "antibodies", + "absence", + "biotic", + "abiotic", + "factors", ], - "id": "http://purl.obolibrary.org/obo/SO_0002139", - "lbl": "unconfirmed_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002051", + "lbl": "inducible_promoter", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:28:07Z", + "val": "2015-05-14T10:39:56Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.", + "val": "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "TEC", - }, - { - "pred": "hasExactSynonym", - "val": "to_be_experimentally_confirmed_transcript", + "val": "inducible promoter", + "xrefs": [], }, ], }, @@ -7151,25 +7699,15 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000141", - "terminator", - "insdc", - "feature:regulatory", - "qualifier:terminator", - "sequence", - "dna", - "located", - "either", - "end", - "transcript", - "causes", - "rna", - "polymerase", - "terminate", + "so:0000568", + "bidirectional", + "promoter", + "allow", "transcription", + "directions", ], - "id": "http://purl.obolibrary.org/obo/SO_0000141", - "lbl": "terminator", + "id": "http://purl.obolibrary.org/obo/SO_0000568", + "lbl": "bidirectional_promoter", "meta": { "basicPropertyValues": [ { @@ -7177,32 +7715,21 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Definition updated in Aug 2020 by Dave Sant.", + ], "definition": { - "val": "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.", + "val": "A promoter that can allow for transcription in both directions.", "xrefs": [ - "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html", + "PMID:21601935", + "SO:ke", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:terminator", - }, { "pred": "hasExactSynonym", - "val": "terminator sequence", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Terminator_(genetics)", + "val": "bidirectional promoter", + "xrefs": [], }, ], }, @@ -7210,45 +7737,49 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000235", - "tf", - "binding", - "site", - "transcription", - "factor", + "so:0002311", + "viral", + "promoter", + "regulatory", "region", - "nucleotide", - "molecule", - "binds", - "complex", - "go:0005667", + "including", + "transcription", + "start", + "site", + "tss", + "gene", + "found", + "genes", + "viruses", ], - "id": "http://purl.obolibrary.org/obo/SO_0000235", - "lbl": "TF_binding_site", + "id": "http://purl.obolibrary.org/obo/SO_0002311", + "lbl": "viral_promoter", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-08-12T14:01:30Z", + }, ], "definition": { - "val": "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].", + "val": "A regulatory_region including the Transcription Start Site (TSS) of a gene found in genes of viruses.", "xrefs": [ - "SO:ke", + "GREEKC:cl", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "TF binding site", - }, - { - "pred": "hasExactSynonym", - "val": "transcription factor binding site", + "val": "viral promoter", + "xrefs": [], }, ], }, @@ -7256,64 +7787,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000551", - "polya", - "signal", - "sequence", - "insdc", - "feature:regulatory", - "qualifier:polya", - "poly", - "polyadenylation", - "termination", - "recognition", - "necessary", - "endonuclease", - "cleavage", - "rna", - "transcript", - "followed", - "consensus", - "aataaa", + "so:0002310", + "cryptic", + "promoter", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000551", - "lbl": "polyA_signal_sequence", + "id": "http://purl.obolibrary.org/obo/SO_0002310", + "lbl": "cryptic_promoter", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-08-12T14:01:30Z", + }, + ], + "comments": [ + "Added by Dave to be consistent with other ontologies updated with GREEKC initiative.", ], "definition": { - "val": "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.", + "val": "The promoter of a cryptic gene.", "xrefs": [ - "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html", + "GREEKC:cl", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:polyA_signal_sequence", - }, - { - "pred": "hasExactSynonym", - "val": "poly(A) signal", - }, - { - "pred": "hasExactSynonym", - "val": "polyA signal sequence", - }, { "pred": "hasExactSynonym", - "val": "polyadenylation termination signal", + "val": "cryptic promoter", + "xrefs": [], }, ], }, @@ -7321,28 +7830,61 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000752", - "gene", - "group", + "so:0002222", + "prokaryotic", + "promoter", "regulatory", "region", + "essential", + "specific", + "initiation", + "transcription", + "defined", + "location", + "dna", + "molecule", + "although", + "might", + "one", + "single", + "base", + "recognized", + "rna", + "polymerase", + "rnap", + "holoenzyme", + "recognition", + "necessarily", + "autonomous", ], - "id": "http://purl.obolibrary.org/obo/SO_0000752", - "lbl": "gene_group_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002222", + "lbl": "prokaryotic_promoter", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2019-07-31T14:02:26Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], + "definition": { + "val": "A regulatory_region essential for the specific initiation of transcription at a defined location in a DNA molecule, although this location might not be one single base. It is recognized by a specific RNA polymerase(RNAP)-holoenzyme, and this recognition is not necessarily autonomous.", + "xrefs": [ + "PMID:32665585", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "gene group regulatory region", + "val": "Prokaryotic promoter", + "xrefs": [], }, ], }, @@ -7350,55 +7892,54 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001055", - "transcriptional", - "cis", + "so:0002221", + "eukaryotic", + "promoter", "regulatory", "region", - "insdc", - "feature:regulatory", - "qualifier:transcriptional", + "including", "transcription", - "control", - "modulates", + "start", + "site", + "tss", "gene", - "genes", + "serving", + "platform", + "pre", + "initiation", + "complex", + "pic", + "assembly", + "enabling", + "certain", + "conditions", ], - "id": "http://purl.obolibrary.org/obo/SO_0001055", - "lbl": "transcriptional_cis_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002221", + "lbl": "eukaryotic_promoter", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2019-07-31T14:01:20Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, ], "definition": { - "val": "A regulatory_region that modulates the transcription of a gene or genes.", - "xrefs": [ - "PMID:9679020", - "SO:regcreative", - ], + "val": "A regulatory_region including the Transcription Start Site (TSS) of a gene and serving as a platform for Pre-Initiation Complex (PIC) assembly, enabling transcription of a gene under certain conditions.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:transcriptional_cis_regulatory_region", - }, { "pred": "hasExactSynonym", - "val": "transcription-control region", - }, - { - "pred": "hasExactSynonym", - "val": "transcriptional cis regulatory region", + "val": "Eukaryotic promoter", + "xrefs": [], }, ], }, @@ -7406,34 +7947,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001056", - "splicing", - "regulatory", - "region", - "modulates", + "so:0002050", + "constitutive", + "promoter", + "allows", + "continual", + "transcription", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0001056", - "lbl": "splicing_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0002050", + "lbl": "constitutive_promoter", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2015-05-14T10:39:09Z", + }, ], "definition": { - "val": "A regulatory_region that modulates splicing.", + "val": "A promoter that allows for continual transcription of gene.", "xrefs": [ "SO:ke", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "splicing regulatory region", + "val": "constitutive promoter", + "xrefs": [], }, ], }, @@ -7441,40 +7990,47 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001427", - "cis", - "regulatory", - "frameshift", - "element", - "structural", - "region", - "rna", - "molecule", - "promotes", - "ribosomal", - "frameshifting", - "coding", - "sequence", + "so:0001741", + "pseudogenic", + "gene", + "segment", + "incorporated", + "somatic", + "recombination", + "final", + "transcript", + "results", + "nonfunctional", + "product", ], - "id": "http://purl.obolibrary.org/obo/SO_0001427", - "lbl": "cis_regulatory_frameshift_element", + "id": "http://purl.obolibrary.org/obo/SO_0001741", + "lbl": "pseudogenic_gene_segment", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "batchelorc", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2011-02-15T05:07:52Z", + }, ], "definition": { - "val": "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.", + "val": "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.", "xrefs": [ - "RFAM:jd", + "SO:hd", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "cis regulatory frameshift element", + "val": "pseudogenic gene segment", + "xrefs": [], }, ], }, @@ -7482,15 +8038,36 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001492", - "intronic", - "regulatory", + "so:0001720", + "epigenetically", + "modified", "region", - "part", - "intron", + "biological", + "dna", + "implicated", + "epigenomic", + "changes", + "caused", + "mechanisms", + "underlying", + "sequence", + "includes", + "nucleosomal", + "histone", + "post", + "translational", + "modifications", + "nucleosome", + "depletion", + "render", + "accessible", + "replicational", + "base", + "cytosine", + "modification", ], - "id": "http://purl.obolibrary.org/obo/SO_0001492", - "lbl": "intronic_regulatory_region", + "id": "http://purl.obolibrary.org/obo/SO_0001720", + "lbl": "epigenetically_modified_region", "meta": { "basicPropertyValues": [ { @@ -7499,23 +8076,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2009-11-08T02:48:02Z", + "val": "2010-03-27T12:02:29Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534.", + ], "definition": { - "val": "A regulatory region that is part of an intron.", + "val": "A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification.", "xrefs": [ "SO:ke", + "http://en.wikipedia.org/wiki/Epigenetics", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { - "pred": "hasExactSynonym", - "val": "intronic regulatory region", + "pred": "hasRelatedSynonym", + "val": "epigenetically modified region", + "xrefs": [], }, ], }, @@ -7523,58 +8108,66 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002047", - "transcription", - "pause", - "site", - "sites", + "so:0002223", + "inert", + "dna", + "spacer", + "sequences", + "decrease", + "interactions", + "biological", "regions", - "gene", - "rna", - "polymerase", - "may", - "functional", - "role", - "pausing", - "facilitate", - "factor", - "recruitment", - "folding", - "synchronization", + "promoter", + "context", + "translational", + "unit", + "regulates", + "spacers", + "affect", + "regulation", "translation", - "consensus", - "observed", - "e", - "coli", + "transcription", + "processes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002047", - "lbl": "transcription_pause_site", + "id": "http://purl.obolibrary.org/obo/SO_0002223", + "lbl": "inert_DNA_spacer", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-02-09T15:32:52Z", + "val": "2019-09-06T19:05:52Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Updated by Evan Christensen on May 27, 2021 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/494", ], "definition": { - "val": "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli.", + "val": "Sequences that decrease interactions between biological regions, such as between a promoter, its 5' context and/or the translational unit(s) it regulates. Spacers can affect regulation of translation, transcription, and other biological processes.", "xrefs": [ - "PMID:24789973", - "SO:ke", + "PMID:20843779", + "PMID:24933158", + "PMID:27034378", + "PMID:28422998", ], }, "synonyms": [ { - "pred": "hasExactSynonym", - "val": "transcription pause site", + "pred": "hasRelatedSynonym", + "val": "Inert DNA Spacer", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "doi:10.1101/584664", }, ], }, @@ -7582,53 +8175,56 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002205", - "response", - "element", + "so:0001682", + "replication", + "regulatory", + "region", "insdc", + "qualifier:replication", "feature:regulatory", - "qualifier:response", - "regulatory", - "acts", - "stimulus", - "usually", - "via", - "transcription", - "factor", - "binding", + "involved", + "control", + "process", + "nucleotide", ], - "id": "http://purl.obolibrary.org/obo/SO_0002205", - "lbl": "response_element", + "id": "http://purl.obolibrary.org/obo/SO_0001682", + "lbl": "replication_regulatory_region", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2018-01-10T16:33:25Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-10-12T03:54:09Z", }, ], "definition": { - "val": "A regulatory element that acts in response to a stimulus, usually via transcription factor binding.", + "val": "A regulatory region that is involved in the control of the process of nucleotide replication.", + "xrefs": [ + "SO:ke", + ], }, "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:replication_regulatory_region", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:response_element", + "val": "replication regulatory region", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "response element", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], }, ], }, @@ -7636,59 +8232,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000140", - "attenuator", - "insdc", - "feature:regulatory", - "qualifier:attenuator", - "sequence", - "segment", - "located", - "within", - "five", - "prime", - "end", - "mrna", - "causes", - "premature", - "termination", + "so:0001680", "translation", + "regulatory", + "region", + "involved", + "control", + "process", ], - "id": "http://purl.obolibrary.org/obo/SO_0000140", - "lbl": "attenuator", + "id": "http://purl.obolibrary.org/obo/SO_0001680", + "lbl": "translation_regulatory_region", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-10-12T03:52:45Z", + }, ], "definition": { - "val": "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.", + "val": "A regulatory region that is involved in the control of the process of translation.", "xrefs": [ - "SO:as", + "SO:ke", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:attenuator", - }, { "pred": "hasExactSynonym", - "val": "attenuator sequence", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Attenuator", + "val": "translation regulatory region", + "xrefs": [], }, ], }, @@ -7696,43 +8275,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002059", + "so:0001681", "recombination", - "enhancer", "regulatory", "region", - "promotes", - "induces", + "involved", + "control", "process", ], - "id": "http://purl.obolibrary.org/obo/SO_0002059", - "lbl": "recombination_enhancer", + "id": "http://purl.obolibrary.org/obo/SO_0001681", + "lbl": "recombination_regulatory_region", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "kareneilbeck", }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-05-14T13:08:58Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-10-12T03:53:35Z", + }, ], "definition": { - "val": "A regulatory_region that promotes or induces the process of recombination.", + "val": "A regulatory region that is involved in the control of the process of recombination.", "xrefs": [ - "PMID:8861911", - "SGD:se", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "recombination enhancer", + "val": "recombination regulatory region", + "xrefs": [], }, ], }, @@ -7740,15 +8318,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000716", - "dicistronic", - "mrna", - "processed", - "transcript", - "quality", + "so:0001055", + "transcriptional", + "cis", + "regulatory", + "region", + "insdc", + "qualifier:transcriptional", + "transcription", + "control", + "feature:regulatory", + "modulates", + "gene", + "genes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000716", - "lbl": "dicistronic_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0001055", + "lbl": "transcriptional_cis_regulatory_region", "meta": { "basicPropertyValues": [ { @@ -7756,20 +8341,39 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527.", + ], "definition": { - "val": "An mRNA that has the quality dicistronic.", + "val": "A regulatory_region that modulates the transcription of a gene or genes.", "xrefs": [ - "SO:ke", + "PMID:9679020", + "SO:regcreative", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "dicistronic mRNA", + "val": "INSDC_qualifier:transcriptional_cis_regulatory_region", + "xrefs": [], }, { - "pred": "hasRelatedSynonym", - "val": "dicistronic processed transcript", + "pred": "hasExactSynonym", + "val": "transcription-control region", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "transcriptional cis regulatory region", + "xrefs": [], }, ], }, @@ -7777,14 +8381,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:1001197", - "dicistronic", + "so:0000185", "primary", "transcript", - "quality", + "insdc", + "feature:prim", + "initial", + "state", + "requires", + "modification", + "functional", ], - "id": "http://purl.obolibrary.org/obo/SO_1001197", - "lbl": "dicistronic_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000185", + "lbl": "primary_transcript", "meta": { "basicPropertyValues": [ { @@ -7792,16 +8401,33 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "See "precursor_RNA" (SO:0002393) for RNA which may be the result of post-transcriptional processing. If the RNA in question is known not to have been processed, use this class ("primary_transcript"). On 9 Sep 2025, Removed "has_exact_synonym : INSDC_feature:precursor_RNA" and "has_exact_synonym : precursor RNA" from the annotation for this class at the request of Terence Murphy of NCBI. See GitHub Issue #655.", + ], "definition": { - "val": "A primary transcript that has the quality dicistronic.", + "val": "A transcript that in its initial state requires modification to be functional.", "xrefs": [ - "SO:xp", + "SO:ma", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "dicistronic primary transcript", + "val": "primary transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "INSDC_feature:prim_transcript", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Primary_transcript", }, ], }, @@ -7809,24 +8435,49 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000932", - "pre", - "edited", - "mrna", + "so:0002208", + "long", + "terminal", + "repeat", + "transcript", + "ltr", + "rna", + "transcribed", ], - "id": "http://purl.obolibrary.org/obo/SO_0000932", - "lbl": "pre_edited_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002208", + "lbl": "long_terminal_repeat_transcript", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2018-02-07T11:51:45Z", + }, ], + "definition": { + "val": "An RNA that is transcribed from a long terminal repeat.", + "xrefs": [ + "PMID:24256266", + "PomBase:mh", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "pre-edited mRNA", + "val": "LTR transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "long terminal repeat transcript", + "xrefs": [], }, ], }, @@ -7834,45 +8485,30 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002112", - "coding", + "so:0000873", + "edited", "transcript", - "retained", - "intron", - "mrna", - "protein", - "containing", ], - "id": "http://purl.obolibrary.org/obo/SO_0002112", - "lbl": "coding_transcript_with_retained_intron", + "id": "http://purl.obolibrary.org/obo/SO_0000873", + "lbl": "edited_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-07-18T14:09:49Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", - ], "definition": { - "val": "A protein coding transcript containing a retained intron.", + "val": "A transcript that is edited.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { - "pred": "hasRelatedSynonym", - "val": "mRNA with retained intron", + "pred": "hasExactSynonym", + "val": "edited transcript", + "xrefs": [], }, ], }, @@ -7880,69 +8516,64 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002114", - "nmd", - "transcript", - "nonsense", - "mediated", - "decay", - "protein", + "so:0002393", + "precursor", + "rna", + "insdc", + "feature:precursor", + "species", + "yet", + "mature", + "product", + "may", + "include", + "ncrna", + "rrna", + "trna", + "untranslated", + "region", + "utr", "coding", - "contains", + "sequences", "cds", - "one", - "splice", - "junctions", - "50bp", - "downstream", - "stop", - "codon", - "making", - "susceptible", + "exon", + "intervening", + "intron", ], - "id": "http://purl.obolibrary.org/obo/SO_0002114", - "lbl": "NMD_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002393", + "lbl": "precursor_RNA", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-07-18T14:16:13Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "Evan Christensen", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2025-09-09T19:26:13Z", }, ], "comments": [ - "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", + "This term should be used for RNA which may be the result of post-transcriptional processing; if the RNA in question is known not to have been processed, use primary_transcript (SO:0000185). At the time this SO term was created, the INSDC Feature Table has a specific term (i.e. precursor_RNA) for transcripts that may be in various stages of processing between primary_transcript (SO:0000185) and mature_transcript (SO:0000233). See the INSDC Feature Table Definition for the "precursor_RNA" feature key https://www.insdc.org/submitting-standards/feature-table/. Added 9 Sep 2025 at the request of Terence Murphy of NCBI to support transformation between the INSDC Feature Table and GFF3 formats. See GitHub Issue #655.", ], "definition": { - "val": "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay.", - "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", - ], + "val": "Any RNA species that is not yet the mature RNA product; may include ncRNA, rRNA, tRNA, 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron) and 3' untranslated region (3'UTR).", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "NMD transcript", - }, - { - "pred": "hasExactSynonym", - "val": "nonsense mediated decay transcript", + "val": "precursor RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "protein_coding_NMD", - }, - ], - "xrefs": [ - { - "val": "http://www.gencodegenes.org/gencode_biotypes.html", + "val": "INSDC_feature:precursor_RNA", + "xrefs": [], }, ], }, @@ -7950,24 +8581,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000012", - "scrna", - "primary", + "so:0000078", + "polycistronic", "transcript", - "small", - "cytoplasmic", - "rna", - "one", - "several", - "molecules", - "present", - "cytoplasm", - "sometimes", - "nucleus", - "eukaryote", ], - "id": "http://purl.obolibrary.org/obo/SO_0000012", - "lbl": "scRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000078", + "lbl": "polycistronic_transcript", "meta": { "basicPropertyValues": [ { @@ -7976,31 +8595,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.", + "val": "A transcript that is polycistronic.", "xrefs": [ - "http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "scRNA primary transcript", - }, - { - "pred": "hasExactSynonym", - "val": "scRNA transcript", - }, - { - "pred": "hasExactSynonym", - "val": "small cytoplasmic RNA transcript", - }, - { - "pred": "hasRelatedSynonym", - "val": "small cytoplasmic RNA", - }, - { - "pred": "hasRelatedSynonym", - "val": "small_cytoplasmic_RNA", + "val": "polycistronic transcript", + "xrefs": [], }, ], }, @@ -8008,40 +8612,41 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000209", - "rrna", - "primary", + "so:0002138", + "predicted", "transcript", - "ribosomal", - "rna", - "encoding", + "feature", + "yet", + "validated", ], - "id": "http://purl.obolibrary.org/obo/SO_0000209", - "lbl": "rRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002138", + "lbl": "predicted_transcript", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:27:38Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, ], "definition": { - "val": "A primary transcript encoding a ribosomal RNA.", + "val": "A transcript feature that has been predicted but is not yet validated.", "xrefs": [ "SO:ke", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "rRNA primary transcript", - }, - { - "pred": "hasExactSynonym", - "val": "ribosomal RNA primary transcript", + "val": "predicted transcript", + "xrefs": [], }, ], }, @@ -8049,17 +8654,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000210", - "trna", - "primary", + "so:0000681", + "aberrant", + "processed", "transcript", - "encoding", - "transfer", - "rna", - "so:0000253", + "incorrectly", + "example", + "failure", + "splicing", + "one", + "exons", ], - "id": "http://purl.obolibrary.org/obo/SO_0000210", - "lbl": "tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000681", + "lbl": "aberrant_processed_transcript", "meta": { "basicPropertyValues": [ { @@ -8068,7 +8675,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a transfer RNA (SO:0000253).", + "val": "A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.", "xrefs": [ "SO:ke", ], @@ -8076,7 +8683,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "tRNA primary transcript", + "val": "aberrant processed transcript", + "xrefs": [], }, ], }, @@ -8084,35 +8692,47 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000231", - "snrna", - "primary", + "so:0001503", + "processed", "transcript", - "encoding", - "small", - "nuclear", - "rna", - "so:0000274", + "open", + "reading", + "frame", + "identified", + "function", + "determined", ], - "id": "http://purl.obolibrary.org/obo/SO_0000231", - "lbl": "snRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001503", + "lbl": "processed_transcript", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2009-12-21T05:37:14Z", + }, + ], + "comments": [ + "Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.", ], "definition": { - "val": "A primary transcript encoding a small nuclear RNA (SO:0000274).", + "val": "A transcript for which no open reading frame has been identified and for which no other function has been determined.", "xrefs": [ - "SO:ke", + "MGI:hdeen", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "snRNA primary transcript", + "val": "processed transcript", + "xrefs": [], }, ], }, @@ -8120,18 +8740,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000232", - "snorna", - "primary", + "so:0000665", + "monocistronic", "transcript", - "encoding", - "small", - "nucleolar", - "mrna", - "so:0000275", ], - "id": "http://purl.obolibrary.org/obo/SO_0000232", - "lbl": "snoRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000665", + "lbl": "monocistronic_transcript", "meta": { "basicPropertyValues": [ { @@ -8140,15 +8754,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a small nucleolar mRNA (SO:0000275).", + "val": "A transcript that is monocistronic.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "snoRNA primary transcript", + "val": "monocistronic transcript", + "xrefs": [], }, ], }, @@ -8156,18 +8771,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000586", - "tmrna", - "primary", + "so:1001187", + "alternatively", + "spliced", "transcript", - "10sa", - "rna", - "ssra", - "encoding", - "so:0000584", ], - "id": "http://purl.obolibrary.org/obo/SO_0000586", - "lbl": "tmRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_1001187", + "lbl": "alternatively_spliced_transcript", "meta": { "basicPropertyValues": [ { @@ -8176,23 +8786,51 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a tmRNA (SO:0000584).", + "val": "A transcript that is alternatively spliced.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "tmRNA primary transcript", + "val": "alternatively spliced transcript", + "xrefs": [], }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000279", + "transcript", + "bound", + "protein", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000279", + "lbl": "transcript_bound_by_protein", + "meta": { + "basicPropertyValues": [ { - "pred": "hasRelatedSynonym", - "val": "10Sa RNA primary transcript", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, + ], + "comments": [ + "Formerly called transcript_by_bound_protein.", + ], + "definition": { + "val": "A transcript that is bound by a protein.", + "xrefs": [ + "SO:xp", + ], + }, + "synonyms": [ { - "pred": "hasRelatedSynonym", - "val": "ssrA RNA primary transcript", + "pred": "hasExactSynonym", + "val": "transcript bound by protein", + "xrefs": [], }, ], }, @@ -8200,18 +8838,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000589", - "srp", - "rna", - "primary", + "so:0000278", "transcript", - "encoding", - "signal", - "recognition", - "particle", + "bound", + "nucleic", + "acid", ], - "id": "http://purl.obolibrary.org/obo/SO_0000589", - "lbl": "SRP_RNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000278", + "lbl": "transcript_bound_by_nucleic_acid", "meta": { "basicPropertyValues": [ { @@ -8219,16 +8853,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Formerly called transcript_by_bound_nucleic_acid.", + ], "definition": { - "val": "A primary transcript encoding a signal recognition particle RNA.", + "val": "A transcript that is bound by a nucleic acid.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "SRP RNA primary transcript", + "val": "transcript bound by nucleic acid", + "xrefs": [], }, ], }, @@ -8236,56 +8874,50 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000647", - "mirna", - "primary", + "so:0000479", + "trans", + "spliced", "transcript", - "micro", - "rna", - "small", - "temporal", - "strna", - "encoding", + "insdc", + "qualifier:trans", + "splicing", + "feature:trna", ], - "id": "http://purl.obolibrary.org/obo/SO_0000647", - "lbl": "miRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000479", + "lbl": "trans_spliced_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "SO:0000648", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A primary transcript encoding a micro RNA.", + "val": "A transcript that is trans-spliced.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "miRNA primary transcript", - }, - { - "pred": "hasExactSynonym", - "val": "micro RNA primary transcript", + "val": "INSDC_qualifier:trans_splicing", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small temporal RNA primary transcript", + "val": "trans spliced transcript", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "stRNA primary transcript", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:tRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "stRNA_primary_transcript", + "val": "trans-spliced transcript", + "xrefs": [], }, ], }, @@ -8293,39 +8925,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001801", - "tasirna", - "primary", + "so:0000118", "transcript", - "encoding", + "translational", + "frameshift", ], - "id": "http://purl.obolibrary.org/obo/SO_0001801", - "lbl": "tasiRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000118", + "lbl": "transcript_with_translational_frameshift", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2011-05-31T03:27:35Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A primary transcript encoding a tasiRNA.", + "val": "A transcript with a translational frameshift.", "xrefs": [ - "PMID:16145017", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "tasiRNA primary transcript", + "val": "transcript with translational frameshift", + "xrefs": [], }, ], }, @@ -8333,39 +8957,61 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002035", - "lncrna", - "primary", + "so:0000233", + "mature", "transcript", - "encoding", - ], - "id": "http://purl.obolibrary.org/obo/SO_0002035", - "lbl": "lncRNA_primary_transcript", + "undergone", + "necessary", + "modifications", + "function", + "eukaryotes", + "includes", + "example", + "processing", + "introns", + "cleavage", + "base", + "modification", + "ends", + "addition", + "bases", + "bacteria", + "functional", + "mrnas", + "usually", + "modified", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000233", + "lbl": "mature_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:23:03Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "A processed transcript cannot contain introns.", + ], "definition": { - "val": "A primary transcript encoding a lncRNA.", + "val": "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.", "xrefs": [ "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "lncRNA primary transcript", + "val": "mature transcript", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Mature_transcript", }, ], }, @@ -8373,39 +9019,41 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002038", - "shrna", - "primary", - "transcript", - "encoding", + "so:0001204", + "phage", + "rna", + "polymerase", + "promoter", + "region", + "dna", + "bacteriophage", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0002038", - "lbl": "shRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001204", + "lbl": "Phage_RNA_Polymerase_Promoter", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:30:43Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.", + ], "definition": { - "val": "A primary transcript encoding an shRNA.", + "val": "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.", "xrefs": [ - "SO:ke", + "xenbase:jb", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "shRNA primary transcript", + "val": "Phage RNA Polymerase Promoter", + "xrefs": [], }, ], }, @@ -8413,31 +9061,32 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002040", - "vaultrna", - "primary", - "transcript", - "encoding", + "so:0000613", + "bacterial", + "rnapol", + "promoter", + "dna", + "sequence", + "rna", + "polymerase", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0002040", - "lbl": "vaultRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000613", + "lbl": "bacterial_RNApol_promoter", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:33:33Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.", + ], "definition": { - "val": "A primary transcript encoding a vaultRNA.", + "val": "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.", "xrefs": [ "SO:ke", ], @@ -8445,7 +9094,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "vaultRNA primary transcript", + "val": "bacterial RNApol promoter", + "xrefs": [], }, ], }, @@ -8453,32 +9103,33 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002042", - "y", + "so:0000169", + "rnapol", + "promoter", + "pol", "rna", - "primary", - "transcript", - "encoding", + "polymerase", + "dna", + "sequence", + "eukaryotic", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0002042", - "lbl": "Y_RNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000169", + "lbl": "RNApol_I_promoter", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:36:51Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.", + ], "definition": { - "val": "A primary transcript encoding a Y-RNA.", + "val": "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.", "xrefs": [ "SO:ke", ], @@ -8486,7 +9137,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "Y-RNA primary transcript", + "val": "pol I promoter", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "RNA polymerase A promoter", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "polymerase I promoter", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "RNApol I promoter", + "xrefs": [], }, ], }, @@ -8494,13 +9161,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000108", - "mrna", - "frameshift", - "frameshifted", + "so:0000170", + "rnapol", + "ii", + "promoter", + "polymerase", + "rna", + "b", + "pol", + "dna", + "sequence", + "eukaryotic", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0000108", - "lbl": "mRNA_with_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0000170", + "lbl": "RNApol_II_promoter", "meta": { "basicPropertyValues": [ { @@ -8508,20 +9185,35 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.", + ], "definition": { - "val": "An mRNA with a frameshift.", + "val": "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "frameshifted mRNA", + "val": "polymerase II promoter", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "mRNA with frameshift", + "val": "RNA polymerase B promoter", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "pol II promoter", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "RNApol II promoter", + "xrefs": [], }, ], }, @@ -8529,26 +9221,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000734", - "exemplar", - "mrna", - "representative", - "cdna", + "so:0000171", + "rnapol", + "iii", + "promoter", + "polymerase", + "rna", + "c", + "pol", + "dna", "sequence", - "gene", - "approach", - "method", - "usually", - "involves", - "initial", - "clustering", - "groups", - "subsequent", - "selection", - "group", + "eukaryotic", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0000734", - "lbl": "exemplar_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000171", + "lbl": "RNApol_III_promoter", "meta": { "basicPropertyValues": [ { @@ -8557,18 +9246,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "comments": [ - "Added for the MO people.", + "parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.", ], "definition": { - "val": "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.", + "val": "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.", "xrefs": [ - "http://mged.sourceforge.net/ontologies/MGEDontology.php", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "exemplar mRNA", + "val": "RNApol III promoter", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "polymerase III promoter", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "RNA polymerase C promoter", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "pol III promoter", + "xrefs": [], }, ], }, @@ -8576,12 +9281,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000862", - "capped", - "mrna", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000862", - "lbl": "capped_mRNA", + "so:0000305", + "modified", + "dna", + "base", + "site", + "insdc", + "feature:modified", + "nucleotide", + "e", + "c", + "g", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000305", + "lbl": "modified_DNA_base", "meta": { "basicPropertyValues": [ { @@ -8589,16 +9302,28 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Modified base:.", + ], "definition": { - "val": "An mRNA that is capped.", + "val": "A modified nucleotide, i.e. a nucleotide other than A, T, C. G.", "xrefs": [ - "SO:xp", + "http://www.insdc.org/files/feature_table.html", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "capped mRNA", + "val": "modified base site", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "INSDC_feature:modified_base", + "xrefs": [], }, ], }, @@ -8606,56 +9331,57 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000871", - "polyadenylated", - "mrna", + "so:0002332", + "epigenomically", + "modified", + "region", + "biological", + "implicated", + "inherited", + "changes", + "caused", + "mechanisms", + "underlying", + "dna", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000871", - "lbl": "polyadenylated_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002332", + "lbl": "epigenomically_modified_region", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-02-11T21:16:30Z", + }, + ], + "comments": [ + "Added as part of GREEKC terms to differentiate between inherited and not inherited epigenetic changes. See GitHub Issue #532.", ], "definition": { - "val": "An mRNA that is polyadenylated.", + "val": "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.", "xrefs": [ - "SO:xp", + "SO:ds", + "http://en.wikipedia.org/wiki/Epigenetics", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "polyadenylated mRNA", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0000995", - "consensus", - "mrna", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000995", - "lbl": "consensus_mRNA", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "val": "epigenomically modified region", + "xrefs": [], }, ], - "comments": [ - "DO not obsolete without considering MGED mapping.", - ], - "synonyms": [ + "xrefs": [ { - "pred": "hasExactSynonym", - "val": "consensus mRNA", + "val": "https://epi.grants.cancer.gov/epigen/#:~:text=mail.nih.gov-,Overview,a%20cell%20or%20entire%20organism.", }, ], }, @@ -8663,46 +9389,59 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002130", - "nsd", - "transcript", - "non", - "stop", - "decay", - "contains", - "cds", - "codon", - "polya", + "so:0001700", + "histone", + "modification", "site", - "reached", + "post", + "translationally", + "modified", + "region", + "whereby", + "residues", + "protein", + "methylation", + "acetylation", + "phosphorylation", + "ubiquitination", + "sumoylation", + "citrullination", + "adp", + "ribosylation", ], - "id": "http://purl.obolibrary.org/obo/SO_0002130", - "lbl": "NSD_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001700", + "lbl": "histone_modification", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:11:34Z", + "val": "kareneilbeck", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-03-31T10:22:08Z", + }, ], "definition": { - "val": "A transcript that contains a CDS but has no stop codon before the polyA site is reached.", + "val": "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "http:en.wikipedia.org/wiki/Histone", ], }, "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "histone modification site", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "non_stop_decay_transcript", + "val": "histone modification", + "xrefs": [], }, ], }, @@ -8710,22 +9449,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:1001261", - "recoded", - "mrna", - "sequence", - "mature", - "transcript", + "so:0000898", + "epigenetically", "modified", - "translation", - "usually", - "special", - "cis", - "acting", - "signals", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_1001261", - "lbl": "recoded_mRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000898", + "lbl": "epigenetically_modified_gene", "meta": { "basicPropertyValues": [ { @@ -8734,15 +9464,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.", + "val": "A gene that is epigenetically modified.", "xrefs": [ - "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "recoded mRNA", + "val": "epigenetically modified gene", + "xrefs": [], }, ], }, @@ -8750,50 +9481,75 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000013", - "scrna", + "so:0002191", + "imprinting", + "control", + "region", "insdc", - "feature:ncrna", - "qualifier:scrna", - "small", - "cytoplasmic", - "rna", + "feature:regulatory", + "qualifier:imprinting", + "regulatory", + "controls", + "epigenetic", + "affects", + "expression", + "target", + "genes", + "allele", + "parent", + "origin", + "specific", + "manner", + "associated", + "elements", + "may", + "include", + "differentially", + "methylated", + "regions", "non", "coding", - "sequence", - "present", - "cytoplasm", + "rnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0000013", - "lbl": "scRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002191", + "lbl": "imprinting_control_region", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2018-01-04T17:35:34Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Moved from is_a regulatory_region (SO:0005836) to is_a epigenetically_modified_region (SO:0001720) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530.", + ], "definition": { - "val": "A small non coding RNA sequence, present in the cytoplasm.", - "xrefs": [ - "SO:ke", - ], + "val": "A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", + "val": "INSDC_feature:regulatory", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:scRNA", + "val": "INSDC_qualifier:imprinting_control_region", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small cytoplasmic RNA", + "val": "imprinting control region", + "xrefs": [], }, ], }, @@ -8801,26 +9557,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000252", - "rrna", + "so:0000140", + "attenuator", + "sequence", "insdc", - "qualifier:unknown", - "feature:rrna", - "ribosomal", - "rna", - "ribonucleic", - "acid", - "comprises", - "part", - "ribosome", - "provide", - "structural", - "scaffolding", - "catalytic", - "activity", + "qualifier:attenuator", + "feature:regulatory", + "segment", + "located", + "within", + "five", + "prime", + "end", + "mrna", + "causes", + "premature", + "termination", + "translation", ], - "id": "http://purl.obolibrary.org/obo/SO_0000252", - "lbl": "rRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000140", + "lbl": "attenuator", "meta": { "basicPropertyValues": [ { @@ -8829,36 +9585,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.", + "val": "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.", "xrefs": [ - "ISBN:0198506732", - "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html", + "SO:as", ], }, "subsets": [ "http://purl.obolibrary.org/obo/so#SOFA", ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_qualifier:unknown", - }, { "pred": "hasExactSynonym", - "val": "INSDC_feature:rRNA", + "val": "attenuator sequence", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "ribosomal RNA", + "val": "INSDC_qualifier:attenuator", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "ribosomal ribonucleic acid", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/RRNA", + "val": "http://en.wikipedia.org/wiki/Attenuator", }, ], }, @@ -8866,116 +9620,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000253", - "trna", - "insdc", - "qualifier:unknown", - "feature:trna", - "transfer", - "rna", - "ribonucleic", - "acid", - "molecules", - "approximately", - "80", - "nucleotides", - "length", - "secondary", - "structure", - "includes", - "four", - "short", - "double", - "helical", - "elements", - "three", - "loops", - "d", - "anti", - "codon", - "hydrogen", - "bonds", - "mediate", - "characteristic", - "l", - "shaped", - "molecular", - "rnas", - "two", - "regions", - "fundamental", - "functional", - "importance:", - "responsible", - "specific", - "mrna", - "recognition", - "end", - "corresponding", - "amino", - "attached", - "aminoacyl", - "synthetases", - "cope", - "degeneracy", - "genetic", - "code", - "manners:", - "one", - "particular", - "wobble", - "base", - "pairing", - "e", - "permitting", - "non", - "standard", - "3rd", - "position", + "so:0002059", + "recombination", + "enhancer", + "regulatory", + "region", + "promotes", + "induces", + "process", ], - "id": "http://purl.obolibrary.org/obo/SO_0000253", - "lbl": "tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002059", + "lbl": "recombination_enhancer", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "comments": [ - "This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2015-05-14T13:08:58Z", + }, ], "definition": { - "val": "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.", + "val": "A regulatory_region that promotes or induces the process of recombination.", "xrefs": [ - "ISBN:0198506732", - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005", + "PMID:8861911", + "SGD:se", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_qualifier:unknown", - }, { "pred": "hasExactSynonym", - "val": "INSDC_feature:tRNA", - }, - { - "pred": "hasRelatedSynonym", - "val": "transfer RNA", - }, - { - "pred": "hasRelatedSynonym", - "val": "transfer ribonucleic acid", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/TRNA", + "val": "recombination enhancer", + "xrefs": [], }, ], }, @@ -8983,23 +9665,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000274", - "snrna", - "insdc", - "feature:ncrna", - "qualifier:snrna", - "small", - "nuclear", - "rna", - "molecule", - "involved", - "pre", - "mrna", - "splicing", - "processing", + "so:0000057", + "operator", + "segment", + "regulatory", + "element", + "operon", + "activators", + "repressors", + "bind", + "thereby", + "effecting", + "translation", + "genes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000274", - "lbl": "snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000057", + "lbl": "operator", "meta": { "basicPropertyValues": [ { @@ -9008,36 +9689,27 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "comments": [ - "This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", + "Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.", ], "definition": { - "val": "A small nuclear RNA molecule involved in pre-mRNA splicing and processing.", + "val": "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.", "xrefs": [ - "PMID:11733745", - "WB:ems", - "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html", + "SO:ma", ], }, "subsets": [ "http://purl.obolibrary.org/obo/so#SOFA", ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:snRNA", - }, { "pred": "hasExactSynonym", - "val": "small nuclear RNA", + "val": "operator segment", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/SnRNA", + "val": "http://en.wikipedia.org/wiki/Operator_(biology)#Operator", }, ], }, @@ -9045,80 +9717,52 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000275", - "snorna", - "insdc", - "feature:ncrna", - "qualifier:snorna", - "small", - "nucleolar", - "rna", - "one", - "class", - "rnas", - "associated", - "eukaryotic", - "nucleus", - "components", - "ribonucleoproteins", - "participate", - "processing", - "modifications", - "many", - "mostly", - "ribosomal", - "rrnas", - "though", - "snornas", - "also", - "known", - "target", - "classes", - "including", - "spliceosomal", - "trnas", - "mrnas", - "via", - "stretch", - "sequence", - "complementary", - "targeted", + "so:0002382", + "range", + "extender", + "element", + "rex", + "conserved", + "cis", + "acting", + "confers", + "extreme", + "distance", + "regulatory", + "activity", + "enhancer", ], - "id": "http://purl.obolibrary.org/obo/SO_0000275", - "lbl": "snoRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002382", + "lbl": "range_extender_element", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + { + "pred": "http://purl.org/dc/elements/1.1/date", + "val": "2024-06-06T16:53:56Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added at the request of Chris Mungall (Berkeley Lab) on 6 June 2024. See GitHub Issue #649.", + ], "definition": { - "val": "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.", + "val": "A conserved cis-acting element that confers extreme-distance regulatory activity to an enhancer.", "xrefs": [ - "GOC:kgc", + "https://doi.org/10.1101/2024.05.26.595809", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:snoRNA", - }, { "pred": "hasExactSynonym", - "val": "small nucleolar RNA", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/SnoRNA", + "val": "REX", + "xrefs": [], }, ], }, @@ -9126,36 +9770,65 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000370", - "small", + "so:0000727", + "cis", "regulatory", - "ncrna", - "non", - "coding", - "rna", - "less", - "200", - "nucleotides", - "long", - "usually", - "specific", - "secondary", - "structure", - "acts", + "module", + "crm", + "transcription", + "factor", + "tf", + "region", + "binding", + "sites", + "clustered", "regulate", - "gene", + "various", + "aspects", + "activities", + "crms", + "located", + "kb", + "hundreds", + "upstream", + "core", + "promoter", + "coding", + "sequence", + "within", + "introns", + "untranslated", + "regions", + "utr", + "sequences", + "even", + "different", + "chromosome", + "single", + "gene", + "regulated", + "multiple", + "give", + "precise", + "control", + "spatial", + "temporal", "expression", - "include", - "short", - "ncrnas", - "pirna", - "mirna", - "sirnas", - "among", - "others", + "function", + "nodes", + "large", + "intertwined", + "network", + "dna", + "accessibility", + "subject", + "regulation", + "dbtfs", + "co", + "tfs", ], - "id": "http://purl.obolibrary.org/obo/SO_0000370", - "lbl": "small_regulatory_ncRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000727", + "lbl": "cis_regulatory_module", "meta": { "basicPropertyValues": [ { @@ -9163,12 +9836,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534.", + ], "definition": { - "val": "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others).", + "val": "A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs.", "xrefs": [ - "PMID:28541282", - "PomBase:al", - "SO:ma", + "PMID:19660565", + "SO:SG", ], }, "subsets": [ @@ -9177,7 +9852,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "small regulatory ncRNA", + "val": "CRM", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "transcription factor module", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cis regulatory module", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "TF module", + "xrefs": [], }, ], }, @@ -9185,47 +9876,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000385", - "rnase", - "mrp", - "rna", - "insdc", - "feature:ncrna", - "qualifier:rnase", - "molecule", - "essential", - "catalytic", - "activity", - "enzymatically", - "active", - "ribonucleoprotein", - "two", - "distinct", - "roles", - "eukaryotes", - "mitochondria", - "plays", - "direct", - "role", - "initiation", - "mitochondrial", + "so:0000235", + "tf", + "binding", + "site", + "transcription", + "factor", "dna", - "replication", - "nucleus", - "involved", - "precursor", - "rrna", - "processing", - "cleaves", - "internal", - "transcribed", - "spacer", - "18s", - "8s", - "rrnas", + "binds", ], - "id": "http://purl.obolibrary.org/obo/SO_0000385", - "lbl": "RNase_MRP_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000235", + "lbl": "TF_binding_site", "meta": { "basicPropertyValues": [ { @@ -9233,27 +9894,28 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", + ], "definition": { - "val": "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.", + "val": "A DNA site where a transcription factor binds.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030", + "SO:ke", ], }, "subsets": [ "http://purl.obolibrary.org/obo/so#SOFA", ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:RNase_MRP_RNA", + "val": "TF binding site", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "RNase MRP RNA", + "val": "transcription factor binding site", + "xrefs": [], }, ], }, @@ -9261,113 +9923,62 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000386", - "rnase", - "p", + "so:0002047", + "transcription", + "pause", + "site", + "sites", + "regions", + "gene", "rna", - "insdc", - "feature:ncrna", - "qualifier:rnase", - "component", - "ribonuclease", - "ubiquitous", - "endoribonuclease", - "found", - "archaea", - "bacteria", - "eukarya", - "well", - "chloroplasts", - "mitochondria", - "best", - "characterized", - "activity", - "generation", - "mature", - "prime", - "ends", - "trnas", - "cleaving", - "leader", - "elements", - "precursor", - "cellular", - "ps", - "ribonucleoproteins", - "bacterial", - "retains", - "catalytic", - "absence", - "protein", - "subunit", + "polymerase", + "may", + "functional", + "role", + "pausing", + "facilitate", + "factor", + "recruitment", + "folding", + "synchronization", + "translation", + "consensus", + "observed", "e", - "ribozyme", - "isolated", - "eukaryotic", - "archaeal", - "shown", - "retain", - "function", - "still", - "essential", - "holoenzyme", - "although", - "holoenzymes", - "much", - "greater", - "content", - "ones", - "cores", - "three", - "lineages", - "homologous", - "helices", - "corresponding", - "p1", - "p2", - "p3", - "p4", - "p10", - "11", - "common", - "rnas", - "yet", - "considerable", - "sequence", - "variation", - "particularly", - "among", + "coli", ], - "id": "http://purl.obolibrary.org/obo/SO_0000386", - "lbl": "RNase_P_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0002047", + "lbl": "transcription_pause_site", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2015-02-09T15:32:52Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + ], + "comments": [ + "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", ], "definition": { - "val": "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.", + "val": "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010", + "PMID:24789973", + "SO:ke", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:RNase_P_RNA", - }, - { - "pred": "hasExactSynonym", - "val": "RNase P RNA", + "val": "transcription pause site", + "xrefs": [], }, ], }, @@ -9375,21 +9986,28 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000390", - "telomerase", - "rna", + "so:0000551", + "polya", + "signal", + "sequence", "insdc", - "feature:ncrna", - "qualifier:telomerase", - "component", - "reverse", - "transcriptase", - "synthesizes", - "telomeric", - "dna", + "qualifier:polya", + "feature:regulatory", + "polyadenylation", + "termination", + "poly", + "recognition", + "necessary", + "endonuclease", + "cleavage", + "rna", + "transcript", + "followed", + "consensus", + "aataaa", ], - "id": "http://purl.obolibrary.org/obo/SO_0000390", - "lbl": "telomerase_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000551", + "lbl": "polyA_signal_sequence", "meta": { "basicPropertyValues": [ { @@ -9397,10 +10015,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", + ], "definition": { - "val": "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.", + "val": "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025", + "http://www.insdc.org/files/feature_table.html", ], }, "subsets": [ @@ -9408,21 +10029,29 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:polyA_signal_sequence", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:telomerase_RNA", + "val": "polyA signal sequence", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "telomerase RNA", + "val": "polyadenylation termination signal", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Telomerase_RNA", + "pred": "hasExactSynonym", + "val": "poly(A) signal", + "xrefs": [], }, ], }, @@ -9430,72 +10059,60 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000404", - "vault", - "rna", + "so:0002205", + "response", + "element", "insdc", - "feature:ncrna", - "qualifier:vault", - "family", - "rnas", - "found", - "part", - "enigmatic", - "ribonucleoprotein", - "complex", - "consists", - "major", - "protein", - "mvp", - "two", - "minor", - "proteins", - "vparp", - "tep1", - "several", - "small", - "untranslated", - "molecules", - "suggested", - "involved", - "drug", - "resistance", + "qualifier:response", + "feature:regulatory", + "regulatory", + "acts", + "stimulus", + "usually", + "via", + "transcription", + "factor", + "binding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000404", - "lbl": "vault_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0002205", + "lbl": "response_element", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2018-01-10T16:33:25Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + ], + "comments": [ + "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", ], "definition": { - "val": "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.", - "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006", - ], + "val": "A regulatory element that acts in response to a stimulus, usually via transcription factor binding.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:vault_RNA", + "val": "INSDC_qualifier:response_element", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "vault RNA", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Vault_RNA", + "pred": "hasExactSynonym", + "val": "response element", + "xrefs": [], }, ], }, @@ -9503,51 +10120,25 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000405", - "y", - "rna", + "so:0000141", + "terminator", "insdc", - "feature:ncrna", - "qualifier:y", - "rnas", - "components", - "ro", - "ribonucleoprotein", - "particle", - "rnp", - "association", - "ro60", - "la", - "proteins", - "well", - "conserved", - "function", - "known", - "humans", - "component", - "one", - "four", - "small", - "rnas:", - "hy1", - "hy3", - "hy4", - "hy5", - "predicted", - "fold", - "secondary", - "structure", - "containing", - "three", - "stem", - "structures", - "largest", - "contains", - "additional", - "hairpin", + "qualifier:terminator", + "sequence", + "feature:regulatory", + "dna", + "located", + "either", + "end", + "transcript", + "causes", + "rna", + "polymerase", + "terminate", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0000405", - "lbl": "Y_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000141", + "lbl": "terminator", "meta": { "basicPropertyValues": [ { @@ -9555,10 +10146,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", + ], "definition": { - "val": "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.", + "val": "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019", + "http://www.insdc.org/files/feature_table.html", ], }, "subsets": [ @@ -9566,21 +10160,24 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:terminator", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:Y_RNA", + "val": "terminator sequence", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "Y RNA", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Y_RNA", + "val": "http://en.wikipedia.org/wiki/Terminator_(genetics)", }, ], }, @@ -9588,59 +10185,59 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000454", - "rasirna", - "insdc", - "feature:ncrna", - "qualifier:rasirna", - "repeat", - "associated", - "small", - "interfering", - "rna", - "17", - "28", - "nt", - "derived", - "transcripts", - "repetitive", - "elements", + "so:0002297", + "tfrs", + "collection", + "transcription", + "factor", + "regulatory", + "site", + "possible", + "discontinous", + "stretch", + "dna", + "encompass", + "tfrss", + "regulate", + "promoter", ], - "id": "http://purl.obolibrary.org/obo/SO_0000454", - "lbl": "rasiRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002297", + "lbl": "TFRS_collection", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-08-05T11:49:30Z", + }, + ], + "comments": [ + "Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", ], "definition": { - "val": "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.", + "val": "The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter.", "xrefs": [ - "http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284", + "Bacterial_regulation_working_group:CMA", + "PMID:32665585", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", + "pred": "hasExactSynonym", + "val": "TFRS collection", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:rasiRNA", - }, - { - "pred": "hasExactSynonym", - "val": "repeat associated small interfering RNA", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/RasiRNA", + "val": "transcription factor regulatory site collection", + "xrefs": [], }, ], }, @@ -9648,134 +10245,77 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000590", - "srp", - "rna", - "insdc", - "feature:ncrna", - "qualifier:srp", - "7s", - "signal", - "recognition", - "particle", - "universally", - "conserved", - "ribonucleoprotein", - "involved", - "co", - "translational", - "targeting", - "proteins", - "membranes", - "eukaryotic", - "consists", - "300", - "nucleotide", - "six", - "proteins:", - "srps", - "72", - "68", - "54", - "19", - "14", - "archaeal", - "homologues", - "srp19", - "srp54", - "eubacteria", - "5s", - "ffh", - "protein", - "homologue", - "rnas", - "similar", - "secondary", - "structures", - "eight", - "helical", - "elements", - "fold", - "alu", - "domains", - "separated", - "long", - "linker", - "region", - "eubacterial", - "generally", - "simpler", - "structure", - "m", - "domain", + "so:0002296", + "tfrs", + "module", + "transcription", + "factor", + "regulatory", + "site", + "phrase", + "possible", + "discontinuous", + "stretch", + "dna", + "combination", + "one", + "several", + "tfrss", + "whose", "bound", - "corresponds", - "helix", - "gram", - "positive", - "bacteria", - "e", - "g", - "bacillus", - "subtilis", - "however", - "larger", - "also", - "thought", - "mediate", - "peptide", - "chain", - "elongation", - "retardation", - "function", - "interacts", - "mediates", - "sequence", - "eukaryotes", - "archaea", - "complex", - "assembly", - "stabilizes", - "binding", + "tfs", + "work", + "jointly", + "regulation", + "promoter", ], - "id": "http://purl.obolibrary.org/obo/SO_0000590", - "lbl": "SRP_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0002296", + "lbl": "TFRS_module", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-08-05T11:49:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", ], "definition": { - "val": "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.", + "val": "The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter. ", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017", + "Bacterial_regulation_working_group:CMA", + "PMID:32665585", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:SRP_RNA", + "val": "transcription factor regulatory site phrase", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "SRP RNA", + "val": "transcription factor regulatory site module", + "xrefs": [], }, { - "pred": "hasRelatedSynonym", - "val": "7S RNA", + "pred": "hasExactSynonym", + "val": "TFRS phrase", + "xrefs": [], }, { - "pred": "hasRelatedSynonym", - "val": "signal recognition particle RNA", + "pred": "hasExactSynonym", + "val": "TFRS module", + "xrefs": [], }, ], }, @@ -9783,69 +10323,47 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000602", - "guide", - "rna", - "insdc", - "feature:ncrna", - "qualifier:guide", - "grna", - "short", - "uridylated", - "form", - "duplex", - "except", - "post", - "transcriptionally", - "added", - "oligo", - "u", - "tail", - "so:0000609", - "stretch", - "mature", - "edited", - "mrna", + "so:0001952", + "promoter", + "flanking", + "region", + "immediately", + "adjacent", + "may", + "contain", + "transcription", + "factor", + "binding", + "sites", ], - "id": "http://purl.obolibrary.org/obo/SO_0000602", - "lbl": "guide_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0001952", + "lbl": "promoter_flanking_region", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2013-03-06T11:36:25Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.", + "val": "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites.", "xrefs": [ - "http://www.rna.ucla.edu/index.html", + "EBI:nj", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:guide_RNA", - }, - { - "pred": "hasExactSynonym", - "val": "gRNA", - }, { "pred": "hasExactSynonym", - "val": "guide RNA", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Guide_RNA", + "val": "promoter flanking region", + "xrefs": [], }, ], }, @@ -9853,24 +10371,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000644", - "antisense", - "rna", - "insdc", - "feature:ncrna", - "qualifier:antisense", - "transcribed", - "coding", - "rather", - "template", - "strand", - "dna", - "therefore", - "complementary", - "mrna", + "so:0001056", + "splicing", + "regulatory", + "region", + "modulates", ], - "id": "http://purl.obolibrary.org/obo/SO_0000644", - "lbl": "antisense_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0001056", + "lbl": "splicing_regulatory_region", "meta": { "basicPropertyValues": [ { @@ -9878,8 +10386,11 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", + ], "definition": { - "val": "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.", + "val": "A regulatory_region that modulates splicing.", "xrefs": [ "SO:ke", ], @@ -9888,22 +10399,10 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "http://purl.obolibrary.org/obo/so#SOFA", ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:antisense_RNA", - }, - { - "pred": "hasExactSynonym", - "val": "antisense RNA", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Antisense_RNA", + "val": "splicing regulatory region", + "xrefs": [], }, ], }, @@ -9911,52 +10410,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000989", - "class", - "ii", - "rna", - "small", - "non", - "coding", - "59", - "60", - "nt", - "long", - "containing", - "ends", - "predicted", - "come", - "together", - "form", - "stem", - "structure", - "identified", - "social", - "amoeba", - "dictyostelium", - "discoideum", - "localized", - "cytoplasm", + "so:0001492", + "intronic", + "regulatory", + "region", + "part", + "intron", ], - "id": "http://purl.obolibrary.org/obo/SO_0000989", - "lbl": "class_II_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0001492", + "lbl": "intronic_regulatory_region", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2009-11-08T02:48:02Z", + }, + ], + "comments": [ + "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", ], "definition": { - "val": "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.", + "val": "A regulatory region that is part of an intron.", "xrefs": [ - "PMID:15333696", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "class II RNA", + "val": "intronic regulatory region", + "xrefs": [], }, ], }, @@ -9964,38 +10455,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000990", - "class", + "so:0001427", + "cis", + "regulatory", + "frameshift", + "element", + "structural", + "region", "rna", - "small", - "non", + "molecule", + "promotes", + "ribosomal", + "frameshifting", "coding", - "55", - "65", - "nt", - "long", - "containing", - "highly", - "conserved", - "ends", - "16", - "respectively", - "predicted", - "come", - "together", - "form", - "stem", - "structure", - "identified", - "social", - "amoeba", - "dictyostelium", - "discoideum", - "localized", - "cytoplasm", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000990", - "lbl": "class_I_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0001427", + "lbl": "cis_regulatory_frameshift_element", "meta": { "basicPropertyValues": [ { @@ -10004,18 +10480,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "comments": [ - "Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.", + "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.", ], "definition": { - "val": "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.", + "val": "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.", "xrefs": [ - "PMID:15333696", + "RFAM:jd", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "class I RNA", + "val": "cis regulatory frameshift element", + "xrefs": [], }, ], }, @@ -10023,52 +10500,43 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001800", - "tasirna", - "trans", - "acting", - "small", - "interfering", - "rna", - "sequence", - "21", - "nucleotide", - "double", - "stranded", - "polyadenylated", - "non", - "coding", - "transcribed", - "tas", - "gene", + "so:0000483", + "nc", + "primary", + "transcript", + "noncoding", + "never", + "translated", + "protein", ], - "id": "http://purl.obolibrary.org/obo/SO_0001800", - "lbl": "tasiRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000483", + "lbl": "nc_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2011-05-31T03:24:06Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.", + "val": "A primary transcript that is never translated into a protein.", "xrefs": [ - "PMID:16145017", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { - "pred": "hasRelatedSynonym", - "val": "trans acting small interfering RNA", + "pred": "hasExactSynonym", + "val": "noncoding primary transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "nc primary transcript", + "xrefs": [], }, ], }, @@ -10076,45 +10544,43 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001870", - "enhancerrna", - "erna", - "short", - "ncrna", - "transcribed", - "enhancer", - "may", - "regulatory", - "function", + "so:0000635", + "mini", + "exon", + "donor", + "rna", + "primary", + "transcript", + "donates", + "spliced", + "leader", + "mrna", ], - "id": "http://purl.obolibrary.org/obo/SO_0001870", - "lbl": "enhancerRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000635", + "lbl": "mini_exon_donor_RNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-01-17T03:09:35Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A short ncRNA that is transcribed from an enhancer. May have a regulatory function.", + "val": "A primary transcript that donates the spliced leader to other mRNA.", "xrefs": [ - "SO:cjm", - "doi:10.1038/465173a", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "eRNA", + "val": "mini exon donor RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "mini-exon donor RNA", + "xrefs": [], }, ], }, @@ -10122,64 +10588,50 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001877", - "lnc", - "rna", - "insdc", - "feature:ncrna", - "qualifier:lncrna", - "lncrna", - "transcript", - "long", - "non", + "so:0000120", + "protein", "coding", - "200nucleotides", - "length", + "primary", + "transcript", + "pre", + "mrna", + "least", + "part", + "encodes", + "one", + "proteins", ], - "id": "http://purl.obolibrary.org/obo/SO_0001877", - "lbl": "lnc_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000120", + "lbl": "protein_coding_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-02-14T05:18:01Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "May contain introns.", + ], "definition": { - "val": "A non-coding RNA over 200nucleotides in length.", + "val": "A primary transcript that, at least in part, encodes one or more proteins.", "xrefs": [ - "HGNC:mw", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:lncRNA", - }, - { - "pred": "hasExactSynonym", - "val": "lncRNA_transcript", + "pred": "hasRelatedSynonym", + "val": "pre mRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "long non-coding RNA", - }, - ], - "xrefs": [ - { - "val": "http://www.gencodegenes.org/gencode_biotypes.html", + "val": "protein coding primary transcript", + "xrefs": [], }, ], }, @@ -10187,41 +10639,35 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001927", - "telomeric", + "so:0000632", + "monocistronic", + "primary", "transcript", - "non", - "coding", - "derived", - "telomere", + "encoding", + "one", + "gene", + "product", ], - "id": "http://purl.obolibrary.org/obo/SO_0001927", - "lbl": "telomeric_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000632", + "lbl": "monocistronic_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-10-31T01:42:15Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A non-coding transcript derived from the transcript of the telomere.", + "val": "A primary transcript encoding for one gene product.", "xrefs": [ - "PMID:22139915", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "telomeric transcript", + "val": "monocistronic primary transcript", + "xrefs": [], }, ], }, @@ -10229,48 +10675,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002022", - "prirna", - "primal", - "small", - "rna", - "molecule", - "22", - "23", - "nt", - "size", - "product", - "longer", - "production", - "prirnas", - "independent", - "dicer", - "involves", - "binding", - "argonaute", - "trimming", - "triman", - "fission", - "yeast", - "trigger", - "establishment", - "heterochromatin", - "primarily", - "generated", - "centromeric", - "transcripts", - "dg", - "dh", - "repeats", - "may", - "also", - "produced", - "degradation", - "products", - "primary", + "so:0002115", + "pseudogenic", + "transcript", + "retained", + "intron", + "pseudogene", + "supported", + "est", + "mrna", + "evidence", + "aligns", + "unambiguously", + "locus", + "intronic", + "sequence", + "compared", + "reference", ], - "id": "http://purl.obolibrary.org/obo/SO_0002022", - "lbl": "priRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002115", + "lbl": "pseudogenic_transcript_with_retained_intron", "meta": { "basicPropertyValues": [ { @@ -10279,25 +10703,27 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-05-30T15:01:24Z", + "val": "2016-07-18T14:19:04Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.", + ], "definition": { - "val": "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts.", + "val": "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence.", "xrefs": [ - "PMID:20178743", - "PMID:24095277", - "PomBase:al", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "primal small RNA", + "val": "pseudogene retained intron", + "xrefs": [], }, ], }, @@ -10305,61 +10731,68 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002031", - "shrna", - "short", - "hairpin", - "rna", - "small", + "so:0000861", + "capped", + "primary", "transcript", - "makes", - "tight", - "turn", - "used", - "silence", - "target", - "gene", - "expression", - "via", - "interference", ], - "id": "http://purl.obolibrary.org/obo/SO_0002031", - "lbl": "shRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000861", + "lbl": "capped_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-10-23T09:16:29Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference.", + "val": "A primary transcript that is capped.", "xrefs": [ - "PMID:6699500", - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "short hairpin RNA", + "val": "capped primary transcript", + "xrefs": [], }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000645", + "antisense", + "primary", + "transcript", + "reverse", + "complement", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000645", + "lbl": "antisense_primary_transcript", + "meta": { + "basicPropertyValues": [ { - "pred": "hasExactSynonym", - "val": "small hairpin RNA", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, ], - "xrefs": [ + "definition": { + "val": "The reverse complement of the primary transcript.", + "xrefs": [ + "SO:ke", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], + "synonyms": [ { - "val": "http:http:en.wikipedia.org/wiki/Small_hairpin_RNA", + "pred": "hasExactSynonym", + "val": "antisense primary transcript", + "xrefs": [], }, ], }, @@ -10367,47 +10800,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002095", - "scarna", - "small", - "cajal", - "body", - "specific", - "rna", - "ncrna", - "demonstrated", - "function", - "guide", - "site", - "synthesis", - "o", - "ribose", - "methylated", - "nucleotides", - "pseudouridines", - "polymerase", - "ii", + "so:0001905", + "regional", + "centromere", + "outer", + "repeat", + "transcript", + "region", "transcribed", - "u1", - "u2", - "u4", - "u5", - "spliceosomal", - "nuclear", - "rnas", - "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0002095", - "lbl": "scaRNA", + "id": "http://purl.obolibrary.org/obo/SO_0001905", + "lbl": "regional_centromere_outer_repeat_transcript", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-04-11T04:54:22Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-05-19T13:42:45Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -10415,25 +10827,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs).", + "val": "A transcript that is transcribed from the outer repeat region of a regional centromere.", "xrefs": [ - "PMC:126017", - "SO:nrs", + "PomBase:mah", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "small Cajal body specific RNA", + "val": "regional centromere outer repeat region transcript", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small Cajal body-specific RNA", + "val": "centromere outer repeat transcript", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/", + "pred": "hasExactSynonym", + "val": "regional_centromere_outer_repeat_region_transcript", + "xrefs": [], }, ], }, @@ -10441,71 +10854,35 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002120", - "three", - "prime", - "overlapping", - "ncrna", - "3prime", - "noncoding", - "rna", + "so:0000631", + "polycistronic", + "primary", "transcript", - "ditag", - "digital", + "encoding", + "one", "gene", - "expression", - "profiling", - "published", - "experimental", - "data", - "strongly", - "supports", - "existence", - "short", - "non", - "coding", - "transcripts", - "transcribed", - "utr", + "product", ], - "id": "http://purl.obolibrary.org/obo/SO_0002120", - "lbl": "three_prime_overlapping_ncrna", + "id": "http://purl.obolibrary.org/obo/SO_0000631", + "lbl": "polycistronic_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T15:48:21Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.", - ], "definition": { - "val": "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR.", + "val": "A primary transcript encoding for more than one gene product.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "3'_overlapping_ncrna", - }, - { - "pred": "hasExactSynonym", - "val": "3prime_overlapping_ncRNA", - }, - { - "pred": "hasExactSynonym", - "val": "three prime overlapping noncoding rna", + "val": "polycistronic primary transcript", + "xrefs": [], }, ], }, @@ -10513,24 +10890,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0005843", - "rrna", - "cleavage", - "rna", - "ncrna", - "part", - "ribonucleoprotein", - "cleaves", - "primary", - "pre", - "transcript", - "process", - "producing", - "mature", - "molecules", + "so:0000929", + "edited", + "mrna", ], - "id": "http://purl.obolibrary.org/obo/SO_0005843", - "lbl": "rRNA_cleavage_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000929", + "lbl": "edited_mRNA", "meta": { "basicPropertyValues": [ { @@ -10539,15 +10904,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.", + "val": "An mRNA that is edited.", "xrefs": [ - "GOC:kgc", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "rRNA cleavage RNA", + "val": "edited mRNA", + "xrefs": [], }, ], }, @@ -10555,51 +10921,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002116", - "polymorphic", - "pseudogene", - "processed", + "so:0000874", + "edited", "transcript", - "contain", - "cds", - "fullfills", - "annotation", - "criteria", - "necessarily", - "functionally", - "non", - "coding", + "substitution", ], - "id": "http://purl.obolibrary.org/obo/SO_0002116", - "lbl": "polymorphic_pseudogene_processed_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000874", + "lbl": "edited_transcript_by_A_to_I_substitution", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-07-18T14:23:59Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", - ], "definition": { - "val": "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding.", + "val": "A transcript that has been edited by A to I substitution.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "polymorphic pseudogene processed transcript", + "val": "edited transcript by A to I substitution", + "xrefs": [], }, ], }, @@ -10607,14 +10953,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000614", - "bacterial", - "terminator", - "signal", - "transcription", + "so:0000634", + "polycistronic", + "mrna", + "processed", + "transcript", + "encodes", + "multiple", + "proteins", + "least", + "two", + "non", + "overlapping", + "regions", ], - "id": "http://purl.obolibrary.org/obo/SO_0000614", - "lbl": "bacterial_terminator", + "id": "http://purl.obolibrary.org/obo/SO_0000634", + "lbl": "polycistronic_mRNA", "meta": { "basicPropertyValues": [ { @@ -10623,15 +10977,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A terminator signal for bacterial transcription.", + "val": "An mRNA that encodes multiple proteins from at least two non-overlapping regions.", "xrefs": [ - "SO:ke", + "SO:rd", ], }, "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "polycistronic processed transcript", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "bacterial terminator", + "val": "polycistronic mRNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Polycistronic_mRNA", }, ], }, @@ -10639,12 +11004,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000951", - "eukaryotic", - "terminator", + "so:0000079", + "dicistronic", + "transcript", ], - "id": "http://purl.obolibrary.org/obo/SO_0000951", - "lbl": "eukaryotic_terminator", + "id": "http://purl.obolibrary.org/obo/SO_0000079", + "lbl": "dicistronic_transcript", "meta": { "basicPropertyValues": [ { @@ -10652,10 +11017,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "definition": { + "val": "A transcript that is dicistronic.", + "xrefs": [ + "SO:ke", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "eukaryotic terminator", + "val": "dicistronic transcript", + "xrefs": [], }, ], }, @@ -10663,53 +11035,82 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002045", - "pheromone", - "response", - "element", - "pre", - "yeast", - "tfbs", - "consensus", - "site", - "tgaaac", - "g", + "so:0002139", + "unconfirmed", + "transcript", + "tec", + "experimentally", + "confirmed", + "used", + "non", + "spliced", + "est", + "clusters", + "polya", + "features", + "category", + "specifically", + "created", + "encode", + "project", + "highlight", + "regions", + "could", + "indicate", + "presence", + "protein", + "coding", + "genes", + "require", + "experimental", + "validation", + "either", + "race", + "rt", + "pcr", + "extend", + "transcripts", + "confirming", + "expression", + "putatively", + "encoded", + "peptide", + "specific", + "antibodies", ], - "id": "http://purl.obolibrary.org/obo/SO_0002045", - "lbl": "pheromone_response_element", + "id": "http://purl.obolibrary.org/obo/SO_0002139", + "lbl": "unconfirmed_transcript", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "val": "nicole", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-02-09T15:05:43Z", + "val": "2016-08-23T16:28:07Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Requested by Rama, SGD.", - ], "definition": { - "val": "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].", + "val": "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.", "xrefs": [ - "PMID:1489142", - "SO:ke", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "PRE", + "val": "TEC", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "pheromone response element", + "val": "to_be_experimentally_confirmed_transcript", + "xrefs": [], }, ], }, @@ -10717,47 +11118,105 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000057", - "operator", - "segment", - "regulatory", - "element", - "operon", - "activators", - "repressors", - "bind", - "thereby", - "effecting", - "translation", - "genes", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000057", - "lbl": "operator", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], + "so:0002111", + "pseudogene", + "processed", + "transcript", + "supported", + "est", + "mrna", + "evidence", + "aligns", + "unambiguously", + "locus", + "e", + "alignment", + "clearly", + "better", + "parent", + ], + "id": "http://purl.obolibrary.org/obo/SO_0002111", + "lbl": "pseudogene_processed_transcript", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-07-18T14:07:00Z", + }, + ], + "comments": [ + "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", + ], "definition": { - "val": "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.", + "val": "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus).", "xrefs": [ - "SO:ma", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "pseudogene processed transcript", + "xrefs": [], + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000633", + "monocistronic", + "mrna", + "processed", + "transcript", + "either", + "single", + "protein", + "product", + "regions", + "encoding", + "products", + "overlap", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000633", + "lbl": "monocistronic_mRNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, ], + "definition": { + "val": "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.", + "xrefs": [ + "SO:rd", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "operator segment", + "val": "monocistronic processed transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "monocistronic mRNA", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Operator_(biology)#Operator", + "val": "http://en.wikipedia.org/wiki/Monocistronic_mRNA", }, ], }, @@ -10765,20 +11224,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000613", - "bacterial", - "rnapol", - "promoter", - "dna", - "sequence", - "rna", - "polymerase", - "binds", - "begin", - "transcription", + "so:0000872", + "trans", + "spliced", + "mrna", ], - "id": "http://purl.obolibrary.org/obo/SO_0000613", - "lbl": "bacterial_RNApol_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000872", + "lbl": "trans_spliced_mRNA", "meta": { "basicPropertyValues": [ { @@ -10787,15 +11239,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.", + "val": "An mRNA that is trans-spliced.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "bacterial RNApol promoter", + "val": "trans-spliced mRNA", + "xrefs": [], }, ], }, @@ -10803,26 +11256,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000167", - "promoter", + "so:0000234", + "mrna", + "messenger", + "rna", "insdc", - "feature:regulatory", - "qualifier:promoter", - "sequence", - "regulatory", - "region", - "composed", - "tss", - "binding", - "sites", - "tf", - "complexes", - "basal", - "transcription", - "machinery", + "feature:mrna", + "protein", + "coding", + "transcript", + "intermediate", + "molecule", + "dna", + "includes", + "utr", + "sequences", + "contain", + "introns", ], - "id": "http://purl.obolibrary.org/obo/SO_0000167", - "lbl": "promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000234", + "lbl": "mRNA", "meta": { "basicPropertyValues": [ { @@ -10831,12 +11284,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "comments": [ - "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.", + "An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.", ], "definition": { - "val": "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.", + "val": "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.", "xrefs": [ - "SO:regcreative", + "SO:ma", ], }, "subsets": [ @@ -10844,21 +11297,27 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", + "pred": "hasExactSynonym", + "val": "messenger RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:promoter", + "val": "INSDC_feature:mRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "promoter sequence", + "val": "protein_coding_transcript", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Promoter", + "val": "http://www.gencodegenes.org/gencode_biotypes.html", + }, + { + "val": "http://en.wikipedia.org/wiki/MRNA", }, ], }, @@ -10866,34 +11325,23 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000627", - "insulator", + "so:0000655", + "ncrna", "insdc", - "feature:regulatory", - "qualifier:insulator", - "element", - "regulatory", - "region", - "located", - "cm", + "qualifier:other", + "noncoding", + "rna", + "known", + "transcript", + "encode", + "protein", + "rather", + "molecule", "gene", - "promoter", - "prevents", - "crm", - "modulating", - "genes", - "expression", - "acts", - "chromatin", - "boundary", - "barrier", - "block", - "encroachment", - "condensed", - "adjacent", + "product", ], - "id": "http://purl.obolibrary.org/obo/SO_0000627", - "lbl": "insulator", + "id": "http://purl.obolibrary.org/obo/SO_0000655", + "lbl": "ncRNA", "meta": { "basicPropertyValues": [ { @@ -10901,12 +11349,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.", + ], "definition": { - "val": "A regulatory region that 1) when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region.", + "val": "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.", "xrefs": [ - "NCBI:cf", - "PMID:12154228", - "SO:regcreative", + "SO:ke", ], }, "subsets": [ @@ -10915,20 +11364,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", + "val": "INSDC_qualifier:other", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:insulator", + "val": "noncoding RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "insulator element", + "val": "known_ncrna", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Insulator_(genetics)", + "val": "http://www.gencodegenes.org/gencode_biotypes.html", + }, + { + "val": "http://en.wikipedia.org/wiki/NcRNA", }, ], }, @@ -10936,57 +11391,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000727", - "crm", - "tf", - "module", - "cis", - "regulatory", - "transcription", - "factor", - "region", - "binding", - "sites", - "clustered", - "regulate", - "various", - "aspects", - "activities", - "crms", - "located", - "kb", - "hundred", - "upstream", - "basal", + "so:0001206", + "t3", + "rna", + "polymerase", "promoter", - "coding", + "dna", "sequence", - "within", - "introns", - "downstream", - "utr", - "sequences", - "well", - "different", - "chromosome", - "single", - "gene", - "regulated", - "multiple", - "give", - "precise", - "control", - "spatial", - "temporal", - "expression", - "function", - "nodes", - "large", - "intertwined", - "network", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0000727", - "lbl": "CRM", + "id": "http://purl.obolibrary.org/obo/SO_0001206", + "lbl": "T3_RNA_Polymerase_Promoter", "meta": { "basicPropertyValues": [ { @@ -10994,31 +11411,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], - "comments": [ - "Requested by Stephen Grossmann Dec 2004.", - ], "definition": { - "val": "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.", + "val": "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.", "xrefs": [ - "PMID:19660565", - "SO:SG", + "xenbase:jb", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "TF module", + "val": "T3 RNA Polymerase Promoter", + "xrefs": [], }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0001207", + "t7", + "rna", + "polymerase", + "promoter", + "region", + "dna", + "binds", + "begin", + "transcription", + ], + "id": "http://purl.obolibrary.org/obo/SO_0001207", + "lbl": "T7_RNA_Polymerase_Promoter", + "meta": { + "basicPropertyValues": [ { - "pred": "hasExactSynonym", - "val": "cis regulatory module", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, + ], + "definition": { + "val": "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.", + "xrefs": [ + "xenbase:jb", + ], + }, + "synonyms": [ { "pred": "hasExactSynonym", - "val": "transcription factor module", + "val": "T7 RNA Polymerase Promoter", + "xrefs": [], }, ], }, @@ -11026,24 +11467,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001058", + "so:0001205", + "sp6", + "rna", + "polymerase", "promoter", - "targeting", - "sequence", - "transcriptional", - "cis", - "regulatory", "region", - "restricts", - "activity", - "crm", - "single", - "functions", - "insulator", - "located", + "dna", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0001058", - "lbl": "promoter_targeting_sequence", + "id": "http://purl.obolibrary.org/obo/SO_0001205", + "lbl": "SP6_RNA_Polymerase_Promoter", "meta": { "basicPropertyValues": [ { @@ -11052,15 +11488,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.", + "val": "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.", "xrefs": [ - "SO:regcreative", + "xenbase:jb", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "promoter targeting sequence", + "val": "SP6 RNA Polymerase Promoter", + "xrefs": [], }, ], }, @@ -11068,57 +11505,65 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001715", - "isre", - "interferon", - "stimulated", - "response", + "so:0001913", + "bacterial", + "rnapol", + "promoter", + "sigma", + "ecf", "element", - "transcriptional", - "cis", - "regulatory", + "factor", + "binding", + "dependency", + "type", + "promoters", + "requires", + "bind", + "identified", + "10", + "35", + "sequence", + "regions", + "order", + "mediate", + "rna", + "polymerase", "region", - "containing", - "consensus", - "region:", - "yagtttc", - "ytttycc", - "responsible", - "increased", + "part", "transcription", - "via", - "binding", + "initiation", ], - "id": "http://purl.obolibrary.org/obo/SO_0001715", - "lbl": "ISRE", + "id": "http://purl.obolibrary.org/obo/SO_0001913", + "lbl": "bacterial_RNApol_promoter_sigma_ecf_element", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "kareneilbeck", }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-04-05T11:15:08Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-06-11T02:41:33Z", + }, ], "comments": [ - "Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term.", + "Requested by Kevin Clancy - invitrogen -May 2012.", ], "definition": { - "val": "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.", + "val": "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation.", "xrefs": [ - "http://genesdev.cshlp.org/content/2/4/383.abstrac", + "Invitrogen:kc", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "interferon stimulated response element", + "val": "bacterial RNApol promoter sigma ecf ", + "xrefs": [], }, ], }, @@ -11126,30 +11571,32 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001952", + "so:0001671", + "bacterial", + "rnapol", "promoter", - "flanking", - "region", - "immediately", - "adjacent", - "may", - "contain", + "sigma", + "70", + "element", + "rna", + "polymerase", + "dna", + "sequence", + "binds", + "begin", "transcription", - "factor", - "binding", - "sites", ], - "id": "http://purl.obolibrary.org/obo/SO_0001952", - "lbl": "promoter_flanking_region", + "id": "http://purl.obolibrary.org/obo/SO_0001671", + "lbl": "bacterial_RNApol_promoter_sigma_70_element", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-10-06T01:41:34Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2013-03-06T11:36:25Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -11157,15 +11604,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites.", - "xrefs": [ - "EBI:nj", - ], + "val": "A DNA sequence to which bacterial RNA polymerase sigma 70 binds, to begin transcription.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "promoter flanking region", + "val": "bacterial RNA polymerase promoter sigma 70", + "xrefs": [], }, ], }, @@ -11173,36 +11619,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000344", - "splice", - "enhancer", - "region", - "transcript", - "regulates", - "splicing", + "so:0001672", + "bacterial", + "rnapol", + "promoter", + "sigma54", + "element", + "rna", + "polymerase", + "new", + "synonym", + "dna", + "sequence", + "sigma", + "54", + "binds", + "begin", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0000344", - "lbl": "splice_enhancer", + "id": "http://purl.obolibrary.org/obo/SO_0001672", + "lbl": "bacterial_RNApol_promoter_sigma54_element", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-10-06T01:42:37Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "Region of a transcript that regulates splicing.", - "xrefs": [ - "SO:ke", - ], + "val": "A DNA sequence to which bacterial RNA polymerase sigma 54 binds, to begin transcription.", + "xrefs": [], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "splice enhancer", + "val": "bacterial RNA polymerase promoter sigma54", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "", + "xrefs": [], }, ], }, @@ -11210,71 +11675,50 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002118", - "nmd", - "polymorphic", - "pseudogene", - "transcript", - "nonsense", - "mediated", - "decay", - "contains", - "cds", - "one", - "splice", - "junctions", - "50bp", - "downstream", - "stop", - "codon", - "premature", - "introduced", - "directly", - "indirectly", - "result", - "variation", - "e", - "must", - "present", - "protein", - "coding", - "pseudogenic", - "alleles", + "so:0001669", + "rnapol", + "ii", + "core", + "promoter", + "minimal", + "portion", + "required", + "properly", + "initiate", + "transcription", + "rna", + "polymerase", + "transcribed", + "genes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002118", - "lbl": "NMD_polymorphic_pseudogene_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001669", + "lbl": "RNApol_II_core_promoter", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "kareneilbeck", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-07-18T14:28:02Z", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "val": "2010-10-01T03:13:41Z", }, ], - "comments": [ - "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", - ], "definition": { - "val": "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles.", + "val": "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "PMID:16858867", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "NMD polymorphic pseudogene transcript", - }, - { - "pred": "hasExactSynonym", - "val": "nonsense_mediated_decay_polymorphic_pseudogene", + "val": "RNApol II core promoter", + "xrefs": [], }, ], }, @@ -11282,18 +11726,25 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000255", - "rrna", - "small", - "subunit", - "primary", - "transcript", - "encoding", - "ribosomal", + "so:0000618", + "rnapol", + "iii", + "promoter", + "type", + "trna", + "recruits", "rna", + "pol", + "transcribe", + "genes", + "mainly", + "intragenic", + "includes", + "box", + "b", ], - "id": "http://purl.obolibrary.org/obo/SO_0000255", - "lbl": "rRNA_small_subunit_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000618", + "lbl": "RNApol_III_promoter_type_2", "meta": { "basicPropertyValues": [ { @@ -11302,15 +11753,21 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a small ribosomal subunit RNA.", + "val": "This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box.", "xrefs": [ - "SO:ke", + "PMID:12381659", ], }, "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "tRNA promoter", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "rRNA small subunit primary transcript", + "val": "RNApol III promoter type 2", + "xrefs": [], }, ], }, @@ -11318,19 +11775,30 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000325", - "rrna", - "large", - "subunit", - "primary", - "transcript", - "35s", - "encoding", - "ribosomal", + "so:0000617", + "rnapol", + "iii", + "promoter", + "type", + "recruits", "rna", + "pol", + "intragenic", + "includes", + "box", + "intermediate", + "element", + "c", + "well", + "conserved", + "5s", + "rrna", + "promoters", + "across", + "species", ], - "id": "http://purl.obolibrary.org/obo/SO_0000325", - "lbl": "rRNA_large_subunit_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000617", + "lbl": "RNApol_III_promoter_type_1", "meta": { "basicPropertyValues": [ { @@ -11339,22 +11807,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a large ribosomal subunit RNA.", + "val": "This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species.", "xrefs": [ - "SO:ke", + "PMID:12381659", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "35S rRNA primary transcript", - }, - { - "pred": "hasExactSynonym", - "val": "rRNA large subunit primary transcript", + "val": "RNApol III promoter type 1", + "xrefs": [], }, ], }, @@ -11362,16 +11824,37 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000211", - "alanine", - "trna", - "primary", - "transcript", - "encoding", - "alanyl", + "so:0000621", + "rnapol", + "iii", + "promoter", + "type", + "recruits", + "rna", + "pol", + "transcribe", + "predominantly", + "noncoding", + "rnas", + "contains", + "proximal", + "sequence", + "element", + "pse", + "tata", + "box", + "upstream", + "gene", + "regulates", + "transcription", + "also", + "activated", + "distal", + "dse", + "located", ], - "id": "http://purl.obolibrary.org/obo/SO_0000211", - "lbl": "alanine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000621", + "lbl": "RNApol_III_promoter_type_3", "meta": { "basicPropertyValues": [ { @@ -11380,15 +11863,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding alanyl tRNA.", + "val": "This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream. ", "xrefs": [ - "SO:ke", + "PMID:12381659", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "alanine tRNA primary transcript", + "val": "RNApol III promoter type 3", + "xrefs": [], }, ], }, @@ -11396,17 +11880,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000212", - "arginine", - "trna", - "primary", - "transcript", - "encoding", - "arginyl", - "so:0000255", + "so:0000306", + "methylated", + "dna", + "base", + "feature", + "nucleotide", + "modified", + "methylation", ], - "id": "http://purl.obolibrary.org/obo/SO_0000212", - "lbl": "arginine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000306", + "lbl": "methylated_DNA_base_feature", "meta": { "basicPropertyValues": [ { @@ -11415,15 +11899,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding arginyl tRNA (SO:0000255).", + "val": "A nucleotide modified by methylation.", "xrefs": [ "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "arginine tRNA primary transcript", + "val": "methylated base feature", + "xrefs": [], }, ], }, @@ -11431,133 +11919,137 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000213", - "asparagine", - "trna", - "primary", - "transcript", - "encoding", - "asparaginyl", - "so:0000256", + "so:0001963", + "modified", + "cytosine", + "dna", + "base", + "feature", ], - "id": "http://purl.obolibrary.org/obo/SO_0000213", - "lbl": "asparagine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001963", + "lbl": "modified_cytosine", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2013-05-20T01:23:47Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "A primary transcript encoding asparaginyl tRNA (SO:0000256).", + "val": "A modified cytosine DNA base feature.", "xrefs": [ "SO:ke", ], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "asparagine tRNA primary transcript", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000214", - "aspartic", - "acid", - "trna", - "primary", - "transcript", - "encoding", - "aspartyl", - "so:0000257", + "so:0001962", + "modified", + "adenine", + "dna", + "base", + "feature", ], - "id": "http://purl.obolibrary.org/obo/SO_0000214", - "lbl": "aspartic_acid_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001962", + "lbl": "modified_adenine", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2013-05-20T01:22:30Z", + }, ], "definition": { - "val": "A primary transcript encoding aspartyl tRNA (SO:0000257).", + "val": "A modified adenine DNA base feature.", "xrefs": [ "SO:ke", ], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "aspartic acid tRNA primary transcript", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000215", - "cysteine", - "trna", - "primary", - "transcript", - "encoding", - "cysteinyl", - "so:0000258", + "so:0001964", + "modified", + "guanine", + "dna", + "base", + "feature", ], - "id": "http://purl.obolibrary.org/obo/SO_0000215", - "lbl": "cysteine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001964", + "lbl": "modified_guanine", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2013-05-20T01:25:31Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, ], "definition": { - "val": "A primary transcript encoding cysteinyl tRNA (SO:0000258).", + "val": "A modified guanine DNA base feature.", "xrefs": [ "SO:ke", ], }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "cysteine tRNA primary transcript", - }, - ], }, "type": "CLASS", }, { "fullTextWords": [ - "so:0000216", - "glutamic", - "acid", - "trna", - "primary", - "transcript", - "encoding", - "glutaminyl", - "so:0000260", + "so:0001701", + "histone", + "methylation", + "site", + "modification", + "residue", ], - "id": "http://purl.obolibrary.org/obo/SO_0000216", - "lbl": "glutamic_acid_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001701", + "lbl": "histone_methylation_site", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-03-31T10:23:02Z", + }, ], "definition": { - "val": "A primary transcript encoding glutaminyl tRNA (SO:0000260).", + "val": "A histone modification site where the modification is the methylation of the residue.", "xrefs": [ "SO:ke", ], @@ -11565,7 +12057,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "glutamic acid tRNA primary transcript", + "val": "histone methylation site", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "histone methylation", + "xrefs": [], }, ], }, @@ -11573,26 +12071,33 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000217", - "glutamine", - "trna", - "primary", - "transcript", - "encoding", - "glutamyl", - "so:0000260", + "so:0001702", + "histone", + "acetylation", + "site", + "modification", + "acylation", + "residue", ], - "id": "http://purl.obolibrary.org/obo/SO_0000217", - "lbl": "glutamine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001702", + "lbl": "histone_acetylation_site", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-03-31T10:23:27Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "A primary transcript encoding glutamyl tRNA (SO:0000260).", + "val": "A histone modification where the modification is the acylation of the residue.", "xrefs": [ "SO:ke", ], @@ -11600,7 +12105,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "glutamine tRNA primary transcript", + "val": "histone acetylation site", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "histone acetylation", + "xrefs": [], }, ], }, @@ -11608,34 +12119,45 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000218", - "glycine", - "trna", - "primary", - "transcript", - "encoding", - "glycyl", - "so:0000263", + "so:0001737", + "histone", + "acylation", + "region", + "modification", + "whereby", + "protein", + "acylated", + "multiple", + "sites", ], - "id": "http://purl.obolibrary.org/obo/SO_0000218", - "lbl": "glycine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001737", + "lbl": "histone_acylation_region", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-04-13T01:58:21Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A primary transcript encoding glycyl tRNA (SO:0000263).", + "val": "A histone modification, whereby the histone protein is acylated at multiple sites in a region.", "xrefs": [ "SO:ke", ], }, "synonyms": [ { - "pred": "hasExactSynonym", - "val": "glycine tRNA primary transcript", + "pred": "hasRelatedSynonym", + "val": "histone acylation region", + "xrefs": [], }, ], }, @@ -11643,34 +12165,44 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000219", - "histidine", - "trna", - "primary", - "transcript", - "encoding", - "histidyl", - "so:0000262", + "so:0001716", + "histone", + "ubiqitination", + "site", + "ubiquitination", + "modification", + "ubiquitin", + "may", + "added", ], - "id": "http://purl.obolibrary.org/obo/SO_0000219", - "lbl": "histidine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001716", + "lbl": "histone_ubiqitination_site", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-04-13T10:12:18Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "A primary transcript encoding histidyl tRNA (SO:0000262).", + "val": "A histone modification site where ubiquitin may be added.", "xrefs": [ "SO:ke", ], }, "synonyms": [ { - "pred": "hasExactSynonym", - "val": "histidine tRNA primary transcript", + "pred": "hasRelatedSynonym", + "val": "histone ubiquitination site", + "xrefs": [], }, ], }, @@ -11678,17 +12210,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000220", - "isoleucine", - "trna", - "primary", - "transcript", - "encoding", - "isoleucyl", - "so:0000263", + "so:0000897", + "allelically", + "excluded", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000220", - "lbl": "isoleucine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000897", + "lbl": "allelically_excluded_gene", "meta": { "basicPropertyValues": [ { @@ -11697,15 +12225,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding isoleucyl tRNA (SO:0000263).", + "val": "A gene that is allelically_excluded.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "isoleucine tRNA primary transcript", + "val": "allelically excluded gene", + "xrefs": [], }, ], }, @@ -11713,17 +12242,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000221", - "leucine", - "trna", - "primary", - "transcript", - "encoding", - "leucyl", - "so:0000264", + "so:0000888", + "maternally", + "imprinted", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000221", - "lbl": "leucine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000888", + "lbl": "maternally_imprinted_gene", "meta": { "basicPropertyValues": [ { @@ -11732,15 +12257,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding leucyl tRNA (SO:0000264).", + "val": "A gene that is maternally_imprinted.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "leucine tRNA primary transcript", + "val": "maternally imprinted gene", + "xrefs": [], }, ], }, @@ -11748,17 +12274,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000222", - "lysine", - "trna", - "primary", - "transcript", - "encoding", - "lysyl", - "so:0000265", + "so:0000138", + "gene", + "rearranged", + "dna", + "level", + "epigenetically", + "modified", ], - "id": "http://purl.obolibrary.org/obo/SO_0000222", - "lbl": "lysine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000138", + "lbl": "gene_rearranged_at_DNA_level", "meta": { "basicPropertyValues": [ { @@ -11767,15 +12292,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding lysyl tRNA (SO:0000265).", + "val": "An epigenetically modified gene, rearranged at the DNA level.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "lysine tRNA primary transcript", + "val": "gene rearranged at DNA level", + "xrefs": [], }, ], }, @@ -11783,17 +12309,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000223", - "methionine", - "trna", - "primary", - "transcript", - "encoding", - "methionyl", - "so:0000266", + "so:0000889", + "paternally", + "imprinted", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000223", - "lbl": "methionine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000889", + "lbl": "paternally_imprinted_gene", "meta": { "basicPropertyValues": [ { @@ -11802,15 +12324,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding methionyl tRNA (SO:0000266).", + "val": "A gene that is paternally imprinted.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "methionine tRNA primary transcript", + "val": "paternally imprinted gene", + "xrefs": [], }, ], }, @@ -11818,17 +12341,24 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000224", - "phenylalanine", - "trna", - "primary", - "transcript", - "encoding", - "phenylalanyl", - "so:0000267", + "so:0000625", + "silencer", + "insdc", + "feature:regulatory", + "qualifier:silencer", + "regulatory", + "region", + "upon", + "binding", + "transcription", + "factors", + "suppress", + "gene", + "genes", + "control", ], - "id": "http://purl.obolibrary.org/obo/SO_0000224", - "lbl": "phenylalanine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000625", + "lbl": "silencer", "meta": { "basicPropertyValues": [ { @@ -11837,33 +12367,65 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding phenylalanyl tRNA (SO:0000267).", + "val": "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.", "xrefs": [ "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "phenylalanine tRNA primary transcript", + "val": "INSDC_qualifier:silencer", + "xrefs": [], }, ], - }, - "type": "CLASS", - }, + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Silencer_(DNA)", + }, + ], + }, + "type": "CLASS", + }, { "fullTextWords": [ - "so:0000225", - "proline", - "trna", - "primary", - "transcript", - "encoding", - "prolyl", - "so:0000268", + "so:0000037", + "locus", + "control", + "region", + "insdc", + "feature:regulatory", + "lcr", + "qualifier:locus", + "element", + "dna", + "includes", + "dnase", + "hypersensitive", + "sites", + "located", + "near", + "gene", + "confers", + "high", + "level", + "position", + "independent", + "copy", + "number", + "dependent", + "expression", ], - "id": "http://purl.obolibrary.org/obo/SO_0000225", - "lbl": "proline_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000037", + "lbl": "locus_control_region", "meta": { "basicPropertyValues": [ { @@ -11871,16 +12433,45 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Definition updated Nov 10 2020, Colin Logie from GREEKC helped us realize that LCRs can also be located 3' to a gene.", + ], "definition": { - "val": "A primary transcript encoding prolyl tRNA (SO:0000268).", + "val": "A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.", "xrefs": [ - "SO:ke", + "SO:ma", ], }, "synonyms": [ + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "proline tRNA primary transcript", + "val": "LCR", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:locus_control_region", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "locus control region", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "locus control element", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Locus_control_region", }, ], }, @@ -11888,17 +12479,33 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000226", - "serine", - "trna", - "primary", - "transcript", - "encoding", - "seryl", - "so:000269", + "so:0000627", + "insulator", + "insdc", + "feature:regulatory", + "qualifier:insulator", + "element", + "regulatory", + "region", + "located", + "crm", + "gene", + "promoter", + "prevents", + "modulating", + "genes", + "expression", + "acts", + "chromatin", + "boundary", + "barrier", + "block", + "encroachment", + "condensed", + "adjacent", ], - "id": "http://purl.obolibrary.org/obo/SO_0000226", - "lbl": "serine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000627", + "lbl": "insulator", "meta": { "basicPropertyValues": [ { @@ -11906,16 +12513,40 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.", + ], "definition": { - "val": "A primary transcript encoding seryl tRNA (SO:000269).", + "val": "A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region.", "xrefs": [ - "SO:ke", + "NCBI:cf", + "PMID:12154228", + "SO:regcreative", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "serine tRNA primary transcript", + "val": "INSDC_qualifier:insulator", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "insulator element", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Insulator_(genetics)", }, ], }, @@ -11923,17 +12554,29 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000227", - "threonine", - "trna", - "primary", - "transcript", - "encoding", - "threonyl", - "so:000270", + "so:0000165", + "enhancer", + "insdc", + "feature:regulatory", + "qualifier:enhancer", + "cis", + "acting", + "sequence", + "increases", + "utilization", + "eukaryotic", + "promoters", + "function", + "either", + "orientation", + "location", + "upstream", + "downstream", + "relative", + "promoter", ], - "id": "http://purl.obolibrary.org/obo/SO_0000227", - "lbl": "threonine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000165", + "lbl": "enhancer", "meta": { "basicPropertyValues": [ { @@ -11941,16 +12584,33 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.", + ], "definition": { - "val": "A primary transcript encoding threonyl tRNA (SO:000270).", + "val": "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.", "xrefs": [ - "SO:ke", + "http://www.insdc.org/files/feature_table.html", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:regulatory", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "threonine tRNA primary transcript", + "val": "INSDC_qualifier:enhancer", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Enhancer_(genetics)", }, ], }, @@ -11958,34 +12618,58 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000228", - "tryptophan", - "trna", - "primary", - "transcript", - "encoding", - "tryptophanyl", - "so:000271", + "so:0002308", + "dna", + "loop", + "anchor", + "ends", + "two", + "strands", + "held", + "close", + "physical", + "proximity", + "interphase", + "anchors", + "loops", + "convergently", + "oriented", + "ctcf", + "binding", + "sites", ], - "id": "http://purl.obolibrary.org/obo/SO_0000228", - "lbl": "tryptophan_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002308", + "lbl": "DNA_loop_anchor", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-08-12T14:01:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.", + ], "definition": { - "val": "A primary transcript encoding tryptophanyl tRNA (SO:000271).", + "val": "The ends of a DNA loop where the two strands of DNA are held in close physical proximity. During interphase the anchors of DNA loops are convergently oriented CTCF binding sites.", "xrefs": [ - "SO:ke", + "GREEKC:cl", + "PMID:32782014", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "tryptophan tRNA primary transcript", + "val": "DNA loop anchor", + "xrefs": [], }, ], }, @@ -11993,34 +12677,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000229", - "tyrosine", - "trna", - "primary", - "transcript", - "encoding", - "tyrosyl", - "so:000272", + "so:0002045", + "pheromone", + "response", + "element", + "pre", + "yeast", + "tfbs", + "consensus", + "site", + "tgaaac", + "g", ], - "id": "http://purl.obolibrary.org/obo/SO_0000229", - "lbl": "tyrosine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002045", + "lbl": "pheromone_response_element", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2015-02-09T15:05:43Z", + }, + ], + "comments": [ + "Requested by Rama, SGD.", ], "definition": { - "val": "A primary transcript encoding tyrosyl tRNA (SO:000272).", + "val": "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].", "xrefs": [ + "PMID:1489142", "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "tyrosine tRNA primary transcript", + "val": "pheromone response element", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "PRE", + "xrefs": [], }, ], }, @@ -12028,34 +12733,65 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000230", - "valine", - "trna", - "primary", - "transcript", - "encoding", - "valyl", - "so:000273", + "so:0001653", + "retinoic", + "acid", + "responsive", + "element", + "rare", + "transcription", + "factor", + "binding", + "site", + "variable", + "direct", + "repeats", + "sequence", + "puggtca", + "spaced", + "five", + "nucleotides", + "dr5", + "found", + "promoters", + "genes", + "receptors", + "bind", ], - "id": "http://purl.obolibrary.org/obo/SO_0000230", - "lbl": "valine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001653", + "lbl": "retinoic_acid_responsive_element", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2010-08-03T10:46:12Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "A primary transcript encoding valyl tRNA (SO:000273).", + "val": "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.", "xrefs": [ - "SO:ke", + "PMID:11327309", + "PMID:19917671", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "valine tRNA primary transcript", + "val": "retinoic acid responsive element", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "RARE", + "xrefs": [], }, ], }, @@ -12063,34 +12799,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001178", - "pyrrolysine", - "trna", - "primary", - "transcript", - "encoding", - "pyrrolysyl", - "so:0000766", + "so:0002295", + "transcription", + "factor", + "regulatory", + "site", + "tfrs", + "tf", + "binding", + "involved", + "regulation", + "expression", ], - "id": "http://purl.obolibrary.org/obo/SO_0001178", - "lbl": "pyrrolysine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002295", + "lbl": "transcription_factor_regulatory_site", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-08-05T11:49:30Z", + }, + ], + "comments": [ + "Added as per Mejia-Almonte et.al PMID:32665585", ], "definition": { - "val": "A primary transcript encoding pyrrolysyl tRNA (SO:0000766).", + "val": "A TF_binding_site that is involved in regulation of expression.", "xrefs": [ - "RSC:cb", + "Bacterial_regulation_working_group:CMA", + "PMID:32665585", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "pyrrolysine tRNA primary transcript", + "val": "transcription factor regulatory site", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "TFRS", + "xrefs": [], }, ], }, @@ -12098,24 +12855,29 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002037", - "mir", - "encoding", - "trna", - "primary", - "transcript", - "also", - "encodes", - "pre", - "sequence", - "processed", - "form", - "functionally", - "active", - "mirna", + "so:0001715", + "isre", + "interferon", + "stimulated", + "response", + "element", + "transcriptional", + "cis", + "regulatory", + "region", + "containing", + "consensus", + "region:", + "yagtttc", + "ytttycc", + "responsible", + "increased", + "transcription", + "via", + "binding", ], - "id": "http://purl.obolibrary.org/obo/SO_0002037", - "lbl": "miR_encoding_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001715", + "lbl": "ISRE", "meta": { "basicPropertyValues": [ { @@ -12124,23 +12886,27 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:28:23Z", + "val": "2010-04-05T11:15:08Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021.", + ], "definition": { - "val": "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.", + "val": "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.", "xrefs": [ - "SO:ke", + "http://genesdev.cshlp.org/content/2/4/383.abstrac", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "miR encoding tRNA primary transcript", + "val": "interferon stimulated response element", + "xrefs": [], }, ], }, @@ -12148,34 +12914,57 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0005856", - "selenocysteine", - "trna", - "primary", - "transcript", - "encoding", - "seryl", - "so:000269", + "so:0001840", + "gata", + "box", + "element", + "transcription", + "factor", + "containing", + "consensus", + "sequence", + "wgatar", + "w", + "indicates", + "r", + "g", ], - "id": "http://purl.obolibrary.org/obo/SO_0005856", - "lbl": "selenocysteine_tRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0001840", + "lbl": "GATA_box", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2011-10-07T03:42:05Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Changed to is_a SO:0001055 transcriptional_cis_regulatory_region from core_eukaryotic_promoter_element SO:0001660 after Ruth Lovering from GREEKC initiative pointed out that GATA boxes are frequently in enhancer regions, Dave Sant Aug 2020. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021.", + ], "definition": { - "val": "A primary transcript encoding seryl tRNA (SO:000269).", + "val": "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G).", "xrefs": [ - "SO:ke", + "PMID:8321208", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "selenocysteine tRNA primary transcript", + "val": "GATA box", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "GATA element", + "xrefs": [], }, ], }, @@ -12183,19 +12972,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000580", - "methylation", - "guide", - "snorna", - "primary", - "transcript", - "encoding", - "small", - "nucleolar", + "so:0000951", + "eukaryotic", + "terminator", + "signal", "rna", + "polymerase", + "terminate", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0000580", - "lbl": "methylation_guide_snoRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000951", + "lbl": "eukaryotic_terminator", "meta": { "basicPropertyValues": [ { @@ -12204,15 +12991,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a methylation guide small nucleolar RNA.", - "xrefs": [ - "SO:ke", - ], + "val": "A signal for RNA polymerase to terminate transcription.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "methylation guide snoRNA primary transcript", + "val": "eukaryotic terminator", + "xrefs": [], }, ], }, @@ -12220,16 +13006,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000582", - "rrna", - "cleavage", - "snorna", - "primary", - "transcript", - "encoding", + "so:0000614", + "bacterial", + "terminator", + "signal", + "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0000582", - "lbl": "rRNA_cleavage_snoRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000614", + "lbl": "bacterial_terminator", "meta": { "basicPropertyValues": [ { @@ -12237,8 +13021,11 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.", + ], "definition": { - "val": "A primary transcript encoding an rRNA cleavage snoRNA.", + "val": "A terminator signal for bacterial transcription.", "xrefs": [ "SO:ke", ], @@ -12246,7 +13033,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "rRNA cleavage snoRNA primary transcript", + "val": "bacterial terminator", + "xrefs": [], }, ], }, @@ -12254,21 +13042,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000595", - "c", - "d", - "box", - "snorna", - "primary", + "so:0000344", + "splice", + "enhancer", + "region", "transcript", - "encoding", - "small", - "nucleolar", - "rna", - "family", + "regulates", + "splicing", ], - "id": "http://purl.obolibrary.org/obo/SO_0000595", - "lbl": "C_D_box_snoRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000344", + "lbl": "splice_enhancer", "meta": { "basicPropertyValues": [ { @@ -12277,15 +13060,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a small nucleolar RNA of the box C/D family.", + "val": "Region of a transcript that regulates splicing.", "xrefs": [ "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "C/D box snoRNA primary transcript", + "val": "splice enhancer", + "xrefs": [], }, ], }, @@ -12293,21 +13080,17 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000596", - "h", - "aca", - "box", - "snorna", + "so:0000210", + "trna", "primary", "transcript", "encoding", - "small", - "nucleolar", + "transfer", "rna", - "family", + "so:0000253", ], - "id": "http://purl.obolibrary.org/obo/SO_0000596", - "lbl": "H_ACA_box_snoRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000210", + "lbl": "tRNA_primary_transcript", "meta": { "basicPropertyValues": [ { @@ -12316,7 +13099,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A primary transcript encoding a small nucleolar RNA of the box H/ACA family.", + "val": "A primary transcript encoding a transfer RNA (SO:0000253).", "xrefs": [ "SO:ke", ], @@ -12324,7 +13107,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "H ACA box snoRNA primary transcript", + "val": "tRNA primary transcript", + "xrefs": [], }, ], }, @@ -12332,24 +13116,55 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002034", - "mir", - "encoding", + "so:0000232", "snorna", "primary", "transcript", - "also", - "encodes", - "pre", - "sequence", - "processed", - "form", - "functionally", - "active", - "mirna", + "encoding", + "one", + "small", + "nucleolar", + "rnas", + "so:0000275", ], - "id": "http://purl.obolibrary.org/obo/SO_0002034", - "lbl": "miR_encoding_snoRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000232", + "lbl": "snoRNA_primary_transcript", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "comments": [ + "This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520).", + ], + "definition": { + "val": "A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).", + "xrefs": [ + "SO:ke", + ], + }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "snoRNA primary transcript", + "xrefs": [], + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0001801", + "tasirna", + "primary", + "transcript", + "encoding", + ], + "id": "http://purl.obolibrary.org/obo/SO_0001801", + "lbl": "tasiRNA_primary_transcript", "meta": { "basicPropertyValues": [ { @@ -12358,7 +13173,7 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:02:13Z", + "val": "2011-05-31T03:27:35Z", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -12366,15 +13181,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.", + "val": "A primary transcript encoding a tasiRNA.", "xrefs": [ - "SO:ke", + "PMID:16145017", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "miR encoding snoRNA primary transcript", + "val": "tasiRNA primary transcript", + "xrefs": [], }, ], }, @@ -12382,30 +13198,18 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0005837", - "u14", - "snorna", + "so:0000586", + "tmrna", "primary", "transcript", - "5s", - "snrna", - "evolutionarily", - "conserved", - "eukaryotic", - "low", - "molecular", - "weight", + "ssra", "rna", - "capable", - "intermolecular", - "hybridization", - "homologous", - "heterologous", - "18s", - "rrna", + "10sa", + "encoding", + "so:0000584", ], - "id": "http://purl.obolibrary.org/obo/SO_0005837", - "lbl": "U14_snoRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000586", + "lbl": "tmRNA_primary_transcript", "meta": { "basicPropertyValues": [ { @@ -12414,19 +13218,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.", + "val": "A primary transcript encoding a tmRNA (SO:0000584).", "xrefs": [ - "PMID:2251119", + "SO:ke", ], }, "synonyms": [ { - "pred": "hasExactSynonym", - "val": "4.5S snRNA primary transcript", + "pred": "hasRelatedSynonym", + "val": "ssrA RNA primary transcript", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "10Sa RNA primary transcript", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "U14 snoRNA primary transcript", + "val": "tmRNA primary transcript", + "xrefs": [], }, ], }, @@ -12434,41 +13245,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002036", - "mir", - "encoding", - "lncrna", + "so:0002038", + "shrna", "primary", "transcript", - "also", - "encodes", - "pre", - "sequence", - "processed", - "form", - "functionally", - "active", - "mirna", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0002036", - "lbl": "miR_encoding_lncRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0002038", + "lbl": "shRNA_primary_transcript", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:23:48Z", + "val": "2015-01-09T15:30:43Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", }, ], "definition": { - "val": "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.", + "val": "A primary transcript encoding an shRNA.", "xrefs": [ "SO:ke", ], @@ -12476,7 +13277,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "miR encoding lncRNA primary transcript", + "val": "shRNA primary transcript", + "xrefs": [], }, ], }, @@ -12484,47 +13286,40 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002113", + "so:0002035", "lncrna", - "retained", - "intron", + "primary", "transcript", - "containing", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0002113", - "lbl": "lncRNA_with_retained_intron", + "id": "http://purl.obolibrary.org/obo/SO_0002035", + "lbl": "lncRNA_primary_transcript", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "kareneilbeck", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-07-18T14:13:07Z", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "val": "2015-01-09T15:23:03Z", }, ], - "comments": [ - "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", - ], "definition": { - "val": "A lncRNA transcript containing a retained intron.", + "val": "A primary transcript encoding a lncRNA.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "lncRNA with retained intron", - }, - { - "pred": "hasExactSynonym", - "val": "lncRNA_retained_intron", + "val": "lncRNA primary transcript", + "xrefs": [], }, ], }, @@ -12532,49 +13327,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002039", - "mir", - "encoding", - "shrna", + "so:0000209", + "rrna", "primary", "transcript", - "also", - "encodes", - "pre", - "sequence", - "processed", - "form", - "functionally", - "active", - "mirna", + "ribosomal", + "rna", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0002039", - "lbl": "miR_encoding_shRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000209", + "lbl": "rRNA_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:32:00Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.", + "val": "A primary transcript encoding a ribosomal RNA.", "xrefs": [ "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "miR encoding shRNA primary transcript", + "val": "ribosomal RNA primary transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "rRNA primary transcript", + "xrefs": [], }, ], }, @@ -12582,41 +13370,27 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002041", - "mir", - "encoding", - "vaultrna", + "so:0000589", + "srp", + "rna", "primary", "transcript", - "also", - "encodes", - "pre", - "sequence", - "processed", - "form", - "functionally", - "active", - "mirna", + "encoding", + "signal", + "recognition", + "particle", ], - "id": "http://purl.obolibrary.org/obo/SO_0002041", - "lbl": "miR_encoding_vaultRNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000589", + "lbl": "SRP_RNA_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:34:32Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.", + "val": "A primary transcript encoding a signal recognition particle RNA.", "xrefs": [ "SO:ke", ], @@ -12624,7 +13398,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "miR encoding vaultRNA primary transcript", + "val": "SRP RNA primary transcript", + "xrefs": [], }, ], }, @@ -12632,42 +13407,27 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002043", - "mir", - "encoding", - "y", - "rna", + "so:0000231", + "snrna", "primary", "transcript", - "also", - "encodes", - "pre", - "sequence", - "processed", - "form", - "functionally", - "active", - "mirna", + "encoding", + "small", + "nuclear", + "rna", + "so:0000274", ], - "id": "http://purl.obolibrary.org/obo/SO_0002043", - "lbl": "miR_encoding_Y_RNA_primary_transcript", + "id": "http://purl.obolibrary.org/obo/SO_0000231", + "lbl": "snRNA_primary_transcript", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T15:37:46Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.", + "val": "A primary transcript encoding a small nuclear RNA (SO:0000274).", "xrefs": [ "SO:ke", ], @@ -12675,7 +13435,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "miR encoding Y-RNA primary transcript", + "val": "snRNA primary transcript", + "xrefs": [], }, ], }, @@ -12683,30 +13444,41 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000282", - "mrna", - "minus", - "frameshift", + "so:0002042", + "y", + "rna", + "primary", + "transcript", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000282", - "lbl": "mRNA_with_minus_1_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0002042", + "lbl": "Y_RNA_primary_transcript", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2015-01-09T15:36:51Z", + }, ], "definition": { - "val": "An mRNA with a minus 1 frameshift.", + "val": "A primary transcript encoding a Y-RNA.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "mRNA with minus 1 frameshift", + "val": "Y-RNA primary transcript", + "xrefs": [], }, ], }, @@ -12714,22 +13486,31 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000321", - "mrna", - "plus", - "frameshift", + "so:0002040", + "vaultrna", + "primary", + "transcript", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000321", - "lbl": "mRNA_with_plus_1_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0002040", + "lbl": "vaultRNA_primary_transcript", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2015-01-09T15:33:33Z", + }, ], "definition": { - "val": "An mRNA with a plus 1 frameshift.", + "val": "A primary transcript encoding a vaultRNA.", "xrefs": [ "SO:ke", ], @@ -12737,7 +13518,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "mRNA with plus 1 frameshift", + "val": "vaultRNA primary transcript", + "xrefs": [], }, ], }, @@ -12745,30 +13527,61 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000329", - "mrna", - "plus", - "frameshift", + "so:0000647", + "mirna", + "primary", + "transcript", + "micro", + "rna", + "strna", + "small", + "temporal", + "encoding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000329", - "lbl": "mRNA_with_plus_2_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0000647", + "lbl": "miRNA_primary_transcript", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val": "SO:0000648", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "An mRNA with a plus 2 frameshift.", + "val": "A primary transcript encoding a micro RNA.", "xrefs": [ - "SO:xp", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "mRNA with plus 2 frameshift", + "val": "micro RNA primary transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "stRNA primary transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "small temporal RNA primary transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "miRNA primary transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "stRNA_primary_transcript", + "xrefs": [], }, ], }, @@ -12776,13 +13589,24 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000335", - "mrna", - "minus", - "frameshift", + "so:0000012", + "scrna", + "primary", + "transcript", + "small", + "cytoplasmic", + "rna", + "one", + "several", + "molecules", + "present", + "cytoplasm", + "sometimes", + "nucleus", + "eukaryote", ], - "id": "http://purl.obolibrary.org/obo/SO_0000335", - "lbl": "mRNA_with_minus_2_frameshift", + "id": "http://purl.obolibrary.org/obo/SO_0000012", + "lbl": "scRNA_primary_transcript", "meta": { "basicPropertyValues": [ { @@ -12791,15 +13615,36 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A mRNA with a minus 2 frameshift.", + "val": "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.", "xrefs": [ - "SO:ke", + "http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "mRNA with minus 2 frameshift", + "val": "scRNA transcript", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "small cytoplasmic RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "small cytoplasmic RNA transcript", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "scRNA primary transcript", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "small_cytoplasmic_RNA", + "xrefs": [], }, ], }, @@ -12807,39 +13652,46 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:1001264", + "so:0002112", + "coding", + "transcript", + "retained", + "intron", "mrna", - "recoded", - "translational", - "bypass", - "translation", - "suspended", - "particular", - "codon", - "resumed", - "non", - "overlapping", - "downstream", + "protein", + "containing", ], - "id": "http://purl.obolibrary.org/obo/SO_1001264", - "lbl": "mRNA_recoded_by_translational_bypass", + "id": "http://purl.obolibrary.org/obo/SO_0002112", + "lbl": "coding_transcript_with_retained_intron", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-07-18T14:09:49Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + ], + "comments": [ + "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", ], "definition": { - "val": "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.", + "val": "A protein coding transcript containing a retained intron.", "xrefs": [ - "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { - "pred": "hasExactSynonym", - "val": "mRNA recoded by translational bypass", + "pred": "hasRelatedSynonym", + "val": "mRNA with retained intron", + "xrefs": [], }, ], }, @@ -12847,17 +13699,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:1001265", + "so:0000932", + "pre", + "edited", "mrna", - "recoded", - "codon", - "redefinition", - "modified", - "alteration", - "meaning", + "primary", + "transcript", + "least", + "part", + "encodes", + "one", + "proteins", ], - "id": "http://purl.obolibrary.org/obo/SO_1001265", - "lbl": "mRNA_recoded_by_codon_redefinition", + "id": "http://purl.obolibrary.org/obo/SO_0000932", + "lbl": "pre_edited_mRNA", "meta": { "basicPropertyValues": [ { @@ -12866,15 +13721,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A recoded_mRNA that was modified by an alteration of codon meaning.", - "xrefs": [ - "SO:ma", - ], + "val": "A primary transcript that, at least in part, encodes one or more proteins that has not been edited.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "mRNA recoded by codon redefinition", + "val": "pre-edited mRNA", + "xrefs": [], }, ], }, @@ -12882,53 +13736,72 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000650", - "small", - "subunit", - "rrna", - "ssu", - "rna", - "ribosomal", + "so:0002114", + "nmd", "transcript", - "structures", - "ribosome", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000650", - "lbl": "small_subunit_rRNA", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "protein", + "coding", + "nonsense", + "mediated", + "decay", + "contains", + "cds", + "one", + "splice", + "junctions", + "50bp", + "downstream", + "stop", + "codon", + "making", + "susceptible", + ], + "id": "http://purl.obolibrary.org/obo/SO_0002114", + "lbl": "NMD_transcript", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-07-18T14:16:13Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, ], + "comments": [ + "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", + ], "definition": { - "val": "Ribosomal RNA transcript that structures the small subunit of the ribosome.", + "val": "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay.", "xrefs": [ - "SO:ke", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "SSU RNA", - "xrefs": [ - "RSC:cb", - ], + "val": "protein_coding_NMD", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "SSU rRNA", - "xrefs": [ - "RSC:cb", - ], + "val": "nonsense mediated decay transcript", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small subunit rRNA", + "val": "NMD transcript", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://www.gencodegenes.org/gencode_biotypes.html", }, ], }, @@ -12936,19 +13809,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000651", - "large", - "subunit", - "rrna", - "lsu", - "rna", - "ribosomal", + "so:1001197", + "dicistronic", + "primary", "transcript", - "structures", - "ribosome", + "quality", ], - "id": "http://purl.obolibrary.org/obo/SO_0000651", - "lbl": "large_subunit_rRNA", + "id": "http://purl.obolibrary.org/obo/SO_1001197", + "lbl": "dicistronic_primary_transcript", "meta": { "basicPropertyValues": [ { @@ -12957,32 +13825,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "Ribosomal RNA transcript that structures the large subunit of the ribosome.", + "val": "A primary transcript that has the quality dicistronic.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "LSU RNA", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "LSU rRNA", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "large subunit rRNA", + "val": "dicistronic primary transcript", + "xrefs": [], }, ], }, @@ -12990,44 +13842,38 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002128", - "mt", - "rrna", - "mitochondrial", - "ribosomal", - "rna", + "so:0000716", + "dicistronic", + "mrna", + "processed", + "transcript", + "quality", ], - "id": "http://purl.obolibrary.org/obo/SO_0002128", - "lbl": "mt_rRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000716", + "lbl": "dicistronic_mRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:08:59Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "Mitochondrial ribosomal RNA.", + "val": "An mRNA that has the quality dicistronic.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "Mt_rRNA", + "val": "dicistronic mRNA", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "mitochondrial_rRNA", + "pred": "hasRelatedSynonym", + "val": "dicistronic processed transcript", + "xrefs": [], }, ], }, @@ -13035,46 +13881,52 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000254", - "alanyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", - "sequence", - "alanine", - "anticodon", - "binding", - "region", + "so:0002116", + "polymorphic", + "pseudogene", + "processed", + "transcript", + "contain", + "cds", + "fullfills", + "annotation", + "criteria", + "necessarily", + "functionally", + "non", + "coding", ], - "id": "http://purl.obolibrary.org/obo/SO_0000254", - "lbl": "alanyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002116", + "lbl": "polymorphic_pseudogene_processed_transcript", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-07-18T14:23:59Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + ], + "comments": [ + "Term added as part of collaboration with Gencode, adding biotypes used in annotation.", ], "definition": { - "val": "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.", + "val": "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding.", "xrefs": [ - "SO:ke", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "alanyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "alanyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "alanyl-transfer ribonucleic acid", + "val": "polymorphic pseudogene processed transcript", + "xrefs": [], }, ], }, @@ -13082,21 +13934,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000256", - "asparaginyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", + "so:1001261", + "recoded", + "mrna", "sequence", - "asparagine", - "anticodon", - "binding", - "region", + "mature", + "transcript", + "modified", + "translation", + "usually", + "special", + "cis", + "acting", + "signals", ], - "id": "http://purl.obolibrary.org/obo/SO_0000256", - "lbl": "asparaginyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_1001261", + "lbl": "recoded_mRNA", "meta": { "basicPropertyValues": [ { @@ -13105,23 +13958,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.", + "val": "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.", "xrefs": [ - "SO:ke", + "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "asparaginyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "asparaginyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "asparaginyl-transfer ribonucleic acid", + "val": "recoded mRNA", + "xrefs": [], }, ], }, @@ -13129,21 +13975,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000257", - "aspartyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", - "sequence", - "aspartic", - "anticodon", - "binding", - "region", + "so:0000871", + "polyadenylated", + "mrna", ], - "id": "http://purl.obolibrary.org/obo/SO_0000257", - "lbl": "aspartyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000871", + "lbl": "polyadenylated_mRNA", "meta": { "basicPropertyValues": [ { @@ -13152,23 +13989,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.", + "val": "An mRNA that is polyadenylated.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "aspartyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "aspartyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "aspartyl-transfer ribonucleic acid", + "val": "polyadenylated mRNA", + "xrefs": [], }, ], }, @@ -13176,46 +14006,62 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000258", - "cysteinyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", - "sequence", - "cysteine", - "anticodon", - "binding", - "region", + "so:0002292", + "circular", + "mrna", + "coding", + "circrna", + "generated", + "backsplicing", + "exons", + "introns", + "resulting", + "covalently", + "closed", + "loop", + "without", + "cap", + "polya", + "tail", ], - "id": "http://purl.obolibrary.org/obo/SO_0000258", - "lbl": "cysteinyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002292", + "lbl": "circular_mRNA", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-07-01T11:49:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)", ], "definition": { - "val": "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.", + "val": "An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail.", "xrefs": [ - "SO:ke", + "PMID:29086764", + "PMID:29182528", + "PMID:29576969", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "cysteinyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "cysteinyl-transfer RNA", + "val": "circular mRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "cysteinyl-transfer ribonucleic acid", + "val": "coding circRNA", + "xrefs": [], }, ], }, @@ -13223,21 +14069,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000259", - "glutaminyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", + "so:0000995", + "consensus", + "mrna", "sequence", - "glutamine", - "anticodon", - "binding", - "region", + "produced", + "aligment", + "algorithm", + "uses", + "multiple", + "sequences", + "input", ], - "id": "http://purl.obolibrary.org/obo/SO_0000259", - "lbl": "glutaminyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000995", + "lbl": "consensus_mRNA", "meta": { "basicPropertyValues": [ { @@ -13245,24 +14090,18 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "DO not obsolete without considering MGED mapping.", + ], "definition": { - "val": "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.", - "xrefs": [ - "SO:ke", - ], + "val": "An mRNA sequence produced from an aligment algorithm that uses multiple sequences as input.", + "xrefs": [], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "glutaminyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "glutaminyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "glutaminyl-transfer ribonucleic acid", + "val": "consensus mRNA", + "xrefs": [], }, ], }, @@ -13270,46 +14109,47 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000260", - "glutamyl", - "trna", - "transfer", - "ribonucleic", - "acid", - "rna", - "sequence", - "glutamic", - "anticodon", - "binding", - "region", + "so:0002130", + "nsd", + "transcript", + "non", + "stop", + "decay", + "contains", + "cds", + "codon", + "polya", + "site", + "reached", ], - "id": "http://purl.obolibrary.org/obo/SO_0000260", - "lbl": "glutamyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002130", + "lbl": "NSD_transcript", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:11:34Z", + }, ], "definition": { - "val": "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.", + "val": "A transcript that contains a CDS but has no stop codon before the polyA site is reached.", "xrefs": [ - "SO:ke", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "glutamyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "glutamyl-transfer ribonucleic acid", - }, - { - "pred": "hasRelatedSynonym", - "val": "glutamyl-transfer RNA", + "val": "non_stop_decay_transcript", + "xrefs": [], }, ], }, @@ -13317,21 +14157,26 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000261", - "glycyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", + "so:0000734", + "exemplar", + "mrna", + "representative", + "cdna", "sequence", - "glycine", - "anticodon", - "binding", - "region", + "gene", + "approach", + "method", + "usually", + "involves", + "initial", + "clustering", + "groups", + "subsequent", + "selection", + "group", ], - "id": "http://purl.obolibrary.org/obo/SO_0000261", - "lbl": "glycyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000734", + "lbl": "exemplar_mRNA", "meta": { "basicPropertyValues": [ { @@ -13339,24 +14184,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Added for the MO people.", + ], "definition": { - "val": "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.", + "val": "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.", "xrefs": [ - "SO:ke", + "http://mged.sourceforge.net/ontologies/MGEDontology.php", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "glycyl tRNA", - }, - { - "pred": "hasRelatedSynonym", - "val": "glycyl-transfer RNA", - }, - { - "pred": "hasRelatedSynonym", - "val": "glycyl-transfer ribonucleic acid", + "val": "exemplar mRNA", + "xrefs": [], }, ], }, @@ -13364,21 +14205,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000262", - "histidyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", - "sequence", - "histidine", - "anticodon", - "binding", - "region", + "so:0000108", + "mrna", + "frameshift", + "frameshifted", ], - "id": "http://purl.obolibrary.org/obo/SO_0000262", - "lbl": "histidyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000108", + "lbl": "mRNA_with_frameshift", "meta": { "basicPropertyValues": [ { @@ -13387,23 +14220,21 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.", + "val": "An mRNA with a frameshift.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "histidyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "histidyl-transfer RNA", + "val": "mRNA with frameshift", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "histidyl-transfer ribonucleic acid", + "val": "frameshifted mRNA", + "xrefs": [], }, ], }, @@ -13411,21 +14242,12 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000263", - "isoleucyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", - "sequence", - "isoleucine", - "anticodon", - "binding", - "region", + "so:0000862", + "capped", + "mrna", ], - "id": "http://purl.obolibrary.org/obo/SO_0000263", - "lbl": "isoleucyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000862", + "lbl": "capped_mRNA", "meta": { "basicPropertyValues": [ { @@ -13434,23 +14256,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.", + "val": "An mRNA that is capped.", "xrefs": [ - "SO:ke", + "SO:xp", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "isoleucyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "isoleucyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "isoleucyl-transfer ribonucleic acid", + "val": "capped mRNA", + "xrefs": [], }, ], }, @@ -13458,46 +14273,72 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000264", - "leucyl", - "trna", - "transfer", + "so:0002340", "rna", - "ribonucleic", - "acid", - "sequence", - "leucine", - "anticodon", - "binding", - "region", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000264", - "lbl": "leucyl_tRNA", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "7sk", + "abundant", + "small", + "nuclear", + "together", + "associated", + "cellular", + "proteins", + "regulates", + "activity", + "positive", + "transcription", + "elongation", + "factor", + "b", + "p", + "tefb", + "often", + "described", + "literature", + "similar", + "snrna", + "except", + "longer", + "length", + ], + "id": "http://purl.obolibrary.org/obo/SO_0002340", + "lbl": "RNA_7SK", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-04-27T14:50:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as a request from FlyBase. See GitHub Issue #512", + ], "definition": { - "val": "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.", + "val": "An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length.", "xrefs": [ - "SO:ke", + "PMID:19246988", + "PMID:21853533", + "PMID:27369380", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "leucyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "leucyl-transfer RNA", + "val": "RNA 7SK", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "leucyl-transfer ribonucleic acid", + "val": "7SK RNA", + "xrefs": [], }, ], }, @@ -13505,46 +14346,49 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000265", - "lysyl", - "trna", - "transfer", + "so:0002247", + "sncrna", + "small", + "noncoding", "rna", - "ribonucleic", - "acid", - "sequence", - "lysine", - "anticodon", - "binding", - "region", + "non", + "coding", + "less", + "200", + "nucleotides", + "length", ], - "id": "http://purl.obolibrary.org/obo/SO_0000265", - "lbl": "lysyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002247", + "lbl": "sncRNA", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-05-13T11:07:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485)", ], "definition": { - "val": "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.", + "val": "A non-coding RNA less than 200 nucleotides in length.", "xrefs": [ - "SO:ke", + "PMID:30069443", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "lysyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "lysyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "lysyl-transfer ribonucleic acid", + "val": "Small noncoding RNA", + "xrefs": [], }, ], }, @@ -13552,46 +14396,46 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000266", - "methionyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", - "sequence", - "methionine", - "anticodon", - "binding", - "region", + "so:0001870", + "enhancerrna", + "erna", + "short", + "ncrna", + "transcribed", + "enhancer", + "may", + "regulatory", + "function", ], - "id": "http://purl.obolibrary.org/obo/SO_0000266", - "lbl": "methionyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0001870", + "lbl": "enhancerRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-01-17T03:09:35Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.", + "val": "A short ncRNA that is transcribed from an enhancer. May have a regulatory function.", "xrefs": [ - "SO:ke", + "SO:cjm", + "doi:10.1038/465173a", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "methionyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "methionyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "methionyl-transfer ribonucleic acid", + "val": "eRNA", + "xrefs": [], }, ], }, @@ -13599,21 +14443,38 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000267", - "phenylalanyl", - "trna", - "transfer", + "so:0000990", + "class", "rna", - "ribonucleic", - "acid", - "sequence", - "phenylalanine", - "anticodon", - "binding", - "region", + "small", + "non", + "coding", + "55", + "65", + "nt", + "long", + "containing", + "highly", + "conserved", + "ends", + "16", + "respectively", + "predicted", + "come", + "together", + "form", + "stem", + "structure", + "identified", + "social", + "amoeba", + "dictyostelium", + "discoideum", + "localized", + "cytoplasm", ], - "id": "http://purl.obolibrary.org/obo/SO_0000267", - "lbl": "phenylalanyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000990", + "lbl": "class_I_RNA", "meta": { "basicPropertyValues": [ { @@ -13621,24 +14482,20 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.", + ], "definition": { - "val": "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.", + "val": "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.", "xrefs": [ - "SO:ke", + "PMID:15333696", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "phenylalanyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "phenylalanyl-transfer RNA", - }, - { - "pred": "hasExactSynonym", - "val": "phenylalanyl-transfer ribonucleic acid", + "val": "class I RNA", + "xrefs": [], }, ], }, @@ -13646,46 +14503,91 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000268", - "prolyl", - "trna", - "transfer", + "so:0001877", + "lncrna", + "insdc", + "qualifier:lncrna", + "feature:ncrna", + "long", + "non", + "coding", "rna", - "ribonucleic", - "acid", - "sequence", - "proline", - "anticodon", - "binding", - "region", + "transcript", + "generally", + "longer", + "200", + "nucleotides", + "cannot", + "classified", + "ncrna", + "subtype", + "similar", + "mrnas", + "lncrnas", + "mainly", + "transcribed", + "polymerase", + "ii", + "often", + "capped", + "methyl", + "guanosine", + "ends", + "polyadenylated", + "may", + "spliced", ], - "id": "http://purl.obolibrary.org/obo/SO_0000268", - "lbl": "prolyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0001877", + "lbl": "lncRNA", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-02-14T05:18:01Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + ], + "comments": [ + "Updated the definition of lncRNA (SO:0001877) from "A non-coding RNA over 200nucleotides in length." to "A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced." See GitHub Issue #575", ], "definition": { - "val": "A tRNA sequence that has a proline anticodon, and a 3' proline binding region.", + "val": "A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced.", "xrefs": [ - "SO:ke", + "HGNC:mw", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "prolyl tRNA", + "val": "INSDC_qualifier:lncRNA", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "prolyl-transfer RNA", + "val": "long non-coding RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "prolyl-transfer ribonucleic acid", + "val": "lncRNA_transcript", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://www.gencodegenes.org/gencode_biotypes.html", }, ], }, @@ -13693,21 +14595,24 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000269", - "seryl", - "trna", - "transfer", + "so:0005843", + "rrna", + "cleavage", "rna", - "ribonucleic", - "acid", - "sequence", - "serine", - "anticodon", - "binding", - "region", + "ncrna", + "part", + "ribonucleoprotein", + "cleaves", + "primary", + "pre", + "transcript", + "process", + "producing", + "mature", + "molecules", ], - "id": "http://purl.obolibrary.org/obo/SO_0000269", - "lbl": "seryl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0005843", + "lbl": "rRNA_cleavage_RNA", "meta": { "basicPropertyValues": [ { @@ -13716,23 +14621,16 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tRNA sequence that has a serine anticodon, and a 3' serine binding region.", + "val": "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.", "xrefs": [ - "SO:ke", + "GOC:kgc", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "seryl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "seryl-transfer RNA", - }, - { - "pred": "hasRelatedSynonym", - "val": "seryl-transfer ribonucleic acid", + "val": "rRNA cleavage RNA", + "xrefs": [], }, ], }, @@ -13740,46 +14638,63 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000270", - "threonyl", - "trna", - "transfer", - "ribonucleic", - "acid", + "so:0002031", + "shrna", + "small", + "hairpin", "rna", - "sequence", - "threonine", - "anticodon", - "binding", - "region", + "short", + "transcript", + "makes", + "tight", + "turn", + "used", + "silence", + "target", + "gene", + "expression", + "via", + "interference", ], - "id": "http://purl.obolibrary.org/obo/SO_0000270", - "lbl": "threonyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002031", + "lbl": "shRNA", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2014-10-23T09:16:29Z", + }, ], "definition": { - "val": "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.", + "val": "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference.", "xrefs": [ + "PMID:6699500", "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "threonyl tRNA", + "val": "small hairpin RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "threonyl-transfer ribonucleic acid", + "val": "short hairpin RNA", + "xrefs": [], }, + ], + "xrefs": [ { - "pred": "hasRelatedSynonym", - "val": "threonyl-transfer RNA", + "val": "http:http:en.wikipedia.org/wiki/Small_hairpin_RNA", }, ], }, @@ -13787,46 +14702,72 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000271", - "tryptophanyl", - "trna", - "transfer", + "so:0002291", + "circular", + "ncrna", + "circrna", + "noncoding", + "non", + "coding", "rna", - "ribonucleic", - "acid", - "sequence", - "tryptophan", - "anticodon", - "binding", - "region", + "generated", + "backsplicing", + "exons", + "introns", + "resulting", + "covalently", + "closed", + "loop", + "without", + "cap", + "polya", + "tail", ], - "id": "http://purl.obolibrary.org/obo/SO_0000271", - "lbl": "tryptophanyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002291", + "lbl": "circular_ncRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-07-01T11:49:30Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)", + ], "definition": { - "val": "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.", + "val": "A non-coding RNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail.", "xrefs": [ - "SO:ke", + "PMID:29086764", + "PMID:29182528", + "PMID:29230098", + "PMID:29576969", + "PMID:29626935", ], }, "synonyms": [ { - "pred": "hasExactSynonym", - "val": "tryptophanyl tRNA", + "pred": "hasBroadSynonym", + "val": "circRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "tryptophanyl-transfer RNA", + "val": "circular ncRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "tryptophanyl-transfer ribonucleic acid", + "val": "noncoding circRNA", + "xrefs": [], }, ], }, @@ -13834,46 +14775,67 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000272", - "tyrosyl", - "trna", - "transfer", - "ribonucleic", - "acid", + "so:0002356", + "hprna", + "hairpin", "rna", - "sequence", - "tyrosine", - "anticodon", - "binding", - "region", + "comprising", + "extended", + "inverted", + "repeat", + "stem", + "typically", + "much", + "longer", + "mirna", + "precursors", + "400", + "base", + "pairs", + "length", + "hprnas", + "processed", + "dicer", + "generate", + "endogenous", + "short", + "interfering", + "rnas", + "sirnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0000272", - "lbl": "tyrosyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002356", + "lbl": "hpRNA", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-10-07T17:35:56Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + ], + "comments": [ + "See GitHub Issue #518.", ], "definition": { - "val": "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.", + "val": "An RNA comprising an extended inverted repeat, the stem of which is typically much longer than that of miRNA precursors and can be up to 400 base pairs in length. hpRNAs are processed by Dicer-2 to generate endogenous short interfering RNAs (siRNAs).", "xrefs": [ - "SO:ke", + "PMID:18463630", + "PMID:18719707", + "PMID:25544562", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "tyrosyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "tyrosyl-transfer ribonucleic acid", - }, - { - "pred": "hasRelatedSynonym", - "val": "tyrosyl-transfer RNA", + "val": "Hairpin RNA", + "xrefs": [], }, ], }, @@ -13881,46 +14843,61 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000273", - "valyl", - "trna", - "transfer", - "ribonucleic", - "acid", + "so:0002354", + "sbrna", + "stem", + "bulge", "rna", - "sequence", - "valine", - "anticodon", - "binding", - "region", + "small", + "non", + "coding", + "loop", + "present", + "nematodes", + "insects", + "functionally", + "structurally", + "related", + "vertebrate", + "y", ], - "id": "http://purl.obolibrary.org/obo/SO_0000273", - "lbl": "valyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002354", + "lbl": "sbRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-09-30T21:29:19Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, + ], + "comments": [ + "See GitHub Issue #516.", ], "definition": { - "val": "A tRNA sequence that has a valine anticodon, and a 3' valine binding region.", + "val": "A small non-coding stem-loop RNA present in nematodes and insects, functionally and structurally related to vertebrate Y RNA.", "xrefs": [ - "SO:ke", + "PMID:25908866", + "PMID:30666901", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "valyl tRNA", + "val": "Stem-bulge RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "valyl-transfer ribonucleic acid", - }, - { - "pred": "hasRelatedSynonym", - "val": "valyl-transfer RNA", + "val": "stem_bulge_RNA", + "xrefs": [], }, ], }, @@ -13928,46 +14905,69 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000766", - "pyrrolysyl", - "trna", - "transfer", - "rna", - "ribonucleic", - "acid", + "so:0002352", + "sisrna", + "stable", + "intronic", "sequence", - "pyrrolysine", - "anticodon", - "binding", - "region", + "rna", + "non", + "coding", + "typically", + "derived", + "sense", + "strand", + "cognate", + "host", + "gene", + "rapidly", + "degraded", + "may", + "contain", + "exonic", + "sequences", + "caps", + "polya", + "tails", ], - "id": "http://purl.obolibrary.org/obo/SO_0000766", - "lbl": "pyrrolysyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002352", + "lbl": "sisRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-09-30T21:07:18Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, ], - "definition": { - "val": "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.", + "comments": [ + "See GitHub Issue #515.", + ], + "definition": { + "val": "A non-coding RNA typically derived from intronic sequence of the sense strand of a cognate host gene, that is not rapidly degraded. It may contain exonic sequences, 5′ caps, and/or polyA tails.", "xrefs": [ - "SO:ke", + "PMID:27147469", + "PMID:29397203", + "PMID:30391089", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "pyrrolysyl tRNA", - }, - { - "pred": "hasExactSynonym", - "val": "pyrrolysyl-transfer RNA", + "val": "stable_intronic_sequence_RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "pyrrolysyl-transfer ribonucleic acid", + "val": "Stable intronic sequence RNA", + "xrefs": [], }, ], }, @@ -13975,17 +14975,51 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001036", - "arginyl", - "trna", - "sequence", - "arginine", - "anticodon", - "binding", - "region", + "so:0000405", + "y", + "rna", + "insdc", + "feature:ncrna", + "qualifier:y", + "rnas", + "components", + "ro", + "ribonucleoprotein", + "particle", + "rnp", + "association", + "ro60", + "la", + "proteins", + "well", + "conserved", + "function", + "known", + "humans", + "component", + "one", + "four", + "small", + "rnas:", + "hy1", + "hy3", + "hy4", + "hy5", + "predicted", + "fold", + "secondary", + "structure", + "containing", + "three", + "stem", + "structures", + "largest", + "contains", + "additional", + "hairpin", ], - "id": "http://purl.obolibrary.org/obo/SO_0001036", - "lbl": "arginyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000405", + "lbl": "Y_RNA", "meta": { "basicPropertyValues": [ { @@ -13994,15 +15028,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.", + "val": "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.", "xrefs": [ - "SO:ke", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "arginyl tRNA", + "val": "INSDC_qualifier:Y_RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "Y RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Y_RNA", }, ], }, @@ -14010,44 +15063,136 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002129", - "mt", - "trna", - "mitochondrial", - "transfer", + "so:0000404", + "vault", "rna", + "insdc", + "qualifier:vault", + "feature:ncrna", + "family", + "rnas", + "found", + "part", + "enigmatic", + "ribonucleoprotein", + "complex", + "consists", + "major", + "protein", + "mvp", + "two", + "minor", + "proteins", + "vparp", + "tep1", + "several", + "small", + "untranslated", + "molecules", + "suggested", + "involved", + "drug", + "resistance", ], - "id": "http://purl.obolibrary.org/obo/SO_0002129", - "lbl": "mt_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000404", + "lbl": "vault_RNA", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, + ], + "definition": { + "val": "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], + "synonyms": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:10:17Z", + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:vault_RNA", + "xrefs": [], }, + { + "pred": "hasExactSynonym", + "val": "vault RNA", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Vault_RNA", + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000644", + "antisense", + "rna", + "insdc", + "feature:ncrna", + "qualifier:antisense", + "transcribed", + "coding", + "rather", + "template", + "strand", + "dna", + "therefore", + "complementary", + "mrna", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000644", + "lbl": "antisense_RNA", + "meta": { + "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "Mitochondrial transfer RNA.", + "val": "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.", "xrefs": [ - "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "Mt_tRNA", + "val": "antisense RNA", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "mitochondrial_tRNA", + "val": "INSDC_qualifier:antisense_RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Antisense_RNA", }, ], }, @@ -14055,21 +15200,21 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0005857", - "selenocysteinyl", - "trna", - "transfer", + "so:0000390", + "telomerase", "rna", - "ribonucleic", - "acid", - "sequence", - "selenocysteine", - "anticodon", - "binding", - "region", + "insdc", + "feature:ncrna", + "qualifier:telomerase", + "component", + "reverse", + "transcriptase", + "synthesizes", + "telomeric", + "dna", ], - "id": "http://purl.obolibrary.org/obo/SO_0005857", - "lbl": "selenocysteinyl_tRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000390", + "lbl": "telomerase_RNA", "meta": { "basicPropertyValues": [ { @@ -14078,23 +15223,34 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.", + "val": "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.", "xrefs": [ - "SO:ke", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "selenocysteinyl tRNA", + "val": "telomerase RNA", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "selenocysteinyl-transfer RNA", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "selenocysteinyl-transfer ribonucleic acid", + "val": "INSDC_qualifier:telomerase_RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Telomerase_RNA", }, ], }, @@ -14102,108 +15258,53 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000391", - "u1", - "snrna", + "so:0001800", + "tasirna", + "trans", + "acting", "small", - "nuclear", + "interfering", "rna", - "component", - "spliceosome", - "involved", - "pre", - "mrna", - "splicing", - "end", - "forms", - "complementary", - "base", - "pairs", - "splice", - "junction", - "thus", - "defining", - "donor", - "site", - "intron", - "significant", - "differences", "sequence", - "secondary", - "structure", - "metazoan", - "yeast", - "snrnas", - "latter", - "much", - "longer", - "568", - "nucleotides", - "compared", - "164", - "human", - "nevertheless", - "predictions", - "suggest", - "share", - "common", - "core", - "consisting", - "helices", - "ii", - "proximal", - "region", - "iii", - "iv", + "21", + "nucleotide", + "double", + "stranded", + "polyadenylated", + "non", + "coding", + "transcribed", + "tas", + "gene", ], - "id": "http://purl.obolibrary.org/obo/SO_0000391", - "lbl": "U1_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0001800", + "lbl": "tasiRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2011-05-31T03:24:06Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.", + "val": "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003", + "PMID:16145017", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { - "pred": "hasExactSynonym", - "val": "U1 small nuclear RNA", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "U1 snRNA", - }, - { - "pred": "hasExactSynonym", - "val": "small nuclear RNA U1", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "snRNA U1", - "xrefs": [ - "RSC:cb", - ], - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/U1_snRNA", + "pred": "hasRelatedSynonym", + "val": "trans acting small interfering RNA", + "xrefs": [], }, ], }, @@ -14211,49 +15312,32 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000392", - "u2", - "snrna", - "small", - "nuclear", + "so:0000602", + "guide", "rna", - "component", - "spliceosome", - "involved", - "pre", + "insdc", + "feature:ncrna", + "grna", + "qualifier:guide", + "short", + "uridylated", + "form", + "duplex", + "except", + "post", + "transcriptionally", + "added", + "oligo", + "u", + "tail", + "so:0000609", + "stretch", + "mature", + "edited", "mrna", - "splicing", - "complementary", - "binding", - "area", - "lying", - "towards", - "end", - "hairpin", - "branchpoint", - "sequence", - "bps", - "intron", - "results", - "bulging", - "unpaired", - "adenine", - "initiates", - "nucleophilic", - "attack", - "intronic", - "splice", - "site", - "thus", - "starting", - "first", - "two", - "transesterification", - "reactions", - "mediate", ], - "id": "http://purl.obolibrary.org/obo/SO_0000392", - "lbl": "U2_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000602", + "lbl": "guide_RNA", "meta": { "basicPropertyValues": [ { @@ -14262,9 +15346,9 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.", + "val": "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004", + "http://www.rna.ucla.edu/index.html", ], }, "subsets": [ @@ -14273,33 +15357,28 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "U2 small nuclear RNA", - "xrefs": [ - "RSC:CB", - ], + "val": "guide RNA", + "xrefs": [], }, { - "pred": "hasExactSynonym", - "val": "U2 snRNA", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small nuclear RNA U2", - "xrefs": [ - "RSC:CB", - ], + "val": "gRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snRNA U2", - "xrefs": [ - "RSC:CB", - ], + "val": "INSDC_qualifier:guide_RNA", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/U2_snRNA", + "val": "http://en.wikipedia.org/wiki/Guide_RNA", }, ], }, @@ -14307,87 +15386,139 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000393", - "u4", - "snrna", - "small", - "nuclear", + "so:0000590", + "srp", "rna", - "component", - "major", - "u2", - "dependent", - "spliceosome", - "forms", - "duplex", - "u6", - "splicing", - "round", - "displaced", - "atp", - "manner", - "allowing", - "refold", - "create", - "active", - "site", - "catalysis", - "recycling", - "process", - "involving", - "protein", - "prp24", - "re", - "anneals", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000393", - "lbl": "U4_snRNA", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", - }, - ], - "definition": { - "val": "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.", - "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015", - ], - }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "U4 small nuclear RNA", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "U4 snRNA", + "7s", + "signal", + "recognition", + "particle", + "insdc", + "feature:ncrna", + "qualifier:srp", + "universally", + "conserved", + "ribonucleoprotein", + "involved", + "co", + "translational", + "targeting", + "proteins", + "membranes", + "eukaryotic", + "consists", + "300", + "nucleotide", + "six", + "proteins:", + "srps", + "72", + "68", + "54", + "19", + "14", + "archaeal", + "homologues", + "srp19", + "srp54", + "eubacteria", + "5s", + "ffh", + "protein", + "homologue", + "rnas", + "similar", + "secondary", + "structures", + "eight", + "helical", + "elements", + "fold", + "alu", + "domains", + "separated", + "long", + "linker", + "region", + "eubacterial", + "generally", + "simpler", + "structure", + "m", + "domain", + "bound", + "corresponds", + "helix", + "gram", + "positive", + "bacteria", + "e", + "g", + "bacillus", + "subtilis", + "however", + "larger", + "also", + "thought", + "mediate", + "peptide", + "chain", + "elongation", + "retardation", + "function", + "interacts", + "mediates", + "sequence", + "eukaryotes", + "archaea", + "complex", + "assembly", + "stabilizes", + "binding", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000590", + "lbl": "SRP_RNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, + ], + "definition": { + "val": "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], + "synonyms": [ { - "pred": "hasExactSynonym", - "val": "small nuclear RNA U4", - "xrefs": [ - "RSC:cb", - ], + "pred": "hasRelatedSynonym", + "val": "7S RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snRNA U4", - "xrefs": [ - "RSC:cb", - ], + "val": "SRP RNA", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/U4_snRNA", + "pred": "hasRelatedSynonym", + "val": "signal recognition particle RNA", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:SRP_RNA", + "xrefs": [], }, ], }, @@ -14395,29 +15526,22 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000394", - "u4atac", - "snrna", + "so:0000013", + "scrna", + "insdc", + "feature:ncrna", "small", - "nuclear", + "cytoplasmic", "rna", - "required", - "splicing", - "minor", - "u12", - "dependent", - "class", - "eukaryotic", - "introns", - "forms", - "base", - "paired", - "complex", - "u6atac", - "so:0000397", + "qualifier:scrna", + "non", + "coding", + "sequence", + "present", + "cytoplasm", ], - "id": "http://purl.obolibrary.org/obo/SO_0000394", - "lbl": "U4atac_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000013", + "lbl": "scRNA", "meta": { "basicPropertyValues": [ { @@ -14426,9 +15550,9 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).", + "val": "A small non coding RNA sequence, present in the cytoplasm.", "xrefs": [ - "PMID:=12409455", + "SO:ke", ], }, "subsets": [ @@ -14436,29 +15560,19 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` ], "synonyms": [ { - "pred": "hasExactSynonym", - "val": "U4atac small nuclear RNA", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "U4atac snRNA", + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small nuclear RNA U4atac", - "xrefs": [ - "RSC:cb", - ], + "val": "small cytoplasmic RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snRNA U4atac", - "xrefs": [ - "RSC:cb", - ], + "val": "INSDC_qualifier:scRNA", + "xrefs": [], }, ], }, @@ -14466,37 +15580,25 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000395", - "u5", - "snrna", - "small", - "nuclear", + "so:0000252", + "rrna", + "insdc", + "qualifier:unknown", + "ribosomal", "rna", + "ribonucleic", + "acid", + "feature:rrna", "component", - "types", - "known", - "spliceosome", - "precise", - "function", - "molecule", - "unknown", - "though", - "loop", - "required", - "splice", - "site", - "selection", - "p220", - "binding", - "stem", - "sm", - "important", - "protein", - "cap", - "methylation", + "ribosome", + "provide", + "structural", + "scaffolding", + "catalytic", + "activity", ], - "id": "http://purl.obolibrary.org/obo/SO_0000395", - "lbl": "U5_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000252", + "lbl": "rRNA", "meta": { "basicPropertyValues": [ { @@ -14504,10 +15606,14 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493", + ], "definition": { - "val": "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.", + "val": "rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020", + "ISBN:0198506732", + "http://www.insdc.org/files/feature_table.html", ], }, "subsets": [ @@ -14515,34 +15621,29 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` ], "synonyms": [ { - "pred": "hasExactSynonym", - "val": "U5 small nuclear RNA", - "xrefs": [ - "RSC:cb", - ], + "pred": "hasBroadSynonym", + "val": "INSDC_qualifier:unknown", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "U5 snRNA", + "val": "ribosomal RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small nuclear RNA U5", - "xrefs": [ - "RSC:cb", - ], + "val": "ribosomal ribonucleic acid", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snRNA U5", - "xrefs": [ - "RSC:cb", - ], + "val": "INSDC_feature:rRNA", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/U5_snRNA", + "val": "http://en.wikipedia.org/wiki/RRNA", }, ], }, @@ -14550,37 +15651,18 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000396", - "u6", - "snrna", - "small", - "nuclear", + "so:0000372", + "enzymatic", "rna", - "component", - "spliceosome", - "involved", - "splicing", - "pre", - "mrna", - "putative", - "secondary", - "structure", - "consensus", - "base", - "pairing", - "confined", - "short", - "stem", - "loop", - "thought", - "form", - "extensive", - "pair", - "interactions", - "u4", + "sequence", + "catalytic", + "activity", + "without", + "associated", + "ribonucleoprotein", ], - "id": "http://purl.obolibrary.org/obo/SO_0000396", - "lbl": "U6_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000372", + "lbl": "enzymatic_RNA", "meta": { "basicPropertyValues": [ { @@ -14588,10 +15670,13 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. Moved under ncRNA on 18 Nov 2021. See GitHub Issue #533.", + ], "definition": { - "val": "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.", + "val": "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015", + "RSC:cb", ], }, "subsets": [ @@ -14600,33 +15685,8 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "synonyms": [ { "pred": "hasExactSynonym", - "val": "U6 small nuclear RNA", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "U6 snRNA", - }, - { - "pred": "hasExactSynonym", - "val": "small nuclear RNA U6", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "snRNA U6", - "xrefs": [ - "RSC:cb", - ], - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/U6_snRNA", + "val": "enzymatic RNA", + "xrefs": [], }, ], }, @@ -14634,66 +15694,74 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000397", - "u6atac", - "snrna", - "small", - "nuclear", + "so:0002120", + "three", + "prime", + "overlapping", + "ncrna", + "noncoding", "rna", - "required", - "splicing", - "minor", - "u12", - "dependent", - "class", - "eukaryotic", - "introns", - "forms", - "base", - "paired", - "complex", - "u4atac", - "so:0000394", + "3prime", + "transcript", + "ditag", + "digital", + "gene", + "expression", + "profiling", + "published", + "experimental", + "data", + "strongly", + "supports", + "existence", + "short", + "non", + "coding", + "transcripts", + "transcribed", + "utr", ], - "id": "http://purl.obolibrary.org/obo/SO_0000397", - "lbl": "U6atac_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002120", + "lbl": "three_prime_overlapping_ncrna", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T15:48:21Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.", + ], "definition": { - "val": "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).", + "val": "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR.", "xrefs": [ - "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "U6atac small nuclear RNA", - "xrefs": [ - "RSC:cb", - ], + "val": "3'_overlapping_ncrna", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "U6atac snRNA", - "xrefs": [ - "RSC:cb", - ], + "val": "three prime overlapping noncoding rna", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snRNA U6atac", - "xrefs": [ - "RSC:cb", - ], + "val": "3prime_overlapping_ncRNA", + "xrefs": [], }, ], }, @@ -14701,80 +15769,42 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000398", - "u11", - "snrna", - "small", - "nuclear", - "rna", - "plays", - "role", - "splicing", - "minor", - "u12", - "dependent", - "class", - "eukaryotic", - "introns", - "similar", - "u1", - "major", - "spliceosome", - "base", - "pairs", - "conserved", - "splice", - "site", - "sequence", + "so:0001927", + "telomeric", + "transcript", + "non", + "coding", + "derived", + "telomere", ], - "id": "http://purl.obolibrary.org/obo/SO_0000398", - "lbl": "U11_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0001927", + "lbl": "telomeric_transcript", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2012-10-31T01:42:15Z", + }, ], "definition": { - "val": "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.", + "val": "A non-coding transcript derived from the transcript of the telomere.", "xrefs": [ - "PMID:9622129", + "PMID:22139915", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "U11 small nuclear RNA", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "U11 snRNA", - }, - { - "pred": "hasExactSynonym", - "val": "small nuclear RNA U11", - "xrefs": [ - "RSC:cb", - ], - }, - { - "pred": "hasExactSynonym", - "val": "snRNA U11", - "xrefs": [ - "RSC:cb", - ], - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/U11_snRNA", + "val": "telomeric transcript", + "xrefs": [], }, ], }, @@ -14782,44 +15812,158 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000399", - "u12", - "snrna", + "so:0002022", + "prirna", + "primal", "small", - "nuclear", "rna", - "together", - "u4atac", - "u6atac", - "u5", - "u11", - "snrnas", - "associated", - "proteins", - "forms", - "spliceosome", - "cleaves", - "divergent", - "class", - "low", - "abundance", - "pre", - "mrna", - "introns", + "molecule", + "22", + "23", + "nt", + "size", + "product", + "longer", + "production", + "prirnas", + "independent", + "dicer", + "involves", + "binding", + "argonaute", + "trimming", + "triman", + "fission", + "yeast", + "trigger", + "establishment", + "heterochromatin", + "primarily", + "generated", + "centromeric", + "transcripts", + "dg", + "dh", + "repeats", + "may", + "also", + "produced", + "degradation", + "products", + "primary", ], - "id": "http://purl.obolibrary.org/obo/SO_0000399", - "lbl": "U12_snRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002022", + "lbl": "priRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2014-05-30T15:01:24Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "kareneilbeck", + }, ], "definition": { - "val": "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.", + "val": "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007", + "PMID:20178743", + "PMID:24095277", + "PomBase:al", + ], + }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "primal small RNA", + "xrefs": [], + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000989", + "class", + "ii", + "rna", + "small", + "non", + "coding", + "59", + "60", + "nt", + "long", + "containing", + "ends", + "predicted", + "come", + "together", + "form", + "stem", + "structure", + "identified", + "social", + "amoeba", + "dictyostelium", + "discoideum", + "localized", + "cytoplasm", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000989", + "lbl": "class_II_RNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "definition": { + "val": "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. 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They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." to "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing." to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578.", + ], + "definition": { + "val": "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. 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Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.", + "xrefs": [ + "PMID:11081512", + "PMID:12592000", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "stRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "micro RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "microRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:miRNA", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "small temporal RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/StRNA", + }, + { + "val": "http://en.wikipedia.org/wiki/MiRNA", + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000646", + "sirna", + "insdc", + "qualifier:sirna", + "small", + "interfering", + "rna", + "feature:ncrna", + "molecule", + "product", + "longer", + "exogenous", + "endogenous", + "dsrna", + "either", + "bimolecular", + "duplex", + "long", + "hairpin", + "processed", + "via", + "dicer", + "pathway", + "numerous", + "sirnas", + "accumulate", + "strands", + "trigger", + "cleavage", + "target", + "molecules", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000646", + "lbl": "siRNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "definition": { + "val": "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules.", + "xrefs": [ + "PMID:12592000", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:siRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "small interfering RNA", + "xrefs": [], + }, + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/SiRNA", + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000377", + "csrb", + "rsmb", + "rna", + "enterobacterial", + "binds", + "csra", + "protein", + "rnas", + "contain", + "conserved", + "motif", + "caggxxg", + "found", + "18", + "copies", + "suggested", + "bind", + "csr", + "regulatory", + "system", + "strong", + "negative", + "effect", + "glycogen", + "biosynthesis", + "glyconeogenesis", + "catabolism", + "positive", + "glycolysis", + "bacteria", + "erwinia", + "caratovara", + "rsma", + "shown", + "regulate", + "production", + "virulence", + "determinants", + "extracellular", + "enzymes", + "also", + "member", + "family", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000377", + "lbl": "CsrB_RsmB_RNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "definition": { + "val": "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018", + ], + }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "CsrB RsmB RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "CsrB-RsmB RNA", + "xrefs": [], + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000378", + "dsra", + "rna", + "regulates", + "transcription", + "overcoming", + "transcriptional", + "silencing", + "nucleoid", + "associated", + "h", + "ns", + "protein", + "translation", + "promoting", + "efficient", + "stress", + "sigma", + "factor", + "rpos", + "two", + "activities", + "separated", + "mutation:", + "first", + "three", + "stem", + "loops", + "85", + "nucleotide", + "necessary", + "anti", + "action", + "second", + "loop", + "essential", + "antisilencing", + "less", + "critical", + "third", + "behaves", + "terminator", + "substituted", + "trp", + "without", + "loss", + "either", + "function", + "sequence", + "complementary", + "upstream", + "leader", + "portion", + "messenger", + "suggesting", + "pairing", + "message", + "might", + "important", + "translational", + "regulation", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000378", + "lbl": "DsrA_RNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "definition": { + "val": "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014", + ], + }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "DsrA RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/DsrA_RNA", + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000388", + "rre", + "rna", + "rev", + "response", + "element", + "encoded", + "within", + "hiv", + "env", + "gene", + "essential", + "regulatory", + "protein", + "binds", + "internal", + "loop", + "leading", + "encouraging", + "binding", + "rnp", + "complex", + "critical", + "mrna", + "export", + "hence", + "expression", + "structural", + "proteins", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000388", + "lbl": "RRE_RNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "definition": { + "val": "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036", + ], + }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "RRE RNA", + "xrefs": [], + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000389", + "spot", + "42", + "rna", + "109", + "nucleotide", + "e", + "coli", + "seems", + "regulatory", + "role", + "galactose", + "operon", + "changes", + "levels", + "implicated", + "affecting", + "dna", + "polymerase", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000389", + "lbl": "spot_42_RNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "definition": { + "val": "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021", + ], + }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "spot-42 RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Spot_42_RNA", + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000387", + "rpra", + "rna", + "translational", + "regulation", + "stationary", + "phase", + "sigma", + "factor", + "rpos", + "mediated", + "formation", + "double", + "stranded", + "stem", + "loop", + "structure", + "upstream", + "region", + "messenger", + "occluding", + "translation", + "initiation", + "site", + "clones", + "carrying", + "regulator", + "increased", + "gene", + "encodes", + "106", + "nucleotide", + "regulatory", + "dsra", + "rfam:rf00014", + "predicted", + "form", + "three", + "loops", + "thus", + "least", + "two", + "small", + "rnas", + "participate", + "positive", + "unlike", + "extensive", + "complementarity", + "leader", + "leaving", + "mechanism", + "action", + "unclear", + "non", + "essential", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000387", + "lbl": "RprA_RNA", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", + }, + ], + "definition": { + "val": "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034", + ], + }, + "synonyms": [ + { + "pred": "hasExactSynonym", + "val": "RprA RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/RprA_RNA", + }, + ], + }, + "type": "CLASS", + }, + { + "fullTextWords": [ + "so:0000384", + "oxys", + "rna", + "small", + "untranslated", + "induced", + "response", + "oxidative", + "stress", + "escherichia", + "coli", + "acts", + "global", + "regulator", + "activate", + "repress", + "expression", + "many", + "40", + "genes", + "including", + "fhla", + "encoded", + "transcriptional", + "activator", + "rpos", + "sigma", + "subunit", + "polymerase", + "bound", + "hfq", + "protein", + "increases", + "interaction", + "target", + "messages", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000384", + "lbl": "OxyS_RNA", "meta": { "basicPropertyValues": [ { @@ -14923,26 +24358,21 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.", + "val": "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.", "xrefs": [ - "http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "C D box snoRNA", - }, - { - "pred": "hasExactSynonym", - "val": "C/D box snoRNA", + "val": "OxyS RNA", + "xrefs": [], }, + ], + "xrefs": [ { - "pred": "hasExactSynonym", - "val": "box C/D snoRNA", + "val": "http://en.wikipedia.org/wiki/OxyS_RNA", }, ], }, @@ -14950,55 +24380,29 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000594", - "h", - "aca", - "box", - "snorna", - "members", - "family", - "contain", - "triplet", - "exactly", - "nt", - "upstream", - "end", - "hinge", - "region", - "links", - "two", - "structurally", - "similar", - "functional", - "domains", - "molecule", - "boxes", - "important", - "biosynthesis", - "function", - "snornas", - "involved", - "rrna", - "processing", - "others", - "known", - "predicted", - "participate", - "selection", - "uridine", - "nucleosides", - "converted", - "pseudouridines", - "site", - "mediated", - "direct", + "so:0000397", + "u6atac", + "snrna", + "small", + "nuclear", + "rna", + "required", + "splicing", + "minor", + "u12", + "dependent", + "class", + "eukaryotic", + "introns", + "forms", "base", - "pairing", - "one", - "targeting", + "paired", + "complex", + "u4atac", + "so:0000394", ], - "id": "http://purl.obolibrary.org/obo/SO_0000594", - "lbl": "H_ACA_box_snoRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000397", + "lbl": "U6atac_snRNA", "meta": { "basicPropertyValues": [ { @@ -15007,23 +24411,35 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.", + "val": "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).", "xrefs": [ - "http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html", + "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "H ACA box snoRNA", + "val": "U6atac snRNA", + "xrefs": [ + "RSC:cb", + ], }, { "pred": "hasExactSynonym", - "val": "H/ACA box snoRNA", + "val": "U6atac small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], }, { "pred": "hasExactSynonym", - "val": "box H/ACA snoRNA", + "val": "snRNA U6atac", + "xrefs": [ + "RSC:cb", + ], }, ], }, @@ -15031,109 +24447,81 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000276", - "mirna", - "insdc", - "feature:ncrna", - "qualifier:mirna", - "micro", - "rna", - "microrna", + "so:0000398", + "u11", + "snrna", "small", - "temporal", - "strna", - "22", - "nt", - "molecule", - "endogenous", - "transcript", - "gene", - "product", - "non", - "coding", - "genes", - "rnas", - "produced", - "precursor", - "molecules", - "so:0000647", - "form", - "local", - "hairpin", - "structures", - "ordinarily", - "processed", - "usually", - "via", - "dicer", - "pathway", - "single", - "accumulates", - "one", - "arm", - "may", - "trigger", - "cleavage", - "target", - "act", - "translational", - "repressors", + "nuclear", + "rna", + "plays", + "role", + "splicing", + "minor", + "u12", + "dependent", + "class", + "eukaryotic", + "introns", + "similar", + "u1", + "major", + "spliceosome", + "base", + "pairs", + "conserved", + "splice", + "site", + "sequence", ], - "id": "http://purl.obolibrary.org/obo/SO_0000276", - "lbl": "miRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000398", + "lbl": "U11_snRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "SO:0000649", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.", + "val": "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.", "xrefs": [ - "PMID:11081512", - "PMID:12592000", + "PMID:9622129", ], }, "subsets": [ "http://purl.obolibrary.org/obo/so#SOFA", ], "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:miRNA", - }, - { - "pred": "hasExactSynonym", - "val": "micro RNA", + "val": "snRNA U11", + "xrefs": [ + "RSC:cb", + ], }, { "pred": "hasExactSynonym", - "val": "microRNA", + "val": "U11 snRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small temporal RNA", + "val": "small nuclear RNA U11", + "xrefs": [ + "RSC:cb", + ], }, { "pred": "hasExactSynonym", - "val": "stRNA", + "val": "U11 small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/MiRNA", - }, - { - "val": "http://en.wikipedia.org/wiki/StRNA", + "val": "http://en.wikipedia.org/wiki/U11_snRNA", }, ], }, @@ -15141,33 +24529,33 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000376", - "rna", - "6s", + "so:0000399", + "u12", + "snrna", "small", - "184", - "nt", - "e", - "coli", + "nuclear", + "rna", + "together", + "u4atac", + "u6atac", + "u5", + "u11", + "snrnas", + "associated", + "proteins", "forms", - "hairpin", - "type", - "structure", - "associates", - "polymerase", - "highly", - "specific", - "manner", - "represses", - "expression", - "sigma70", - "dependent", - "promoter", - "stationary", - "phase", + "spliceosome", + "cleaves", + "divergent", + "class", + "low", + "abundance", + "pre", + "mrna", + "introns", ], - "id": "http://purl.obolibrary.org/obo/SO_0000376", - "lbl": "RNA_6S", + "id": "http://purl.obolibrary.org/obo/SO_0000399", + "lbl": "U12_snRNA", "meta": { "basicPropertyValues": [ { @@ -15176,24 +24564,45 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.", + "val": "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "6S RNA", + "val": "small nuclear RNA U12", + "xrefs": [ + "RSC:cb", + ], }, { "pred": "hasExactSynonym", - "val": "RNA 6S", + "val": "U12 small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "snRNA U12", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "U12 snRNA", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/6S_RNA", + "val": "http://en.wikipedia.org/wiki/U12_snRNA", }, ], }, @@ -15201,53 +24610,37 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000377", - "csrb", - "rsmb", + "so:0000395", + "u5", + "snrna", + "small", + "nuclear", "rna", - "enterobacterial", - "binds", - "csra", + "component", + "types", + "known", + "spliceosome", + "precise", + "function", + "molecule", + "unknown", + "though", + "loop", + "required", + "splice", + "site", + "selection", + "p220", + "binding", + "stem", + "sm", + "important", "protein", - "rnas", - "contain", - "conserved", - "motif", - "caggxxg", - "found", - "18", - "copies", - "suggested", - "bind", - "csr", - "regulatory", - "system", - "strong", - "negative", - "effect", - "glycogen", - "biosynthesis", - "glyconeogenesis", - "catabolism", - "positive", - "glycolysis", - "bacteria", - "erwinia", - "caratovara", - "rsma", - "shown", - "regulate", - "production", - "virulence", - "determinants", - "extracellular", - "enzymes", - "also", - "member", - "family", + "cap", + "methylation", ], - "id": "http://purl.obolibrary.org/obo/SO_0000377", - "lbl": "CsrB_RsmB_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000395", + "lbl": "U5_snRNA", "meta": { "basicPropertyValues": [ { @@ -15256,112 +24649,45 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.", + "val": "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "CsrB RsmB RNA", + "val": "small nuclear RNA U5", + "xrefs": [ + "RSC:cb", + ], }, { "pred": "hasExactSynonym", - "val": "CsrB-RsmB RNA", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0000378", - "dsra", - "rna", - "regulates", - "transcription", - "overcoming", - "transcriptional", - "silencing", - "nucleoid", - "associated", - "h", - "ns", - "protein", - "translation", - "promoting", - "efficient", - "stress", - "sigma", - "factor", - "rpos", - "two", - "activities", - "separated", - "mutation:", - "first", - "three", - "stem", - "loops", - "85", - "nucleotide", - "necessary", - "anti", - "action", - "second", - "loop", - "essential", - "antisilencing", - "less", - "critical", - "third", - "behaves", - "terminator", - "substituted", - "trp", - "without", - "loss", - "either", - "function", - "sequence", - "complementary", - "upstream", - "leader", - "portion", - "messenger", - "suggesting", - "pairing", - "message", - "might", - "important", - "translational", - "regulation", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000378", - "lbl": "DsrA_RNA", - "meta": { - "basicPropertyValues": [ + "val": "U5 small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], + }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "hasExactSynonym", + "val": "U5 snRNA", + "xrefs": [], }, - ], - "definition": { - "val": "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.", - "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014", - ], - }, - "synonyms": [ { "pred": "hasExactSynonym", - "val": "DsrA RNA", + "val": "snRNA U5", + "xrefs": [ + "RSC:cb", + ], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/DsrA_RNA", + "val": "http://en.wikipedia.org/wiki/U5_snRNA", }, ], }, @@ -15369,67 +24695,71 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000384", - "oxys", - "rna", + "so:0002338", + "u7", + "snrna", "small", - "untranslated", - "induced", - "response", - "oxidative", - "stress", - "escherichia", - "coli", - "acts", - "global", - "regulator", - "activate", - "repress", - "expression", - "many", - "40", - "genes", - "including", - "fhla", - "encoded", - "transcriptional", - "activator", - "rpos", - "sigma", - "subunit", - "polymerase", - "bound", - "hfq", - "protein", - "increases", - "interaction", - "target", - "messages", + "nuclear", + "rna", + "57", + "71", + "nucleotide", + "component", + "ribonucleoprotein", + "complex", + "snrnp", + "required", + "histone", + "pre", + "mrna", + "processing", ], - "id": "http://purl.obolibrary.org/obo/SO_0000384", - "lbl": "OxyS_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0002338", + "lbl": "U7_snRNA", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-04-24T16:59:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Added as a request from FlyBase. See GitHub Issue #508", ], "definition": { - "val": "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.", + "val": "A 57 to 71 nucleotide RNA that is a component of the U7 small nuclear ribonucleoprotein complex (U7 snRNP). The U7 snRNP is required for histone pre-mRNA processing.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035", + "PMID:15526162", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "OxyS RNA", + "val": "U7 snRNA", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/OxyS_RNA", + "pred": "hasExactSynonym", + "val": "small nuclear RNA U7", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "U7 small nuclear RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "snRNA U7", + "xrefs": [], }, ], }, @@ -15437,65 +24767,37 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000387", - "rpra", + "so:0000396", + "u6", + "snrna", + "small", + "nuclear", "rna", - "translational", - "regulation", - "stationary", - "phase", - "sigma", - "factor", - "rpos", - "mediated", - "formation", - "double", - "stranded", + "component", + "spliceosome", + "involved", + "splicing", + "pre", + "mrna", + "putative", + "secondary", + "structure", + "consensus", + "base", + "pairing", + "confined", + "short", "stem", "loop", - "structure", - "upstream", - "region", - "messenger", - "occluding", - "translation", - "initiation", - "site", - "clones", - "carrying", - "regulator", - "increased", - "gene", - "encodes", - "106", - "nucleotide", - "regulatory", - "dsra", - "rfam:rf00014", - "predicted", + "thought", "form", - "three", - "loops", - "thus", - "least", - "two", - "small", - "rnas", - "participate", - "positive", - "unlike", "extensive", - "complementarity", - "leader", - "leaving", - "mechanism", - "action", - "unclear", - "non", - "essential", + "pair", + "interactions", + "u4", ], - "id": "http://purl.obolibrary.org/obo/SO_0000387", - "lbl": "RprA_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000396", + "lbl": "U6_snRNA", "meta": { "basicPropertyValues": [ { @@ -15504,20 +24806,45 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.", + "val": "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "RprA RNA", + "val": "U6 small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "U6 snRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "snRNA U6", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "small nuclear RNA U6", + "xrefs": [ + "RSC:cb", + ], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/RprA_RNA", + "val": "http://en.wikipedia.org/wiki/U6_snRNA", }, ], }, @@ -15525,38 +24852,41 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000388", - "rre", + "so:0000393", + "u4", + "snrna", + "small", + "nuclear", "rna", - "rev", - "response", - "element", - "encoded", - "within", - "hiv", - "env", - "gene", - "essential", - "regulatory", + "component", + "major", + "u2", + "dependent", + "spliceosome", + "forms", + "duplex", + "u6", + "splicing", + "round", + "displaced", + "atp", + "manner", + "allowing", + "refold", + "create", + "active", + "site", + "catalysis", + "recycling", + "process", + "involving", "protein", - "binds", - "internal", - "loop", - "leading", - "encouraging", - "binding", - "rnp", - "complex", - "critical", - "mrna", - "export", - "hence", - "expression", - "structural", - "proteins", + "prp24", + "re", + "anneals", ], - "id": "http://purl.obolibrary.org/obo/SO_0000388", - "lbl": "RRE_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000393", + "lbl": "U4_snRNA", "meta": { "basicPropertyValues": [ { @@ -15565,15 +24895,45 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.", + "val": "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "RRE RNA", + "val": "small nuclear RNA U4", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "U4 snRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "U4 small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "snRNA U4", + "xrefs": [ + "RSC:cb", + ], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/U4_snRNA", }, ], }, @@ -15581,28 +24941,29 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000389", - "spot", - "42", + "so:0000394", + "u4atac", + "snrna", + "small", + "nuclear", "rna", - "109", - "nucleotide", - "e", - "coli", - "seems", - "regulatory", - "role", - "galactose", - "operon", - "changes", - "levels", - "implicated", - "affecting", - "dna", - "polymerase", + "required", + "splicing", + "minor", + "u12", + "dependent", + "class", + "eukaryotic", + "introns", + "forms", + "base", + "paired", + "complex", + "u6atac", + "so:0000397", ], - "id": "http://purl.obolibrary.org/obo/SO_0000389", - "lbl": "spot_42_RNA", + "id": "http://purl.obolibrary.org/obo/SO_0000394", + "lbl": "U4atac_snRNA", "meta": { "basicPropertyValues": [ { @@ -15611,20 +24972,40 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.", + "val": "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021", + "PMID:12409455", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "spot-42 RNA", + "val": "U4atac snRNA", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Spot_42_RNA", + "pred": "hasExactSynonym", + "val": "snRNA U4atac", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "small nuclear RNA U4atac", + "xrefs": [ + "RSC:cb", + ], + }, + { + "pred": "hasExactSynonym", + "val": "U4atac small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], }, ], }, @@ -15632,57 +25013,62 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000584", - "tmrna", - "insdc", - "feature:tmrna", - "10sa", + "so:0000391", + "u1", + "snrna", + "small", + "nuclear", "rna", - "ssra", - "liberates", + "component", + "spliceosome", + "involved", + "pre", "mrna", - "stalled", - "ribosome", - "accomplish", - "part", - "used", - "reading", - "frame", - "ends", - "translation", - "stop", - "signal", - "broken", - "replaced", - "leads", - "addition", - "proteolysis", - "tag", - "incomplete", - "protein", - "enabling", - "recognition", - "protease", - "recently", - "number", - "permuted", - "tmrnas", - "genes", - "found", - "encoded", - "two", - "parts", - "identified", - "eubacteria", - "chloroplasts", - "absent", - "archeal", - "eukaryote", - "nuclear", - "genomes", + "splicing", + "end", + "forms", + "complementary", + "base", + "pairs", + "splice", + "junction", + "thus", + "defining", + "donor", + "site", + "intron", + "significant", + "differences", + "sequence", + "secondary", + "structure", + "metazoan", + "yeast", + "snrnas", + "latter", + "much", + "longer", + "568", + "nucleotides", + "compared", + "164", + "human", + "nevertheless", + "predictions", + "suggest", + "share", + "common", + "core", + "consisting", + "helices", + "ii", + "proximal", + "region", + "iii", + "iv", ], - "id": "http://purl.obolibrary.org/obo/SO_0000584", - "lbl": "tmRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000391", + "lbl": "U1_snRNA", "meta": { "basicPropertyValues": [ { @@ -15691,28 +25077,45 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.", + "val": "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "INSDC_feature:tmRNA", + "val": "snRNA U1", + "xrefs": [ + "RSC:cb", + ], }, { - "pred": "hasRelatedSynonym", - "val": "10Sa RNA", + "pred": "hasExactSynonym", + "val": "U1 small nuclear RNA", + "xrefs": [ + "RSC:cb", + ], }, { - "pred": "hasRelatedSynonym", - "val": "ssrA", + "pred": "hasExactSynonym", + "val": "U1 snRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "small nuclear RNA U1", + "xrefs": [ + "RSC:cb", + ], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/TmRNA", + "val": "http://en.wikipedia.org/wiki/U1_snRNA", }, ], }, @@ -15720,41 +25123,49 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0000646", - "sirna", - "insdc", - "feature:ncrna", - "qualifier:sirna", + "so:0000392", + "u2", + "snrna", "small", - "interfering", + "nuclear", "rna", - "molecule", - "product", - "longer", - "exogenous", - "endogenous", - "dsrna", - "either", - "bimolecular", - "duplex", - "long", + "component", + "spliceosome", + "involved", + "pre", + "mrna", + "splicing", + "complementary", + "binding", + "area", + "lying", + "towards", + "end", "hairpin", - "processed", - "via", - "dicer", - "pathway", - "numerous", - "sirnas", - "accumulate", - "strands", - "srnas", - "trigger", - "cleavage", - "target", - "molecules", + "branchpoint", + "sequence", + "bps", + "intron", + "results", + "bulging", + "unpaired", + "adenine", + "initiates", + "nucleophilic", + "attack", + "intronic", + "splice", + "site", + "thus", + "starting", + "first", + "two", + "transesterification", + "reactions", + "mediate", ], - "id": "http://purl.obolibrary.org/obo/SO_0000646", - "lbl": "siRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000392", + "lbl": "U2_snRNA", "meta": { "basicPropertyValues": [ { @@ -15763,9 +25174,9 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, ], "definition": { - "val": "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.", + "val": "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.", "xrefs": [ - "PMID:12592000", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004", ], }, "subsets": [ @@ -15773,21 +25184,35 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", + "pred": "hasExactSynonym", + "val": "snRNA U2", + "xrefs": [ + "RSC:CB", + ], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:siRNA", + "val": "U2 small nuclear RNA", + "xrefs": [ + "RSC:CB", + ], }, { "pred": "hasExactSynonym", - "val": "small interfering RNA", + "val": "small nuclear RNA U2", + "xrefs": [ + "RSC:CB", + ], + }, + { + "pred": "hasExactSynonym", + "val": "U2 snRNA", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/SiRNA", + "val": "http://en.wikipedia.org/wiki/U2_snRNA", }, ], }, @@ -15795,28 +25220,60 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0001035", - "pirna", - "insdc", - "feature:ncrna", - "qualifier:pirna", - "piwi", - "associated", - "rna", + "so:0000593", + "c", + "d", + "box", + "snorna", + "snord", + "snornas", + "also", + "contain", + "long", + "10", + "nt", + "sequences", + "complementary", + "rrna", + "boxes", + "well", + "usually", + "located", + "close", + "proximity", + "form", + "structure", + "known", + "motif", + "important", + "stability", + "processing", + "nucleolar", + "targeting", + "function", "small", - "non", - "coding", - "part", - "silencing", - "system", - "prevents", - "spreading", - "selfish", - "genetic", - "elements", + "number", + "involved", + "however", + "predicted", + "serve", + "guide", + "rnas", + "ribose", + "methylation", + "involves", + "direct", + "base", + "pairing", + "site", + "modified", + "selection", + "nucleotide", + "fixed", + "distance", ], - "id": "http://purl.obolibrary.org/obo/SO_0001035", - "lbl": "piRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000593", + "lbl": "C_D_box_snoRNA", "meta": { "basicPropertyValues": [ { @@ -15824,29 +25281,40 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` "val": "sequence", }, ], + "comments": [ + "Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577.", + ], "definition": { - "val": "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.", + "val": "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.", "xrefs": [ - "SO:ke", + "http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:ncRNA", + "pred": "hasExactSynonym", + "val": "C/D box snoRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:piRNA", + "val": "SNORD", + "xrefs": [ + "PMID:31828325", + ], }, { "pred": "hasExactSynonym", - "val": "piwi-associated RNA", + "val": "C D box snoRNA", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/PiRNA", + "pred": "hasExactSynonym", + "val": "box C/D snoRNA", + "xrefs": [], }, ], }, @@ -15854,56 +25322,94 @@ exports[`OntologyStore can query SO gene terms and parts of genes 2`] = ` }, { "fullTextWords": [ - "so:0002032", - "mor", - "microrna", - "offset", - "rna", - "non", - "coding", - "transcript", - "encoded", - "sequences", - "adjacent", - "ends", - "mir", - "encoding", - "abut", - "loop", - "precursor", - "mirna", + "so:0000594", + "h", + "aca", + "box", + "snorna", + "snora", + "members", + "family", + "contain", + "triplet", + "exactly", + "nt", + "upstream", + "end", + "hinge", + "region", + "links", + "two", + "structurally", + "similar", + "functional", + "domains", + "molecule", + "boxes", + "important", + "biosynthesis", + "function", + "snornas", + "involved", + "rrna", + "processing", + "others", + "known", + "predicted", + "participate", + "selection", + "uridine", + "nucleosides", + "converted", + "pseudouridines", + "site", + "mediated", + "direct", + "base", + "pairing", + "one", + "targeting", ], - "id": "http://purl.obolibrary.org/obo/SO_0002032", - "lbl": "moR", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T13:57:43Z", - }, + "id": "http://purl.obolibrary.org/obo/SO_0000594", + "lbl": "H_ACA_box_snoRNA", + "meta": { + "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "comments": [ - "MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do. -Requested by Thomas Desvignes, Jan 2015.", + "Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577.", ], "definition": { - "val": "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA.", + "val": "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.", "xrefs": [ - "SO:ke", + "http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "microRNA-offset RNA", + "val": "H/ACA box snoRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "H ACA box snoRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "SNORA", + "xrefs": [ + "PMID:31828325", + ], + }, + { + "pred": "hasExactSynonym", + "val": "box H/ACA snoRNA", + "xrefs": [], }, ], }, @@ -15911,32 +25417,47 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002033", - "lor", - "loop", - "origin", - "mirs", - "short", - "non", - "coding", - "transcript", - "derived", - "sequences", - "encoded", - "precursor", - "mirna", + "so:0002095", + "scarna", + "small", + "cajal", + "body", + "specific", + "rna", + "ncrna", + "demonstrated", + "function", + "guide", + "site", + "synthesis", + "o", + "ribose", + "methylated", + "nucleotides", + "pseudouridines", + "polymerase", + "ii", + "transcribed", + "u1", + "u2", + "u4", + "u5", + "spliceosomal", + "nuclear", + "rnas", + "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0002033", - "lbl": "loR", + "id": "http://purl.obolibrary.org/obo/SO_0002095", + "lbl": "scaRNA", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-05-19T13:42:45Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-01-09T14:02:02Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -15944,70 +25465,32 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "comments": [ - "MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do. -Requested by Thomas Desvignes, Jan 2015.", + "Moved from is_a ncRNA (SO:0000655) to is_a snoRNA (SO:0000275) as per request from FlyBase by Dave Sant 24 April 2021. See GitHub Issue #509.", ], "definition": { - "val": "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA.", + "val": "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs).", "xrefs": [ - "SO:ke", + "PMC:126017", + "PMID:27775477", + "PMID:28869095", + "SO:nrs", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "loop-origin miRs", - }, - ], - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0000383", - "micf", - "rna", - "non", - "translated", - "93", - "nt", - "antisense", - "binds", - "target", - "ompf", - "mrna", - "regulates", - "expression", - "inhibiting", - "translation", - "inducing", - "degradation", - "message", - ], - "id": "http://purl.obolibrary.org/obo/SO_0000383", - "lbl": "MicF_RNA", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "val": "small Cajal body specific RNA", + "xrefs": [], }, - ], - "definition": { - "val": "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.", - "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033", - ], - }, - "synonyms": [ { "pred": "hasExactSynonym", - "val": "MicF RNA", + "val": "small Cajal body-specific RNA", + "xrefs": [], }, ], "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/MicF_RNA", + "val": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/", }, ], }, @@ -16015,29 +25498,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001463", - "lincrna", - "large", - "intervening", - "non", - "coding", + "so:0000258", + "cysteinyl", + "trna", + "transfer", "rna", - "long", - "intergenic", - "transcript", - "overlap", - "within", - "start", - "end", - "genomic", - "coordinates", - "gene", - "pseudogene", - "either", - "strand", + "ribonucleic", + "acid", + "sequence", + "cysteine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0001463", - "lbl": "lincRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000258", + "lbl": "cysteinyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -16046,26 +25521,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "definition": { - "val": "Long, intervening non-coding RNA. A transcript that does not overlap within the start or end genomic coordinates of a coding gene or pseudogene on either strand.", + "val": "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.", "xrefs": [ - "PMID:19182780", - "PMID:23463798", "SO:ke", - "http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "large intervening non-coding RNA", + "val": "cysteinyl tRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "long intergenic non-coding RNA", + "val": "cysteinyl-transfer RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "long intervening non-coding RNA", + "val": "cysteinyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -16073,55 +25548,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001904", - "antisense", - "lncrna", - "natural", - "transcript", - "non", - "coding", + "so:0000259", + "glutaminyl", + "trna", + "transfer", + "ribonucleic", + "acid", "rna", - "transcribed", - "opposite", - "dna", - "strand", - "compared", - "transcripts", - "overlap", - "part", - "sense", + "sequence", + "glutamine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0001904", - "lbl": "antisense_lncRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000259", + "lbl": "glutaminyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-04-06T04:36:44Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.", + "val": "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.", "xrefs": [ - "PMID:19638999", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "natural antisense transcript", + "val": "glutaminyl-transfer ribonucleic acid", + "xrefs": [], }, { - "pred": "hasRelatedSynonym", - "val": "antisense lncRNA", + "pred": "hasExactSynonym", + "val": "glutaminyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "glutaminyl tRNA", + "xrefs": [], }, ], }, @@ -16129,67 +25598,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002131", - "sense", - "intronic", - "ncrna", - "lncrna", - "non", - "coding", + "so:0000256", + "asparaginyl", + "trna", + "transfer", "rna", - "long", - "transcript", - "found", - "within", - "intron", - "gene", - "overlap", - "exonic", + "ribonucleic", + "acid", "sequence", + "asparagine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0002131", - "lbl": "sense_intronic_ncRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000256", + "lbl": "asparaginyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:15:02Z", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "SO:0001903", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence.", + "val": "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.", "xrefs": [ - "GENECODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "sense intronic lncRNA", - }, - { - "pred": "hasExactSynonym", - "val": "sense_intronic", + "val": "asparaginyl-transfer RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense_intronic_lncRNA", + "val": "asparaginyl-transfer ribonucleic acid", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense_intronic_non-coding_RNA", + "val": "asparaginyl tRNA", + "xrefs": [], }, ], }, @@ -16197,60 +25648,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002132", - "sense", - "overlap", - "ncrna", - "lncrna", - "overlapping", - "long", - "non", - "coding", - "transcript", - "contains", - "protein", - "gene", - "within", - "intronic", + "so:0000257", + "aspartyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", "sequence", - "strand", - "exonic", + "aspartic", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0002132", - "lbl": "sense_overlap_ncRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000257", + "lbl": "aspartyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2016-08-23T16:16:13Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence.", + "val": "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.", "xrefs": [ - "GENECODE:http://www.gencodegenes.org/gencode_biotypes.html", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "sense overlap lncRNA", + "val": "aspartyl tRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense_overlap_lncRNA", + "val": "aspartyl-transfer RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "sense_overlapping", + "val": "aspartyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -16258,63 +25698,46 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001923", - "terra", - "telomeric", - "repeat", - "containing", + "so:0002129", + "mt", + "trna", + "mitochondrial", + "transfer", "rna", - "non", - "coding", - "transcript", - "derived", - "transcription", - "telomere", - "transcripts", - "contain", - "g", - "rich", - "repeats", - "tracts", - "corresponding", - "adjacent", - "subtelomeric", - "sequences", - "100", - "9000", - "bases", - "long", ], - "id": "http://purl.obolibrary.org/obo/SO_0001923", - "lbl": "TERRA", + "id": "http://purl.obolibrary.org/obo/SO_0002129", + "lbl": "mt_tRNA", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-08-23T16:10:17Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-10-31T01:06:40Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.", - ], "definition": { - "val": "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long.", + "val": "Mitochondrial transfer RNA.", "xrefs": [ - "PMID:22139915", + "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", ], }, "synonyms": [ { - "pred": "hasRelatedSynonym", - "val": "telomeric repeat containing RNA", + "pred": "hasExactSynonym", + "val": "Mt_tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "mitochondrial_tRNA", + "xrefs": [], }, ], }, @@ -16322,139 +25745,99 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001924", - "arret", - "non", - "coding", + "so:0000266", + "methionyl", + "trna", + "transfer", "rna", - "transcript", - "complementary", - "subtelomeric", - "tract", - "terra", - "devoid", - "repeats", + "ribonucleic", + "acid", + "sequence", + "methionine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0001924", - "lbl": "ARRET", + "id": "http://purl.obolibrary.org/obo/SO_0000266", + "lbl": "methionyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-10-31T01:11:49Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.", - ], "definition": { - "val": "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats.", + "val": "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.", "xrefs": [ - "PMID:2139915", + "SO:ke", ], }, - }, - "type": "CLASS", - }, - { - "fullTextWords": [ - "so:0001925", - "aria", - "non", - "coding", - "rna", - "transcript", - "derived", - "transcription", - "telomere", - "transcripts", - "consist", - "c", - "rich", - "repeats", - ], - "id": "http://purl.obolibrary.org/obo/SO_0001925", - "lbl": "ARIA", - "meta": { - "basicPropertyValues": [ + "synonyms": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "hasExactSynonym", + "val": "methionyl-transfer RNA", + "xrefs": [], }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-10-31T01:24:37Z", + "pred": "hasExactSynonym", + "val": "methionyl-transfer ribonucleic acid", + "xrefs": [], }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "hasExactSynonym", + "val": "methionyl tRNA", + "xrefs": [], }, ], - "comments": [ - "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.", - ], - "definition": { - "val": "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats.", - "xrefs": [ - "PMID:22139915", - ], - }, }, "type": "CLASS", }, { "fullTextWords": [ - "so:0001926", - "anti", - "arret", - "non", - "coding", + "so:0000267", + "phenylalanyl", + "trna", + "transfer", + "ribonucleic", + "acid", "rna", - "transcript", - "derived", - "transcription", - "telomere", - "transcripts", - "antisense", + "sequence", + "phenylalanine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0001926", - "lbl": "anti_ARRET", + "id": "http://purl.obolibrary.org/obo/SO_0000267", + "lbl": "phenylalanyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-10-31T01:40:22Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.", - ], "definition": { - "val": "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts.", + "val": "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.", "xrefs": [ - "PMID:22139915", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "anti-ARRET", + "val": "phenylalanyl-transfer ribonucleic acid", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "phenylalanyl tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "phenylalanyl-transfer RNA", + "xrefs": [], }, ], }, @@ -16462,14 +25845,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000981", - "rho", - "dependent", - "bacterial", - "terminator", + "so:0000268", + "prolyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", + "sequence", + "proline", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0000981", - "lbl": "rho_dependent_bacterial_terminator", + "id": "http://purl.obolibrary.org/obo/SO_0000268", + "lbl": "prolyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -16477,10 +25867,27 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "definition": { + "val": "A tRNA sequence that has a proline anticodon, and a 3' proline binding region.", + "xrefs": [ + "SO:ke", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "rho dependent bacterial terminator", + "val": "prolyl tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "prolyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "prolyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -16488,14 +25895,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000982", - "rho", - "independent", - "bacterial", - "terminator", + "so:0000264", + "leucyl", + "trna", + "transfer", + "ribonucleic", + "acid", + "rna", + "sequence", + "leucine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0000982", - "lbl": "rho_independent_bacterial_terminator", + "id": "http://purl.obolibrary.org/obo/SO_0000264", + "lbl": "leucyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -16503,10 +25917,27 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "definition": { + "val": "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.", + "xrefs": [ + "SO:ke", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "rho independent bacterial terminator", + "val": "leucyl tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "leucyl-transfer ribonucleic acid", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "leucyl-transfer RNA", + "xrefs": [], }, ], }, @@ -16514,19 +25945,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000615", - "terminator", - "type", - "rnapol", - "iii", - "promoter", - "signal", + "so:0000265", + "lysyl", + "trna", + "transfer", "rna", - "polymerase", - "transcription", + "ribonucleic", + "acid", + "sequence", + "lysine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0000615", - "lbl": "terminator_of_type_2_RNApol_III_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000265", + "lbl": "lysyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -16535,7 +25968,7 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "definition": { - "val": "A terminator signal for RNA polymerase III transcription.", + "val": "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.", "xrefs": [ "SO:ke", ], @@ -16543,7 +25976,18 @@ Requested by Thomas Desvignes, Jan 2015.", "synonyms": [ { "pred": "hasExactSynonym", - "val": "terminator of type 2 RNApol III promoter", + "val": "lysyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "lysyl tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "lysyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -16551,36 +25995,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001671", - "bacterial", - "rnapol", - "promoter", - "sigma", - "70", + "so:0000262", + "histidyl", + "trna", + "transfer", "rna", - "polymerase", + "ribonucleic", + "acid", + "sequence", + "histidine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0001671", - "lbl": "bacterial_RNApol_promoter_sigma_70", + "id": "http://purl.obolibrary.org/obo/SO_0000262", + "lbl": "histidyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-10-06T01:41:34Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "definition": { + "val": "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.", + "xrefs": [ + "SO:ke", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "bacterial RNA polymerase promoter sigma 70", + "val": "histidyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "histidyl tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "histidyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -16588,35 +26045,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001672", - "bacterial", - "rnapol", - "promoter", - "sigma54", + "so:0000263", + "isoleucyl", + "trna", + "transfer", "rna", - "polymerase", + "ribonucleic", + "acid", + "sequence", + "isoleucine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0001672", - "lbl": "bacterial_RNApol_promoter_sigma54", + "id": "http://purl.obolibrary.org/obo/SO_0000263", + "lbl": "isoleucyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-10-06T01:42:37Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "definition": { + "val": "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.", + "xrefs": [ + "SO:ke", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "bacterial RNA polymerase promoter sigma54", + "val": "isoleucyl tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "isoleucyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "isoleucyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -16624,63 +26095,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001913", - "bacterial", - "rnapol", - "promoter", - "sigma", - "ecf", - "factor", - "binding", - "dependency", - "type", - "promoters", - "requires", - "bind", - "identified", - "10", - "35", - "sequence", - "regions", - "order", - "mediate", + "so:0000260", + "glutamyl", + "trna", + "transfer", + "ribonucleic", + "acid", "rna", - "polymerase", - "region", - "part", - "transcription", - "initiation", - ], - "id": "http://purl.obolibrary.org/obo/SO_0001913", - "lbl": "bacterial_RNApol_promoter_sigma_ecf", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2012-06-11T02:41:33Z", - }, + "sequence", + "glutamic", + "anticodon", + "binding", + "region", + ], + "id": "http://purl.obolibrary.org/obo/SO_0000260", + "lbl": "glutamyl_tRNA", + "meta": { + "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Requested by Kevin Clancy - invitrogen -May 2012.", - ], "definition": { - "val": "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation.", + "val": "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.", "xrefs": [ - "Invitrogen:kc", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "bacterial RNApol promoter sigma ecf ", + "val": "glutamyl-transfer ribonucleic acid", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "glutamyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "glutamyl tRNA", + "xrefs": [], }, ], }, @@ -16688,16 +26145,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000568", - "bidirectional", - "promoter", - "unregulated", - "allows", - "continuous", - "expression", + "so:0000261", + "glycyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", + "sequence", + "glycine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0000568", - "lbl": "bidirectional_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000261", + "lbl": "glycyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -16706,15 +26168,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "definition": { - "val": "An unregulated promoter that allows continuous expression.", + "val": "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.", "xrefs": [ "SO:ke", ], }, "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "glycyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "glycyl-transfer ribonucleic acid", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "bidirectional promoter", + "val": "glycyl tRNA", + "xrefs": [], }, ], }, @@ -16722,18 +26195,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001203", + "so:0000269", + "seryl", + "trna", + "transfer", + "ribonucleic", + "acid", "rna", - "polymerase", - "promoter", + "sequence", + "serine", + "anticodon", + "binding", "region", - "dna", - "binds", - "begin", - "transcription", ], - "id": "http://purl.obolibrary.org/obo/SO_0001203", - "lbl": "RNA_polymerase_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000269", + "lbl": "seryl_tRNA", "meta": { "basicPropertyValues": [ { @@ -16742,15 +26218,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "definition": { - "val": "A region (DNA) to which RNA polymerase binds, to begin transcription.", + "val": "A tRNA sequence that has a serine anticodon, and a 3' serine binding region.", "xrefs": [ - "xenbase:jb", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNA polymerase promoter", + "val": "seryl tRNA", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "seryl-transfer ribonucleic acid", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "seryl-transfer RNA", + "xrefs": [], }, ], }, @@ -16758,33 +26245,30 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002050", - "constitutive", - "promoter", - "allows", - "continual", - "transcription", - "gene", + "so:0000271", + "tryptophanyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", + "sequence", + "tryptophan", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0002050", - "lbl": "constitutive_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000271", + "lbl": "tryptophanyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-05-14T10:39:09Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A promoter that allows for continual transcription of gene.", + "val": "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.", "xrefs": [ "SO:ke", ], @@ -16792,7 +26276,18 @@ Requested by Thomas Desvignes, Jan 2015.", "synonyms": [ { "pred": "hasExactSynonym", - "val": "constitutive promoter", + "val": "tryptophanyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "tryptophanyl-transfer ribonucleic acid", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "tryptophanyl tRNA", + "xrefs": [], }, ], }, @@ -16800,45 +26295,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002051", - "inducible", - "promoter", - "whereby", - "activity", - "induced", - "presence", - "absence", - "biotic", - "abiotic", - "factors", + "so:0000272", + "tyrosyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", + "sequence", + "tyrosine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0002051", - "lbl": "inducible_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000272", + "lbl": "tyrosyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-05-14T10:39:56Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "definition": { - "val": "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors.", + "val": "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.", "xrefs": [ "SO:ke", ], }, "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "tyrosyl-transfer RNA", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "inducible promoter", + "val": "tyrosyl-transfer ribonucleic acid", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "tyrosyl tRNA", + "xrefs": [], }, ], }, @@ -16846,54 +26345,49 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002020", - "boundary", - "element", - "insulator", - "elements", - "dna", - "motifs", - "prevent", - "heterochromatin", - "spreading", - "neighboring", - "euchromatic", - "regions", + "so:0000270", + "threonyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", + "sequence", + "threonine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0002020", - "lbl": "boundary_element", + "id": "http://purl.obolibrary.org/obo/SO_0000270", + "lbl": "threonyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2014-05-30T14:45:37Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Requested by Antonia Lock. Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf).", - ], "definition": { - "val": "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions.", + "val": "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.", "xrefs": [ - "PMID:24013502", + "SO:ke", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "boundary element", + "val": "threonyl tRNA", + "xrefs": [], }, { "pred": "hasRelatedSynonym", - "val": "insulator", + "val": "threonyl-transfer RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "threonyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -16901,73 +26395,35 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002190", - "enhancer", - "blocking", - "element", - "insdc", - "feature:regulatory", - "qualifier:enhancer", - "insulator", - "transcriptional", - "cis", - "regulatory", - "region", - "located", - "gene", - "promoter", - "prevents", - "modulating", - "expression", - "sometimes", - "referred", - "may", - "include", - "barrier", - "function", + "so:0001036", + "arginyl", + "trna", + "sequence", + "arginine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0002190", - "lbl": "enhancer_blocking_element", + "id": "http://purl.obolibrary.org/obo/SO_0001036", + "lbl": "arginyl_tRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "nicole", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2018-01-04T17:28:52Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], - "comments": [ - "Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf).", - ], "definition": { - "val": "A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator.", + "val": "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.", "xrefs": [ - "NCBI:cf", + "SO:ke", ], }, "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, - { - "pred": "hasExactSynonym", - "val": "INSDC_qualifier:enhancer_blocking_element", - }, { "pred": "hasExactSynonym", - "val": "enhancer blocking element", - }, - { - "pred": "hasRelatedSynonym", - "val": "insulator", + "val": "arginyl tRNA", + "xrefs": [], }, ], }, @@ -16975,34 +26431,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000037", - "locus", - "control", + "so:0000254", + "alanyl", + "trna", + "transfer", + "ribonucleic", + "acid", + "rna", + "sequence", + "alanine", + "anticodon", + "binding", "region", - "insdc", - "feature:regulatory", - "qualifier:locus", - "lcr", - "element", - "dna", - "includes", - "dnase", - "hypersensitive", - "sites", - "located", - "gene", - "confers", - "high", - "level", - "position", - "independent", - "copy", - "number", - "dependent", - "expression", ], - "id": "http://purl.obolibrary.org/obo/SO_0000037", - "lbl": "locus_control_region", + "id": "http://purl.obolibrary.org/obo/SO_0000254", + "lbl": "alanyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -17011,36 +26454,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "definition": { - "val": "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.", + "val": "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.", "xrefs": [ - "SO:ma", + "SO:ke", ], }, "synonyms": [ - { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", - }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:locus_control_region", + "val": "alanyl tRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "LCR", + "val": "alanyl-transfer ribonucleic acid", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "locus control region", - }, - { - "pred": "hasRelatedSynonym", - "val": "locus control element", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Locus_control_region", + "val": "alanyl-transfer RNA", + "xrefs": [], }, ], }, @@ -17048,29 +26481,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000165", - "enhancer", - "insdc", - "feature:regulatory", - "qualifier:enhancer", - "cis", - "acting", + "so:0005857", + "selenocysteinyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", "sequence", - "increases", - "utilization", - "eukaryotic", - "promoters", - "function", - "either", - "orientation", - "location", - "upstream", - "downstream", - "relative", - "promoter", + "selenocysteine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0000165", - "lbl": "enhancer", + "id": "http://purl.obolibrary.org/obo/SO_0005857", + "lbl": "selenocysteinyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -17078,31 +26503,27 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], - "comments": [ - "An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.", - ], "definition": { - "val": "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.", + "val": "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.", "xrefs": [ - "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html", + "SO:ke", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", + "pred": "hasExactSynonym", + "val": "selenocysteinyl tRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:enhancer", + "val": "selenocysteinyl-transfer RNA", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Enhancer_(genetics)", + "pred": "hasExactSynonym", + "val": "selenocysteinyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -17110,24 +26531,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000625", - "silencer", - "insdc", - "feature:regulatory", - "qualifier:silencer", - "regulatory", - "region", - "upon", + "so:0000766", + "pyrrolysyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", + "sequence", + "pyrrolysine", + "anticodon", "binding", - "transcription", - "factors", - "suppress", - "gene", - "genes", - "control", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0000625", - "lbl": "silencer", + "id": "http://purl.obolibrary.org/obo/SO_0000766", + "lbl": "pyrrolysyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -17136,27 +26554,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "definition": { - "val": "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.", + "val": "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.", "xrefs": [ "SO:ke", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { - "pred": "hasBroadSynonym", - "val": "INSDC_feature:regulatory", + "pred": "hasExactSynonym", + "val": "pyrrolysyl tRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "INSDC_qualifier:silencer", + "val": "pyrrolysyl-transfer RNA", + "xrefs": [], }, - ], - "xrefs": [ { - "val": "http://en.wikipedia.org/wiki/Silencer_(DNA)", + "pred": "hasExactSynonym", + "val": "pyrrolysyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -17164,20 +26581,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000320", - "intronic", - "splice", - "enhancer", - "sequences", - "within", - "intron", - "modulate", - "site", - "selection", - "introns", + "so:0000273", + "valyl", + "trna", + "transfer", + "rna", + "ribonucleic", + "acid", + "sequence", + "valine", + "anticodon", + "binding", + "region", ], - "id": "http://purl.obolibrary.org/obo/SO_0000320", - "lbl": "intronic_splice_enhancer", + "id": "http://purl.obolibrary.org/obo/SO_0000273", + "lbl": "valyl_tRNA", "meta": { "basicPropertyValues": [ { @@ -17186,15 +26604,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "definition": { - "val": "Sequences within the intron that modulate splice site selection for some introns.", + "val": "A tRNA sequence that has a valine anticodon, and a 3' valine binding region.", "xrefs": [ "SO:ke", ], }, "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "valyl-transfer RNA", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "intronic splice enhancer", + "val": "valyl tRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "valyl-transfer ribonucleic acid", + "xrefs": [], }, ], }, @@ -17202,41 +26631,54 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000683", - "exonic", - "splice", - "enhancer", - "splicing", - "enhancers", - "eses", - "facilitate", - "exon", - "definition", - "assisting", - "recruitment", - "factors", - "adjacent", - "intron", + "so:0002347", + "plastid", + "ssu", + "rrna", + "small", + "subunit", + "rna", + "component", + "chloroplast", + "ribosomes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000683", - "lbl": "exonic_splice_enhancer", + "id": "http://purl.obolibrary.org/obo/SO_0002347", + "lbl": "plastid_SSU_rRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-06-10T16:45:30Z", + }, + ], + "comments": [ + "Added as a request from EMBL. See GitHub Issue #493", ], "definition": { - "val": "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.", + "val": "Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes.", "xrefs": [ - "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract", + "PMID: 24572720", + "PMID:3044395", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "exonic splice enhancer", + "val": "plastid SSU rRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "plastid small subunit rRNA", + "xrefs": [], }, ], }, @@ -17244,54 +26686,54 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000407", + "so:0002348", + "plastid", + "lsu", "rrna", - "18s", - "ribosomal", - "rna", "large", - "polynucleotide", - "eukaryotes", - "functions", - "small", "subunit", - "ribosome", + "rna", + "component", + "chloroplast", + "ribosomes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000407", - "lbl": "rRNA_18S", + "id": "http://purl.obolibrary.org/obo/SO_0002348", + "lbl": "plastid_LSU_rRNA", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-06-10T16:45:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + ], + "comments": [ + "Added as a request from EMBL. See GitHub Issue #493", ], "definition": { - "val": "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.", + "val": "Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes.", "xrefs": [ - "SO:ke", + "PMID: 24572720", + "PMID:3044395", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "18S rRNA", - }, - { - "pred": "hasExactSynonym", - "val": "18S ribosomal RNA", + "val": "plastid large subunit rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "rRNA 18S", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/18S_ribosomal_RNA", + "val": "plastid LSU rRNA", + "xrefs": [], }, ], }, @@ -17299,23 +26741,19 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001000", - "rrna", - "16s", + "so:0000650", + "cytosolic", "ssu", - "rna", + "rrna", "ribosomal", - "large", - "polynucleotide", - "bacteria", - "archaea", - "functions", + "rna", "small", "subunit", - "ribosome", + "component", + "ribosomes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001000", - "lbl": "rRNA_16S", + "id": "http://purl.obolibrary.org/obo/SO_0000650", + "lbl": "cytosolic_SSU_rRNA", "meta": { "basicPropertyValues": [ { @@ -17323,8 +26761,11 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Renamed to cytosolic_SSU_rRNA from small_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.", + ], "definition": { - "val": "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.", + "val": "Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.", "xrefs": [ "SO:ke", ], @@ -17335,24 +26776,18 @@ Requested by Thomas Desvignes, Jan 2015.", "synonyms": [ { "pred": "hasExactSynonym", - "val": "16S SSU RNA", + "val": "cytosolic SSU ribosomal RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "16S ribosomal RNA", + "val": "cytosolic small subunit rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "rRNA 16S", - }, - { - "pred": "hasRelatedSynonym", - "val": "16S rRNA", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/16S_ribosomal_RNA", + "val": "cytosolic SSU rRNA", + "xrefs": [], }, ], }, @@ -17360,44 +26795,18 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000375", - "rrna", - "8s", + "so:0000651", + "cytosolic", "lsu", - "ribosomal", - "rna", - "component", + "rrna", "large", "subunit", - "eukaryotic", - "ribosome", - "transcribed", - "polymerase", - "part", - "45s", - "precursor", - "also", - "contains", - "18s", - "28s", - "functionally", - "thought", - "may", - "involved", - "translocation", - "known", - "form", - "covalent", - "linkage", - "p53", - "tumour", - "suppressor", - "protein", - "found", - "archaea", + "rna", + "component", + "ribosomes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000375", - "lbl": "rRNA_5_8S", + "id": "http://purl.obolibrary.org/obo/SO_0000651", + "lbl": "cytosolic_LSU_rRNA", "meta": { "basicPropertyValues": [ { @@ -17405,10 +26814,13 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.", + ], "definition": { - "val": "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.", + "val": "Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002", + "SO:ke", ], }, "subsets": [ @@ -17417,24 +26829,18 @@ Requested by Thomas Desvignes, Jan 2015.", "synonyms": [ { "pred": "hasExactSynonym", - "val": "5.8S LSU rRNA", + "val": "cytosolic LSU rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "5.8S rRNA", + "val": "cytosolic large subunit rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "5.8S ribosomal RNA", - }, - { - "pred": "hasExactSynonym", - "val": "rRNA 5 8S", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA", + "val": "cytosolic LSU RNA", + "xrefs": [], }, ], }, @@ -17442,85 +26848,59 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000652", + "so:0002344", + "mt", + "ssu", "rrna", - "5s", - "lsu", - "ribosomal", + "mitochondrial", + "small", + "subunit", "rna", "component", - "large", - "subunit", - "prokaryotes", - "eukaryotes", - "synthesised", - "polymerase", - "iii", - "eukaryotic", - "rrnas", - "cleaved", - "45s", - "precursor", - "xenopus", - "oocytes", - "shown", - "fingers", - "nine", - "zinc", - "finger", - "transcription", - "factor", - "tfiiia", - "bind", - "central", - "region", - "thus", - "addition", - "positively", - "regulating", - "also", - "stabilizes", - "required", + "ribosomes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000652", - "lbl": "rRNA_5S", + "id": "http://purl.obolibrary.org/obo/SO_0002344", + "lbl": "mt_SSU_rRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-06-10T16:45:30Z", + }, + ], + "comments": [ + "Added as a request from EMBL. See GitHub Issue #493", ], "definition": { - "val": "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.", + "val": "Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001", + "PMID: 24572720", + "PMID:3044395", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "5S LSU rRNA", - }, - { - "pred": "hasExactSynonym", - "val": "5S rRNA", + "val": "mitochondrial small subunit rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "5S ribosomal RNA", + "val": "MT SSU rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "rRNA 5S", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/5S_ribosomal_RNA", + "val": "mitochondrial SSU rRNA", + "xrefs": [], }, ], }, @@ -17528,55 +26908,59 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000653", - "rrna", - "28s", + "so:0002345", + "mt", "lsu", - "ribosomal", - "rna", - "component", + "rrna", + "mitochondrial", "large", "subunit", + "rna", + "component", + "ribosomes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000653", - "lbl": "rRNA_28S", + "id": "http://purl.obolibrary.org/obo/SO_0002345", + "lbl": "mt_LSU_rRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-06-10T16:45:30Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as a request from EMBL. See GitHub Issue #493", + ], "definition": { - "val": "A component of the large ribosomal subunit.", + "val": "Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes.", "xrefs": [ - "SO:ke", + "PMID: 24572720", + "PMID:3044395", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "28S LSU rRNA", - }, - { - "pred": "hasExactSynonym", - "val": "28S rRNA", + "val": "mitochondrial LSU rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "28S ribosomal RNA", + "val": "MT LSU rRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "rRNA 28S", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/28S_ribosomal_RNA", + "val": "mitochondrial large subunit rRNA", + "xrefs": [], }, ], }, @@ -17584,54 +26968,43 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001001", - "rrna", - "23s", - "lsu", - "ribosomal", + "so:0002231", + "self", + "cleaving", + "ribozyme", "rna", - "large", - "polynucleotide", - "bacteria", - "archaea", - "functions", - "subunit", - "ribosome", + "catalyzes", + "cleavage", ], - "id": "http://purl.obolibrary.org/obo/SO_0001001", - "lbl": "rRNA_23S", + "id": "http://purl.obolibrary.org/obo/SO_0002231", + "lbl": "self_cleaving_ribozyme", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "definition": { - "val": "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.", - "xrefs": [ - "SO:ke", - ], - }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], - "synonyms": [ { - "pred": "hasExactSynonym", - "val": "23S LSU rRNA", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2020-03-30T16:02:30Z", }, { - "pred": "hasExactSynonym", - "val": "23S rRNA", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", }, + ], + "comments": [ + "Added as per request by John T. Sexton GitHub issue #470 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/470)", + ], + "definition": { + "val": "An RNA that catalyzes its own cleavage.", + "xrefs": [], + }, + "synonyms": [ { "pred": "hasExactSynonym", - "val": "rRNA 23S", - }, - { - "pred": "hasRelatedSynonym", - "val": "23S ribosomal RNA", + "val": "self cleaving ribozyme", + "xrefs": [], }, ], }, @@ -17639,54 +27012,65 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001002", - "rrna", - "25s", - "lsu", - "ribosomal", - "rna", - "large", - "polynucleotide", - "functions", - "part", - "subunit", - "ribosome", - "eukaryotes", + "so:0002145", + "h2azk4", + "acetylation", + "site", + "h2a", + "zk4ac", + "h2azk4ac", + "kind", + "histone", + "modification", + "whereby", + "4th", + "residue", + "lysine", + "start", + "h2az", + "protein", + "acetylated", ], - "id": "http://purl.obolibrary.org/obo/SO_0001002", - "lbl": "rRNA_25S", + "id": "http://purl.obolibrary.org/obo/SO_0002145", + "lbl": "H2AZK4_acetylation_site", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-10-25T14:19:43Z", + }, ], "definition": { - "val": "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.", + "val": "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated.", "xrefs": [ - "RSC:cb", + "PMID:19385636", + "PMID:24316985", + "PMID:27087541", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "25S LSU rRNA", + "val": "H2A.ZK4ac", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "25S rRNA", + "val": "H2AZK4 acetylation site", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "25S ribosomal RNA", - }, - { - "pred": "hasExactSynonym", - "val": "rRNA 25S", + "val": "H2AZK4ac", + "xrefs": [], }, ], }, @@ -17694,48 +27078,65 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001171", - "rrna", - "21s", - "lsu", - "ribosomal", - "rna", - "component", - "large", - "subunit", - "mitochondrial", + "so:0002149", + "h2azk15", + "acetylation", + "site", + "h2azk15ac", + "h2a", + "zk15ac", + "kind", + "histone", + "modification", + "whereby", + "15th", + "residue", + "lysine", + "start", + "h2az", + "protein", + "acetylated", ], - "id": "http://purl.obolibrary.org/obo/SO_0001171", - "lbl": "rRNA_21S", + "id": "http://purl.obolibrary.org/obo/SO_0002149", + "lbl": "H2AZK15_acetylation_site", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-10-25T14:24:08Z", + }, ], "definition": { - "val": "A component of the large ribosomal subunit in mitochondrial rRNA.", + "val": "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated.", "xrefs": [ - "RSC:cb", + "PMID:19385636", + "PMID:24316985", + "PMID:27087541", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "21S LSU rRNA", + "val": "H2AZK15 acetylation site", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "21S rRNA", + "val": "H2AZK15ac", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "21S ribosomal RNA", - }, - { - "pred": "hasExactSynonym", - "val": "rRNA 21S", + "val": "H2A.ZK15ac", + "xrefs": [], }, ], }, @@ -17743,81 +27144,65 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000403", - "u14", - "snorna", - "small", - "nucleolar", - "rna", - "required", - "early", - "cleavages", - "eukaryotic", - "precursor", - "rrnas", - "yeasts", - "molecule", - "possess", - "stem", - "loop", - "region", - "known", - "y", - "domain", - "essential", - "function", - "similar", - "structure", - "different", - "consensus", - "sequence", - "found", - "plants", - "absent", - "vertebrates", + "so:0002147", + "h2azk11", + "acetylation", + "site", + "h2azk11ac", + "h2a", + "zk11ac", + "kind", + "histone", + "modification", + "whereby", + "11th", + "residue", + "lysine", + "start", + "h2az", + "protein", + "acetylated", ], - "id": "http://purl.obolibrary.org/obo/SO_0000403", - "lbl": "U14_snoRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002147", + "lbl": "H2AZK11_acetylation_site", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "SO:0005839", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "comments": [ - "An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.", + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-10-25T14:23:31Z", + }, ], "definition": { - "val": "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.", + "val": "A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated.", "xrefs": [ - "PMID:2551119", - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016", + "PMID:19385636", + "PMID:24316985", + "PMID:27087541", ], }, - "subsets": [ - "http://purl.obolibrary.org/obo/so#SOFA", - ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "U14 small nucleolar RNA", - }, - { - "pred": "hasExactSynonym", - "val": "U14 snoRNA", + "val": "H2AZK11 acetylation site", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small nucleolar RNA U14", + "val": "H2AZK11ac", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snoRNA U14", + "val": "H2A.ZK11ac", + "xrefs": [], }, ], }, @@ -17825,102 +27210,65 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001179", - "u3", - "snorna", - "small", - "nucleolar", - "rna", - "member", - "box", - "c", - "d", - "class", - "rnas", - "secondary", - "structure", - "characterised", - "domain", - "boxes", - "larger", - "b", - "two", - "domains", - "linked", - "single", - "stranded", - "hinge", - "form", - "motif", - "appears", - "exclusive", - "snornas", - "latter", - "functionally", - "similar", - "motifs", - "found", - "region", - "act", - "pre", - "rrna", - "binding", - "conserved", + "so:0002146", + "h2azk7", + "acetylation", + "site", + "h2a", + "zk7ac", + "h2azk7ac", + "kind", + "histone", + "modification", + "whereby", + "7th", + "residue", + "lysine", + "start", + "h2az", "protein", - "sites", - "sufficient", - "nuclear", - "retention", - "also", - "necessary", - "localization", - "stability", - "hypermethylation", - "involved", - "specific", - "interactions", - "processing", - "functions", + "acetylated", ], - "id": "http://purl.obolibrary.org/obo/SO_0001179", - "lbl": "U3_snoRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002146", + "lbl": "H2AZK7_acetylation_site", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-10-25T14:23:11Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "comments": [ - "The definition is most of the old definition for snoRNA (SO:0000275).", + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, ], "definition": { - "val": "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.", + "val": "A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated.", "xrefs": [ - "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012", + "PMID:19385636", + "PMID:24316985", + "PMID:27087541", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "U3 small nucleolar RNA", - }, - { - "pred": "hasExactSynonym", - "val": "U3 snoRNA", + "val": "H2A.ZK7ac", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "small nucleolar RNA U3", + "val": "H2AZK7ac", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "snoRNA U3", - }, - ], - "xrefs": [ - { - "val": "http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3", + "val": "H2AZK7 acetylation site", + "xrefs": [], }, ], }, @@ -17928,47 +27276,65 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0005841", - "methylation", - "guide", - "snorna", - "specifies", + "so:0002148", + "h2azk13", + "acetylation", "site", - "o", - "ribose", - "rna", - "molecule", - "base", - "pairing", - "short", - "sequence", - "around", - "target", + "h2azk13ac", + "h2a", + "zk13ac", + "kind", + "histone", + "modification", + "whereby", + "13th", "residue", + "lysine", + "start", + "h2az", + "protein", + "acetylated", ], - "id": "http://purl.obolibrary.org/obo/SO_0005841", - "lbl": "methylation_guide_snoRNA", + "id": "http://purl.obolibrary.org/obo/SO_0002148", + "lbl": "H2AZK13_acetylation_site", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2016-10-25T14:23:50Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, - ], - "comments": [ - "Has RNA 2'-O-ribose methylation guide activity (GO:0030561).", + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "nicole", + }, ], "definition": { - "val": "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.", + "val": "A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated.", "xrefs": [ - "GOC:mah", - "PMID:12457565", + "PMID:19385636", + "PMID:24316985", + "PMID:27087541", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "methylation guide snoRNA", + "val": "H2AZK13ac", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "H2AZK13 acetylation site", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "H2A.ZK13ac", + "xrefs": [], }, ], }, @@ -17976,24 +27342,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001187", - "pseudouridylation", - "guide", - "snorna", - "specifies", - "site", + "so:0000454", + "rasirna", + "insdc", + "feature:ncrna", + "repeat", + "associated", + "small", + "interfering", "rna", - "molecule", - "base", - "pairing", - "short", - "sequence", - "around", - "target", - "residue", + "qualifier:rasirna", + "17", + "28", + "nt", + "derived", + "transcripts", + "repetitive", + "elements", ], - "id": "http://purl.obolibrary.org/obo/SO_0001187", - "lbl": "pseudouridylation_guide_snoRNA", + "id": "http://purl.obolibrary.org/obo/SO_0000454", + "lbl": "rasiRNA", "meta": { "basicPropertyValues": [ { @@ -18002,19 +27370,33 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "comments": [ - "Has RNA pseudouridylation guide activity (GO:0030558).", + "Changed parent term from ncRNA (SO:0000655) to piRNA (SO:0001035). See GitHub Issue #573.", ], "definition": { - "val": "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.", + "val": "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.", "xrefs": [ - "GOC:mah", - "PMID:12457565", + "PMID:18032451", + "http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ + { + "pred": "hasBroadSynonym", + "val": "INSDC_feature:ncRNA", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "pseudouridylation guide snoRNA", + "val": "repeat associated small interfering RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "INSDC_qualifier:rasiRNA", + "xrefs": [], }, ], }, @@ -18075,15 +27457,18 @@ Requested by Thomas Desvignes, Jan 2015.", "synonyms": [ { "pred": "hasExactSynonym", - "val": "RefSeq miRNA", + "val": "RefSeq-miRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "RefSeq-miRNA", + "val": "RefSeq miRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", "val": "ref miRNA", + "xrefs": [], }, ], }, @@ -18116,14 +27501,14 @@ Requested by Thomas Desvignes, Jan 2015.", "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "nicole", }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-06-22T11:09:42Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2017-06-22T11:09:42Z", + }, ], "definition": { "val": "IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA.", @@ -18169,6 +27554,7 @@ Requested by Thomas Desvignes, Jan 2015.", { "pred": "hasExactSynonym", "val": "GcvB RNA", + "xrefs": [], }, ], "xrefs": [ @@ -18181,21 +27567,65 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000169", - "rnapol", - "promoter", + "so:0001179", + "u3", + "snorna", + "small", + "nucleolar", "rna", - "polymerase", - "pol", - "dna", - "sequence", - "eukaryotic", - "binds", - "begin", - "transcription", + "member", + "box", + "c", + "d", + "class", + "rnas", + "secondary", + "structure", + "characterised", + "domain", + "boxes", + "larger", + "b", + "two", + "domains", + "linked", + "single", + "stranded", + "hinge", + "form", + "motif", + "appears", + "exclusive", + "snornas", + "latter", + "functionally", + "similar", + "motifs", + "found", + "region", + "act", + "pre", + "rrna", + "binding", + "conserved", + "protein", + "sites", + "sufficient", + "nuclear", + "retention", + "also", + "necessary", + "localization", + "stability", + "hypermethylation", + "involved", + "specific", + "interactions", + "processing", + "functions", ], - "id": "http://purl.obolibrary.org/obo/SO_0000169", - "lbl": "RNApol_I_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0001179", + "lbl": "U3_snoRNA", "meta": { "basicPropertyValues": [ { @@ -18203,28 +27633,40 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "The definition is most of the old definition for snoRNA (SO:0000275).", + ], "definition": { - "val": "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.", + "val": "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.", "xrefs": [ - "SO:ke", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNA polymerase A promoter", + "val": "U3 small nucleolar RNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "RNApol I promoter", + "val": "U3 snoRNA", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "pol I promoter", + "val": "snoRNA U3", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "polymerase I promoter", + "val": "small nucleolar RNA U3", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3", }, ], }, @@ -18232,52 +27674,85 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000170", - "rnapol", - "ii", - "promoter", + "so:0000403", + "u14", + "snorna", + "small", + "nucleolar", "rna", - "polymerase", - "b", - "pol", - "dna", - "sequence", + "required", + "early", + "cleavages", "eukaryotic", - "binds", - "begin", - "transcription", + "precursor", + "rrnas", + "yeasts", + "molecule", + "possess", + "stem", + "loop", + "region", + "known", + "y", + "domain", + "essential", + "function", + "similar", + "structure", + "different", + "consensus", + "sequence", + "found", + "plants", + "absent", + "vertebrates", ], - "id": "http://purl.obolibrary.org/obo/SO_0000170", - "lbl": "RNApol_II_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000403", + "lbl": "U14_snoRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val": "SO:0005839", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.", + ], "definition": { - "val": "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.", + "val": "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.", "xrefs": [ - "SO:ke", + "PMID:2551119", + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNA polymerase B promoter", + "val": "snoRNA U14", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "RNApol II promoter", + "val": "small nucleolar RNA U14", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "polymerase II promoter", + "val": "U14 small nucleolar RNA", + "xrefs": [], }, { - "pred": "hasRelatedSynonym", - "val": "pol II promoter", + "pred": "hasExactSynonym", + "val": "U14 snoRNA", + "xrefs": [], }, ], }, @@ -18285,23 +27760,26 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000171", - "rnapol", - "iii", - "promoter", + "so:0005841", + "methylation", + "guide", + "snorna", + "specifies", + "site", + "o", + "ribose", "rna", - "polymerase", - "c", - "pol", - "dna", + "molecule", + "base", + "pairing", + "short", "sequence", - "eukaryotic", - "binds", - "begin", - "transcription", + "around", + "target", + "residue", ], - "id": "http://purl.obolibrary.org/obo/SO_0000171", - "lbl": "RNApol_III_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0005841", + "lbl": "methylation_guide_snoRNA", "meta": { "basicPropertyValues": [ { @@ -18309,28 +27787,21 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Has RNA 2'-O-ribose methylation guide activity (GO:0030561).", + ], "definition": { - "val": "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.", + "val": "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.", "xrefs": [ - "SO:ke", + "GOC:mah", + "PMID:12457565", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNA polymerase C promoter", - }, - { - "pred": "hasExactSynonym", - "val": "RNApol III promoter", - }, - { - "pred": "hasExactSynonym", - "val": "pol III promoter", - }, - { - "pred": "hasExactSynonym", - "val": "polymerase III promoter", + "val": "methylation guide snoRNA", + "xrefs": [], }, ], }, @@ -18338,20 +27809,24 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001204", - "phage", + "so:0001187", + "pseudouridylation", + "guide", + "snorna", + "specifies", + "site", "rna", - "polymerase", - "promoter", - "region", - "dna", - "bacteriophage", - "binds", - "begin", - "transcription", + "molecule", + "base", + "pairing", + "short", + "sequence", + "around", + "target", + "residue", ], - "id": "http://purl.obolibrary.org/obo/SO_0001204", - "lbl": "Phage_RNA_Polymerase_Promoter", + "id": "http://purl.obolibrary.org/obo/SO_0001187", + "lbl": "pseudouridylation_guide_snoRNA", "meta": { "basicPropertyValues": [ { @@ -18359,16 +27834,21 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Has RNA pseudouridylation guide activity (GO:0030558).", + ], "definition": { - "val": "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.", + "val": "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.", "xrefs": [ - "xenbase:jb", + "GOC:mah", + "PMID:12457565", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "Phage RNA Polymerase Promoter", + "val": "pseudouridylation guide snoRNA", + "xrefs": [], }, ], }, @@ -18376,30 +27856,50 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000166", - "enhancer", - "bound", - "factor", + "so:0002369", + "c", + "d", + "box", + "scarna", + "possessing", + "sequence", + "motif", + "guiding", + "methylation", + "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0000166", - "lbl": "enhancer_bound_by_factor", + "id": "http://purl.obolibrary.org/obo/SO_0002369", + "lbl": "C_D_box_scaRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:34:44Z", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", + ], "definition": { - "val": "An enhancer bound by a factor.", + "val": "A scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs.", "xrefs": [ - "SO:xp", + "PMID:17099227", + "PMID:24659245", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "enhancer bound by factor", + "val": "C/D scaRNA", + "xrefs": [], }, ], }, @@ -18407,31 +27907,53 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001482", - "shadow", - "enhancer", + "so:0002371", + "c", + "d", + "h", + "aca", + "box", + "scarna", + "possessing", + "sequence", + "motifs", + "guiding", + "methylation", + "pseudouridylation", + "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0001482", - "lbl": "shadow_enhancer", + "id": "http://purl.obolibrary.org/obo/SO_0002371", + "lbl": "C-D_H_ACA_box_scaRNA", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "sequence", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2009-09-09T05:29:29Z", + "val": "2021-11-19T05:35:23Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "sequence", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", }, ], + "comments": [ + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", + ], + "definition": { + "val": "A scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs.", + "xrefs": [ + "PMID:17099227", + "PMID:24659245", + ], + }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "shadow enhancer", + "val": "C/D-H/ACA scaRNA", + "xrefs": [], }, ], }, @@ -18439,35 +27961,29 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002056", - "intronic", - "splicing", - "silencer", - "iss", - "regulatory", - "element", - "functions", - "recruit", - "trans", - "acting", - "factors", - "suppress", - "transcription", - "gene", - "genes", - "control", + "so:0002370", + "h", + "aca", + "box", + "scarna", + "possessing", + "sequence", + "motif", + "guiding", + "pseudouridylation", + "snrnas", ], - "id": "http://purl.obolibrary.org/obo/SO_0002056", - "lbl": "intronic_splicing_silencer", + "id": "http://purl.obolibrary.org/obo/SO_0002370", + "lbl": "H_ACA_box_scaRNA", "meta": { "basicPropertyValues": [ { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-11-19T05:35:04Z", }, { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-05-14T12:24:10Z", + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "evan", }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18475,23 +27991,20 @@ Requested by Thomas Desvignes, Jan 2015.", }, ], "comments": [ - "Requested by Javier Diez Perez.", + "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).", ], "definition": { - "val": "An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.", + "val": "A scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs.", "xrefs": [ - "PMID:23241926", - "SO:ke", + "PMID:17099227", + "PMID:24659245", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "ISS", - }, - { - "pred": "hasExactSynonym", - "val": "intronic splicing silencer", + "val": "H/ACA scaRNA", + "xrefs": [], }, ], }, @@ -18499,59 +28012,65 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0002058", - "exonic", - "splicing", - "silencer", - "ess", - "regulatory", - "element", - "functions", - "recruit", - "trans", - "acting", - "factors", - "suppress", - "transcription", - "gene", - "genes", - "control", + "so:0001000", + "cytosolic", + "16s", + "rrna", + "ssu", + "rna", + "ribosomal", + "component", + "small", + "subunit", + "ribosomes", + "prokaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0002058", - "lbl": "exonic_splicing_silencer", + "id": "http://purl.obolibrary.org/obo/SO_0001000", + "lbl": "cytosolic_16S_rRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2015-05-14T12:42:12Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], "comments": [ - "Requested by Javier Diez Perez.", + "Renamed to cytosolic_16S_rRNA from rRNA_16S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.", ], "definition": { - "val": "An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.", + "val": "Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.", "xrefs": [ - "PMID:23241926", "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ + { + "pred": "hasRelatedSynonym", + "val": "cytosolic 16S rRNA", + "xrefs": [], + }, { "pred": "hasExactSynonym", - "val": "ESS", + "val": "cytosolic rRNA 16S", + "xrefs": [], }, { "pred": "hasExactSynonym", - "val": "exonic splicing silencer", + "val": "cytosolic 16S SSU RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 16S ribosomal RNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/16S_ribosomal_RNA", }, ], }, @@ -18559,49 +28078,59 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001669", - "rnapol", - "ii", - "core", - "promoter", - "minimal", - "portion", - "required", - "properly", - "initiate", - "transcription", + "so:0000407", + "cytosolic", + "18s", + "rrna", + "ribosomal", "rna", - "polymerase", - "transcribed", - "genes", + "component", + "small", + "subunit", + "ribosomes", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001669", - "lbl": "RNApol_II_core_promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000407", + "lbl": "cytosolic_18S_rRNA", "meta": { "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "kareneilbeck", - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2010-10-01T03:13:41Z", - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Renamed to cytosolic_18S_rRNA from rRNA_18S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.", + ], "definition": { - "val": "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.", + "val": "Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.", "xrefs": [ - "PMID:16858867", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNApol II core promoter", + "val": "cytosolic rRNA 18S", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 18S ribosomal RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 18S rRNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/18S_ribosomal_RNA", }, ], }, @@ -18609,14 +28138,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000617", - "rnapol", - "iii", - "promoter", - "type", + "so:0001002", + "cytosolic", + "25s", + "rrna", + "lsu", + "ribosomal", + "rna", + "component", + "large", + "subunit", + "ribosomes", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000617", - "lbl": "RNApol_III_promoter_type_1", + "id": "http://purl.obolibrary.org/obo/SO_0001002", + "lbl": "cytosolic_25S_rRNA", "meta": { "basicPropertyValues": [ { @@ -18624,10 +28160,40 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.", + ], + "definition": { + "val": "Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes.", + "xrefs": [ + "PMID:15493135", + "PMID:2100998", + "RSC:cb", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNApol III promoter type 1", + "val": "cytosolic 25S LSU rRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic rRNA 25S", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 25S rRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 25S ribosomal RNA", + "xrefs": [], }, ], }, @@ -18635,15 +28201,22 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000618", - "rnapol", - "iii", - "promoter", - "type", - "trna", + "so:0000652", + "cytosolic", + "5s", + "rrna", + "ribosomal", + "rna", + "lsu", + "component", + "large", + "subunit", + "ribosomes", + "prokaryotes", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000618", - "lbl": "RNApol_III_promoter_type_2", + "id": "http://purl.obolibrary.org/obo/SO_0000652", + "lbl": "cytosolic_5S_rRNA", "meta": { "basicPropertyValues": [ { @@ -18651,14 +28224,43 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.", + ], + "definition": { + "val": "Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes.", + "xrefs": [ + "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNApol III promoter type 2", + "val": "cytosolic 5S ribosomal RNA", + "xrefs": [], }, { - "pred": "hasRelatedSynonym", - "val": "tRNA promoter", + "pred": "hasExactSynonym", + "val": "cytosolic 5S rRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic rRNA 5S", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 5S LSU rRNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/5S_ribosomal_RNA", }, ], }, @@ -18666,14 +28268,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0000621", - "rnapol", - "iii", - "promoter", - "type", + "so:0001001", + "cytosolic", + "23s", + "rrna", + "lsu", + "ribosomal", + "rna", + "component", + "large", + "subunit", + "ribosomes", + "prokaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0000621", - "lbl": "RNApol_III_promoter_type_3", + "id": "http://purl.obolibrary.org/obo/SO_0001001", + "lbl": "cytosolic_23S_rRNA", "meta": { "basicPropertyValues": [ { @@ -18681,10 +28290,38 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.", + ], + "definition": { + "val": "Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes.", + "xrefs": [ + "SO:ke", + ], + }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "RNApol III promoter type 3", + "val": "cytosolic rRNA 23S", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 23S LSU rRNA", + "xrefs": [], + }, + { + "pred": "hasRelatedSynonym", + "val": "cytosolic 23S ribosomal RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 23S rRNA", + "xrefs": [], }, ], }, @@ -18692,19 +28329,22 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001205", - "sp6", + "so:0000653", + "cytosolic", + "28s", + "rrna", + "ribosomal", "rna", - "polymerase", - "promoter", - "region", - "dna", - "binds", - "begin", - "transcription", + "lsu", + "component", + "large", + "subunit", + "ribosomes", + "metazoan", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001205", - "lbl": "SP6_RNA_Polymerase_Promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000653", + "lbl": "cytosolic_28S_rRNA", "meta": { "basicPropertyValues": [ { @@ -18712,16 +28352,43 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.", + ], "definition": { - "val": "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.", + "val": "Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes.", "xrefs": [ - "xenbase:jb", + "SO:ke", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "SP6 RNA Polymerase Promoter", + "val": "cytosolic 28S rRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic rRNA 28S", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 28S ribosomal RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 28S LSU rRNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/28S_ribosomal_RNA", }, ], }, @@ -18729,36 +28396,83 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001206", - "t3", + "so:0002337", + "cytosolic", + "2s", + "rrna", + "30", + "nucleotide", "rna", - "polymerase", - "promoter", - "dna", - "sequence", - "binds", - "begin", - "transcription", + "component", + "large", + "subunit", + "ribosomes", + "drosophila", + "least", + "diptera", + "homologous", + "part", + "8s", + "molecules", + "end", + "molecule", + "able", + "base", + "pair", + "generate", + "helical", + "region", + "equivalent", + "position", + "gc", + "rich", + "hairpin", + "found", + "previously", + "sequenced", ], - "id": "http://purl.obolibrary.org/obo/SO_0001206", - "lbl": "T3_RNA_Polymerase_Promoter", + "id": "http://purl.obolibrary.org/obo/SO_0002337", + "lbl": "cytosolic_2S_rRNA", "meta": { "basicPropertyValues": [ + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "david", + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val": "2021-04-23T22:59:30Z", + }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "sequence", }, ], + "comments": [ + "Added as a request from FlyBase. See GitHub Issue #507. Renamed from rRNA_2S to cytosolic_2S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.", + ], "definition": { - "val": "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.", + "val": "Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules.", "xrefs": [ - "xenbase:jb", + "PMID: 118436", + "PMID: 29474379", + "PMID: 3136294", + "PMID:10788608", + "PMID:407103", + "PMID:4847940", + "PMID:768488", ], }, "synonyms": [ { "pred": "hasExactSynonym", - "val": "T3 RNA Polymerase Promoter", + "val": "cytosolic rRNA 2S", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 2S rRNA", + "xrefs": [], }, ], }, @@ -18766,19 +28480,21 @@ Requested by Thomas Desvignes, Jan 2015.", }, { "fullTextWords": [ - "so:0001207", - "t7", + "so:0000375", + "cytosolic", + "8s", + "rrna", + "lsu", + "ribosomal", "rna", - "polymerase", - "promoter", - "region", - "dna", - "binds", - "begin", - "transcription", + "component", + "large", + "subunit", + "ribosomes", + "eukaryotes", ], - "id": "http://purl.obolibrary.org/obo/SO_0001207", - "lbl": "T7_RNA_Polymerase_Promoter", + "id": "http://purl.obolibrary.org/obo/SO_0000375", + "lbl": "cytosolic_5_8S_rRNA", "meta": { "basicPropertyValues": [ { @@ -18786,16 +28502,43 @@ Requested by Thomas Desvignes, Jan 2015.", "val": "sequence", }, ], + "comments": [ + "Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.", + ], "definition": { - "val": "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.", + "val": "Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.", "xrefs": [ - "xenbase:jb", + "https://rfam.xfam.org/family/RF00002", ], }, + "subsets": [ + "http://purl.obolibrary.org/obo/so#SOFA", + ], "synonyms": [ { "pred": "hasExactSynonym", - "val": "T7 RNA Polymerase Promoter", + "val": "cytosolic rRNA 5 8S", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 5.8S LSU rRNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 5.8S ribosomal RNA", + "xrefs": [], + }, + { + "pred": "hasExactSynonym", + "val": "cytosolic 5.8S rRNA", + "xrefs": [], + }, + ], + "xrefs": [ + { + "val": "http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA", }, ], }, diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts index 8c9d05440..c93aaee18 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts @@ -37,7 +37,10 @@ jest.mock('jsonpath', () => { let so: OntologyStore beforeAll(async () => { - const localPath = path.resolve(__dirname, '../../../test_data/so-v3.1.json') + const localPath = path.resolve( + __dirname, + '../../../test_data/so-2024-11-18.json', + ) so = new OntologyStore( 'Sequence Ontology', 'automated testing', diff --git a/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts b/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts index f7d8b4052..067fa8978 100644 --- a/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts +++ b/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts @@ -1,5 +1,6 @@ import { type AnnotationFeature, + type Children, type TranscriptPartCoding, } from '@apollo-annotation/mst' import { type BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes' @@ -62,6 +63,20 @@ export function selectFeatureAndOpenWidget( } } +export function isGeneFeature( + feature: AnnotationFeature, + session: ApolloSessionModel, +): boolean { + const { featureTypeOntology } = session.apolloDataStore.ontologyManager + if (!featureTypeOntology) { + throw new Error('featureTypeOntology is undefined') + } + return ( + featureTypeOntology.isTypeOf(feature.type, 'gene') || + featureTypeOntology.isTypeOf(feature.type, 'pseudogene') + ) +} + export function isTranscriptFeature( feature: AnnotationFeature, session: ApolloSessionModel, @@ -98,6 +113,36 @@ export function isCDSFeature( return featureTypeOntology.isTypeOf(feature.type, 'CDS') } +export function looksLikeGene( + feature: AnnotationFeature, + session: ApolloSessionModel, +) { + const { featureTypeOntology } = session.apolloDataStore.ontologyManager + if (!featureTypeOntology) { + throw new Error('featureTypeOntology is undefined') + } + const children = feature.children as Children + if (!children?.size) { + return false + } + const isGene = isGeneFeature(feature, session) + if (!isGene) { + return false + } + for (const [, child] of children) { + if (isTranscriptFeature(child, session)) { + const { children: grandChildren } = child as { children?: Children } + if (!grandChildren?.size) { + return false + } + return [...grandChildren.values()].some((grandchild) => + isExonFeature(grandchild, session), + ) + } + } + return false +} + export interface AdjacentExons { upstream: AnnotationFeature | undefined downstream: AnnotationFeature | undefined diff --git a/packages/jbrowse-plugin-apollo/test_data/glyph_types.gff3 b/packages/jbrowse-plugin-apollo/test_data/glyph_types.gff3 new file mode 100644 index 000000000..e12e1c7ea --- /dev/null +++ b/packages/jbrowse-plugin-apollo/test_data/glyph_types.gff3 @@ -0,0 +1,265 @@ +##gff-version 3 +##sequence-region 1 1 1920 +##sequence-region 2 1 3540 +##sequence-region 3 1 1200 +##sequence-region 4 1 600 +##sequence-region 5 1 2220 +##sequence-region 6 1 1020 +### +1 WormBase gene 61 1893 . + . ID=Gene:WBGene00010929;Name=WBGene00010929;locus=srt-45;sequence_name=M162.3;biotype=protein_coding;so_term_name=protein_coding_gene;curie=WB:WBGene00010929;Alias=srt-45,M162.3 +1 WormBase mRNA 61 1874 . + . ID=Transcript:M162.3a.1;Parent=Gene:WBGene00010929;Name=M162.3a.1;wormpep=CE51494;locus=srt-45;uniprot_id=Q9XUC8 +1 WormBase exon 61 406 . + . Parent=Transcript:M162.3a.1 +1 WormBase CDS 61 406 . + 0 ID=CDS:M162.3a;Parent=Transcript:M162.3a.1;Name=M162.3a;prediction_status=Predicted;wormpep=CE51494;protein_id=CAB05255.2;locus=srt-45;uniprot_id=Q9XUC8 +1 WormBase CDS 741 985 . + 2 ID=CDS:M162.3a;Parent=Transcript:M162.3a.1;Name=M162.3a;prediction_status=Predicted;wormpep=CE51494;protein_id=CAB05255.2;locus=srt-45;uniprot_id=Q9XUC8 +1 WormBase CDS 1104 1229 . + 0 ID=CDS:M162.3a;Parent=Transcript:M162.3a.1;Name=M162.3a;prediction_status=Predicted;wormpep=CE51494;protein_id=CAB05255.2;locus=srt-45;uniprot_id=Q9XUC8 +1 WormBase CDS 1567 1782 . + 0 ID=CDS:M162.3a;Parent=Transcript:M162.3a.1;Name=M162.3a;prediction_status=Predicted;wormpep=CE51494;protein_id=CAB05255.2;locus=srt-45;uniprot_id=Q9XUC8 +1 WormBase CDS 1830 1874 . + 0 ID=CDS:M162.3a;Parent=Transcript:M162.3a.1;Name=M162.3a;prediction_status=Predicted;wormpep=CE51494;protein_id=CAB05255.2;locus=srt-45;uniprot_id=Q9XUC8 +1 WormBase nc_primary_transcript 61 1893 . + . ID=Transcript:M162.3b;Parent=Gene:WBGene00010929;Name=M162.3b +1 WormBase exon 61 406 . + . Parent=Transcript:M162.3b +1 WormBase intron 407 740 . + . Parent=Transcript:M162.3a.1 +1 WormBase exon 741 985 . + . Parent=Transcript:M162.3a.1 +1 WormBase exon 741 985 . + . Parent=Transcript:M162.3b +1 WormBase intron 986 1103 . + . Parent=Transcript:M162.3a.1 +1 WormBase exon 1061 1229 . + . Parent=Transcript:M162.3b +1 WormBase exon 1104 1229 . + . Parent=Transcript:M162.3a.1 +1 WormBase intron 1230 1566 . + . Parent=Transcript:M162.3a.1 +1 WormBase exon 1567 1782 . + . Parent=Transcript:M162.3a.1 +1 WormBase exon 1567 1782 . + . Parent=Transcript:M162.3b +1 WormBase intron 1783 1829 . + . Parent=Transcript:M162.3a.1 +1 WormBase exon 1830 1874 . + . Parent=Transcript:M162.3a.1 +1 WormBase exon 1830 1893 . + . Parent=Transcript:M162.3b +### +2 WormBase pseudogene 61 3486 . + . ID=Gene:WBGene00013826;Name=WBGene00013826;interpolated_map_position=23.7297;sequence_name=Y116F11B.10;biotype=pseudogene;so_term_name=pseudogene;curie=WB:WBGene00013826;Alias=Y116F11B.10 +2 WormBase pseudogenic_transcript 61 3484 . + . ID=Pseudogene:Y116F11B.10a;Parent=Gene:WBGene00013826;Name=Y116F11B.10a +2 WormBase exon 61 156 . + . Parent=Pseudogene:Y116F11B.10a +2 WormBase pseudogenic_transcript 61 3486 . + . ID=Pseudogene:Y116F11B.10b;Parent=Gene:WBGene00013826;Name=Y116F11B.10b +2 WormBase exon 61 156 . + . Parent=Pseudogene:Y116F11B.10b +2 WormBase exon 348 539 . + . Parent=Pseudogene:Y116F11B.10a +2 WormBase exon 348 539 . + . Parent=Pseudogene:Y116F11B.10b +2 WormBase exon 587 760 . + . Parent=Pseudogene:Y116F11B.10a +2 WormBase exon 587 2720 . + . Parent=Pseudogene:Y116F11B.10b +2 WormBase exon 2775 2975 . + . Parent=Pseudogene:Y116F11B.10a +2 WormBase exon 2775 2975 . + . Parent=Pseudogene:Y116F11B.10b +2 WormBase exon 3025 3132 . + . Parent=Pseudogene:Y116F11B.10a +2 WormBase exon 3025 3132 . + . Parent=Pseudogene:Y116F11B.10b +2 WormBase exon 3185 3292 . + . Parent=Pseudogene:Y116F11B.10a +2 WormBase exon 3185 3292 . + . Parent=Pseudogene:Y116F11B.10b +2 WormBase exon 3340 3484 . + . Parent=Pseudogene:Y116F11B.10a +2 WormBase exon 3340 3486 . + . Parent=Pseudogene:Y116F11B.10b +### +3 WormBase gene 61 1144 . - . ID=Gene:WBGene00013364;Name=WBGene00013364;interpolated_map_position=23.9937;sequence_name=Y60A3A.16;biotype=protein_coding;so_term_name=protein_coding_gene;curie=WB:WBGene00013364;Alias=Y60A3A.16 +3 WormBase mRNA 61 1144 . - . ID=Transcript:Y60A3A.16.2;Parent=Gene:WBGene00013364;Name=Y60A3A.16.2;wormpep=CE41071;uniprot_id=Q9U1Z0 +3 WormBase exon 61 558 . - . Parent=Transcript:Y60A3A.16.2 +3 WormBase three_prime_UTR 61 444 . - . Parent=Transcript:Y60A3A.16.2 +3 WormBase mRNA 391 1031 . - . ID=Transcript:Y60A3A.16.1;Parent=Gene:WBGene00013364;Name=Y60A3A.16.1;wormpep=CE41071;uniprot_id=Q9U1Z0 +3 WormBase three_prime_UTR 391 444 . - . Parent=Transcript:Y60A3A.16.1 +3 WormBase exon 391 558 . - . Parent=Transcript:Y60A3A.16.1 +3 WormBase CDS 445 558 . - 0 ID=CDS:Y60A3A.16;Parent=Transcript:Y60A3A.16.1,Transcript:Y60A3A.16.2;Name=Y60A3A.16;prediction_status=Confirmed;wormpep=CE41071;protein_id=CAB60401.2;uniprot_id=Q9U1Z0 +3 WormBase CDS 604 721 . - 1 ID=CDS:Y60A3A.16;Parent=Transcript:Y60A3A.16.1,Transcript:Y60A3A.16.2;Name=Y60A3A.16;prediction_status=Confirmed;wormpep=CE41071;protein_id=CAB60401.2;uniprot_id=Q9U1Z0 +3 WormBase CDS 829 1025 . - 0 ID=CDS:Y60A3A.16;Parent=Transcript:Y60A3A.16.1,Transcript:Y60A3A.16.2;Name=Y60A3A.16;prediction_status=Confirmed;wormpep=CE41071;protein_id=CAB60401.2;uniprot_id=Q9U1Z0 +3 WormBase intron 559 603 . - . Parent=Transcript:Y60A3A.16.1;Note=Confirmed_EST yk1679e03.5 %3B Confirmed_EST OSTF164C12_1 %3B Confirmed_EST elegans_PE_SS_GG922%7Cc0_g1_i1 %3B Confirmed_EST elegans_PE_SS_GG922%7Cc0_g1_i1 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B +3 WormBase intron 559 603 . - . Parent=Transcript:Y60A3A.16.2;Note=Confirmed_EST yk1679e03.5 %3B Confirmed_EST OSTF164C12_1 %3B Confirmed_EST elegans_PE_SS_GG922%7Cc0_g1_i1 %3B Confirmed_EST elegans_PE_SS_GG922%7Cc0_g1_i1 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B Confirmed_EST adult_Nanopore_Roach_18471 %3B +3 WormBase exon 604 721 . - . Parent=Transcript:Y60A3A.16.1 +3 WormBase exon 604 721 . - . Parent=Transcript:Y60A3A.16.2 +3 WormBase intron 722 828 . - . Parent=Transcript:Y60A3A.16.1;Note=Confirmed_EST OSTF164C12_1 %3B Confirmed_EST elegans_PE_SS_GG922%7Cc0_g1_i1 %3B Confirmed_EST adult_Nanopore_Roach_29043 %3B Confirmed_EST adult_Nanopore_Roach_29043 %3B +3 WormBase intron 722 828 . - . Parent=Transcript:Y60A3A.16.2;Note=Confirmed_EST OSTF164C12_1 %3B Confirmed_EST elegans_PE_SS_GG922%7Cc0_g1_i1 %3B Confirmed_EST adult_Nanopore_Roach_29043 %3B Confirmed_EST adult_Nanopore_Roach_29043 %3B +3 WormBase exon 829 1031 . - . Parent=Transcript:Y60A3A.16.1 +3 WormBase exon 829 1031 . - . Parent=Transcript:Y60A3A.16.2 +3 WormBase five_prime_UTR 1026 1031 . - . Parent=Transcript:Y60A3A.16.1 +3 WormBase five_prime_UTR 1026 1031 . - . Parent=Transcript:Y60A3A.16.2 +3 WormBase intron 1032 1081 . - . Parent=Transcript:Y60A3A.16.2;Note=Confirmed_EST L4_Nanopore_Roach_52374 %3B +3 WormBase exon 1082 1144 . - . Parent=Transcript:Y60A3A.16.2 +3 WormBase five_prime_UTR 1082 1144 . - . Parent=Transcript:Y60A3A.16.2 +### +4 WormBase gene 61 562 . - . ID=Gene:WBGene00305851;Name=WBGene00305851;interpolated_map_position=23.904;sequence_name=Y60A3A.40;biotype=ncRNA;so_term_name=ncRNA_gene;curie=WB:WBGene00305851;Alias=Y60A3A.40 +4 WormBase circular_ncRNA 61 562 . - . ID=Transcript:Y60A3A.40;Parent=Gene:WBGene00305851;Name=Y60A3A.40 +4 WormBase exon 61 562 . - . Parent=Transcript:Y60A3A.40 +### +5 est EST_match 61 2213 . + . ID=Match1;Name=agt830.5;Target=agt830.5 1 654 +5 est match_part 61 511 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 1 451 +5 est match_part 2011 2213 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 452 654 +### +6 . remark 60 1000 . + . ID=Remark1 +### +##FASTA +>1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +ATGAATCGTCTGCTGGAATACGGTAGTGTTGAAGCAATTCCCTATTACAACTGCTCCCAT +AAAAATTTCACGGAATGGGAGAAGACTGGACAGAAACGACCGTATTTCGGATGGCCACTG +GTAGTTTTTGGAGTCCTCGTGGAGTTGTTGTACATTCCTGTTATCTATATTATATTTAAA +ACCAAACTTATCAGACATCCGTGCTATAAAATAATTGTTCTATTGGCCCTAATTGACATT +ACTGCGACTTGCTGTAGTTGCCTGATTACTGGACCGATGCTGATTATGGGTACCGTGTTC +TGCATGTATCCAACGTTTACTTATGTGGCTGGAGGAATTGCAATAAGTAAGTTTACTGTA +ATAAATAAAGATCTAGTCGGGGCAACTGACGTTAACCGCAAAAAATGCAGACAAATAGAC +AACTCTGTTTCAAATAGTGCTTAATAAAAAATGCAAAGATCAAAATGATGTATCTCTCAT +TTCTTATCGCCTGCAAAAGTATAAAACAACGTTTTCGGTAGCATCAGACAATTCCGGGGT +ACTTAATCACTTTTTTTGACATGCTATCCTGAGTGATTCTAAAGCTCAGTATACGTCAGG +CGCATCATTCATTCAGAATTGGCAAAGCGTCAAAATAGACTTTACCAATCACATTTTCTG +GGAGCTTATAAGTTTTTCAGGTACCTGGTGTATGGCATGTGCCGCCACCACGTCTCTATT +TTCCAATCGGATCATCAGTATTGGCTTCAGGAAGTATGCAGATGTAATCGAGAAGAAACT +CGCCTATACTTCAATCAGTTTTGTACTTTTCTATGGATTCTACATTTGTTGGTTTACACC +CACAACTGCGTATAATTCTGTATTTATGGCATGGATTCCTGATCCATTATCTGAGGAAGT +ACCCAGTAAAGAGGCAGCTGCAATGGTAACTTATTTGGAATATTTTTTTGCAGTTTCAAC +TTTTTATTAAACCAATGTCTAACTTCAATTACTATTTCAGAATTAATAAGAAAACAGTCC +TCAGAGATTAAAAAACGTTTCAGTACAAACACACCATTCTACCGTGGAACAATTGGATTT +TTGTGGCATGCATGTTCATTTTATTTTCTGTGTATTTTATAATGGTAAAACGGATGGCGA +AGGGACAGAAATCAAAGGCTTCCAGATCAGTGAGTCAGACATTTTACCAGTTCCCGATAG +ATTATTTTTCTGTTCTCCACGCTACCAGTATTTTTTTAAATTCTAGTCTTTGAAAAAAAT +TGGAAAAATATATAGGAGTTTCAAGATAGTTGTATATTTGAGACCAACATGCTGTGCTTT +TAATATTTATTTTTTTTTAATTTTAATTTTAAAATGTCTTTTTTGTTTGCAATTGAACAC +GATATGTCTGAGAGGACAGTAATAACTAAGTGTCAAGTTTAAAATCAAAAAGTTGGAACA +GTAGTTATTTTGTTTTTGAATCTTCTATCACATTAACTTATCAATCCAAATAAGAAAATC +TTTCAGATTTTCATTCAATGCTCCATAATTTGCTTCTTCAATACCGGAACTGCTTTGGTC +TACAACGCGCTAGCAATTGTAACCCCTGCTGAATGGATTCTTGCATTTGGACAAATATGT +TGGACATGTAATCATGCAAGTCCTGCTATTATATATGTCTCTTTAAATAGCACTATCCGC +AGGGAATTCTTGAAAATTGTGTTCCGAAACACTTTGGCACCGGTAAATTTAATTTTTGGA +ATTTCTGAATTAAAATCTCTTGTTTTCAGAAAGTGGAAGATGCTACAACAGGTGTTGCAA +AGAACACGATTTAAAATCAATTTTGTAATGTAANNNNNNNNNNNNNNNNNNNNNNNNNNN +>2 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +ATGTCAGCAAAAATTAAAGCTTGGAGCTCCAACGCGGAAAAATTAAATTCGAAACGAAAA +AAAATGGAAATTCGGGAGGAATTATTCCCATCGACGGTAATTCGACAAAATTTTTTCGAA +AAACTGTATAGAATTTCGATATTTTTTTGACATTTTCACGTACTACTGGACGAGATCTTT +CTAAAAAACCAAAAAATCGATACTCTAGTTCAGTTCGTTCAGCTCAATTTTGTCTACTTT +AATTAAGTTGGAGTAGTTTGTTCTAACTTCAAAAACGTGATTTTCAGACGTGCAGCTCGT +CGCCACAGGCTAATCAGGAAATCAGTTCAGAAGATCGAAACTCCCACCATCCCGACATTG +CTTCCAGTAGCTCCGCAACTACATGCAGGTCGTCAAATTGTTTCAATATGGATGAAGGAA +TTCTGACGAGAGACGTGGAAATGGATTTTAGTGACGAAATTCCGACTTTTTCTCACAATG +TAATTTTTTTTCAATATTTCAAAACTAATATTATATGATTTTGCAGAGATTCTCCAATCC +CGTGTTTCCACCGACACCTTCACGAAACTCGTTCAGTACACCGAGGGTTCGAATAATCTC +CAATGTTGAGCAAATTCCGCAGATCAAAATGCTCCGACTAACGATCGAACGACTGAAAAA +TGAAAAAATGAAATATCAGAAGAAATACAAAAGCGGAATGGTGAGTTTGCGGTGTTTTCG +GAAGAAATACTAATAGTCCGCCAAGAAAATATCACTGTAAGAGCATCGAATTCTTCGCTG +CAAATGGAAGTATGCAATATGCGAACGATCGTCAGTGGTATAGAAGGTCGATTGGTGAGA +AGCTGGGCAGATGTGAAGAAAAGTGGCAAAGCTATGGTTCTGAGTCTACAAAGACACGCC +GAAGAAATTGAAAACCTCAAAAAATCAGCTTTTAAAGTTAAATTTTCGAATCTAAGAAAC +AAAAGTTGTATCAAAAATCGATTTCGCAAAGCTCTTCACTTGCTTCAACACGAAATCTGC +CTCGAGGATGACGTCGGACAATTTATTCGAAAATTCACAAAATTCCTGAATTCAGAAGAG +AATCAAAGCTACAAAAACAAGCTTTCAAACTTTGAGGCCGTTGACTTTTTATCAAAATGC +GGATTATCTCTAAGTCAGATGGAAAAAATCAAAAACTATTTGACTAATTCCATTGGCTAT +GATTTGCTTCCATTGGTAAAGAACACAAGAGATTTGTCAATCCAGTTATCAATGATCTCC +AGTTTCAAAGTTTCCACTTCGTTCGACAATAAAGGAAAAGTGATTACCATTGTGCAGTGC +ATGAAAATTGCAGAAGTTTTAGCCTATCGAATAGAGCTTCTATGCAATTCAAATCAATTT +GTGGACGATGGCTACACGAAAGGAGTAATCAAGATTGGAGTCGTTGGTGACGCTGGAGGT +GGAAGCACAAAGTTGGCATTGGTAATCGGAATGTATCTCGACCGAATTCTTCGAGACACG +TTATGGTAATTGCAGTATATGACGGATCCGACAATTACTCGTGTCTGAAAAAATTCATTC +CCGACGTTCTTGAGCAGCTTGGCAAGCTGACAAAAATTCGATATTTGGACAAAGGAGTTC +AAAAAACCGCAAAAATTGTGCAAATTGCAACTGGAGATTGCAAGTTTCAATTTGATATTC +TTGGACACCAAGGACATTCATCCCACAATTTCTGCTTCAAGTGTTTTGCCCAGAATCCAC +GGGGAGCTGAAGAGAGGATGAAAATCAAGGATATGAATGTTGATGAAACATTCCACCCAC +GAACAATCGATCTTTACAAAGCTTGTTGTACTCCACTTCTGCCACACGTTGCGATCATGT +TCTATTTGATTCCTCTTCTGCACATTATCATGGGTATTTTTGACAAATATATCTTCAATC +CCCTCTGGAAATATTCTGTCACTTTGGATAACACTACTTGTTTCCCTATCCTGAAAACGC +GAAAAGCAACTCTAAAAAACGCTGTTAACCTAATCAAAAGTGCGGAAGAAAAGTATCAAG +CAGCCACCGGAAAGATGAAATTGGAGTCGCATGCTGAACTGAAAGCACTTCAATCGGAAA +AATTGTTGCTCGACACAATTGTGAATGGTACTCCCGGAGGAACACTTGAAAAAATGGAAC +AGTGTTGGGCTAAGTTTGGAGCGGACAAGCAGGCTTGGTTCCAATCATTTTGCGGAAACC +ATTTGAAATTGCTGCTAACGCCGGCTATTGTAGAGGAGACTTTCAACATTTTTGGCCCAA +ATTTATGCCCAATGTTGCTCGGATTGAAATCAGCAATGGGAAAGCTTTCAACTATTATGT +CACTTTCGGGAAACAAGTTTTTAAATGATTCCGACGTCTTAATACTTCAAAATTCGATTC +GCGGATTTGTGGAGGATTTGAAAGTAGCGGTTCCCGAAGAAACAATTATTTTAAAGCTGC +ACTTGGTGGTCTACCATGCACCACAAATGGCAAAAGATGTGAGAAACATTGGAAGGATCA +CAGAACCAGGAGTTGAATCTGTCCACGCGATTTTCAATGCACTTGAGAGGAGATTTTGCA +ATTACCGGGACAAGAAAAGGCGTTACATCCATGTTCTGAGAGAGCTCATGTGTCGTAACA +TCATGAATGACATGACTATGGTAATTTTTGTACAGAAAAAAATTTCTGCATTCTTAAAAA +CACAACTATTTCAGAACACGTCCATTCCCGGTCTTTCCATCGTACCAAAAGATGCAACAG +TTCTGCCAATTTCTTCGCAAAATGATCTTCGGGACCCAAAAGTAGTTATTCGGGACGTCA +CGGCTGCCCAAAAAAGAAAAAATTTAGCGAAAAAAAAAATCAATTTTAGCTCCAAGAAAA +GGCTTCCACAATCGACAAAATCTCGAAATGCTGTGGTGAGATTTTTATTTTTCACGAAAA +GTTTCAAATTTTGAACATTTTCAGCCCGACTTCTCACAAAACGTACAAACTTCTATTGCA +TTTGGAGGCAATTCAACGAAAATTGGATTCCGTGGTCTACCGAGCAATGCTCTTTCTCGT +CCGAACCCGATGGTAGGTTCACTGCTTTAAATCAACTCAAAATTGAAATCAAAAATTATT +TCAGGCAATCACACAAACTTGCTCGACAAGCCAGCCAATCACTAGAAGCCATCCACTTGT +TGCTCCACCAGTATCTTATCAACTTCCGAAATGCAGTAATAGTTTAGCTGAAGTGAGTGT +AAAGGTGAAATGACAATTTCAATAAGTTAAAAATTTTAGAAAATTCGAGCAAGTTGTGGG +CAAGCAAGAAGGAGTGCTGCAGAATCTTCTTCGACTGAAAGCCACGTGGACACAAATTCG +AAGAAGAAAGTTTACAGACTAAAATTCGTCCAAAAAAGTCGTGAAATTCCGAAGAAATAG +TAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>3 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +TAAATAAATAAAACTTAATTGTAAAACCTAAAAAAGTACTCAAAAACAATGAAAAAACCT +GGCAATGGAAAAATTGGATGGAAGAATCACAATGGAATATATAAAGCACTTGAAATATAA +ATTAAAAGAGGAAGTATCAAAAACAGAGAGAAATTCAGCAGAAAGCATAGGAAAAATGGG +AAATATCTTATGCTTCTTAGCAATACCAAAAAGTTTGTTACGGTAGTGAGGAAGCAGTAA +AATAATTGCGAGAGGATCTAGAACGAGCACTTTAAGTATTAGTGACTCCTTATTTTTTCT +GGTTTTTTGAGCTTCAAGAGCAAAGGTATCTCTGCATTGGTAAATGATTTATTTTTTCAA +GGGACGTATGAAAAAAACCAGTAATTAAATGTCAAGCTCTTCTGATATTTTTGTGATGAT +ATTCTTAAAGTCGCTCGAGCTTCCCGAAATGCGTTGAAAATGCACACCATTCAAATATAA +GCGTGGTAGTGTGCAGACCTGAAAAACTGGAACTTTCTAATGAAAAATAAATGTTATTTT +GACCTCGATTTCCCACTTTACTGACGCATCAGTGAGAGGATCCACATGGCTACAGCGGAG +CAAGAATCGTTTTTGTTGTTCATAATCAATGCCATAGCTTCCAAGTACTTTTTGAATTTC +TCTGAAACGTATTTTTACAAATTAAGAACGCGTGTTGGTAACATTTCAAAAAAATTATCC +GTAGACAGGCATGTGAATAGGCAAGATGCGCGAAAACCTACCCCTTACTTCAAAATCTCA +TCCGGTTCCAGCATTGAAGTTTTCTTCAGGTTCCAAGTGAACCTCACTGCTCTCGGCATA +TCTTCCTGATCAGTCGTCTCCAGCGCAAACCCAAACCGCTGACGAATAGCAGCCAAAGTT +TCAGACGCTTGCTGCCATTGGAATGCTCCAACATTTTCATCACACTCTTCAATAGGTTCC +ATCATTTTTTACTGAAATTGTACATATTTTTAAAATTAATAAAAAATCGCAAATTTATTA +CCCGGAAAAAAAAGAGTGAAAAGAGGGTCAATCAATTTTCTCTAAACAGAGATTAGCAAC +GCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>4 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +CCTTGACACATGATCCTCCGGTGTCAGTAAAGAGTCGAAATTCTGATAAGTAGTGACGAC +ACGAGGCTCGGATTCACAAATTGTGAAGAGTGGCGAGCGATTTCCTGGAAAAAAGGTGAA +AATTCCAGAAAAATCAATAAATTTCCAGAAAAATCAATAAATTTCCAGAAAAATCAATAA +ATTTCCAGAAAAATCAATAACATTTGAGAAAAAAATTTTTTACAAAATTTATTGATTTTT +CTGAAATTTATTGATTTTTCTGGAAATTTATCGATTTTTCTGGAAATTTATCGAGTTTTC +TGAAATTTCATTGATTTTTCTTCAATTTTCACGTATTTTTTTTACCTGGTTTTCTGTATG +TTTGATGTACATAATCGACAATTCTTCTTTTCAACAAATTCAGCGGATTCGAAGATTCTT +GGAGGATACGGCGATCCAAAAGCCGTCGAACACCTGGTGACAGGTTGTATAATGCGTCTG +GAGTGTATTTTCGACCATCTAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>5 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 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+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>6 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/packages/jbrowse-plugin-apollo/test_data/so-2024-11-18.json b/packages/jbrowse-plugin-apollo/test_data/so-2024-11-18.json new file mode 100644 index 000000000..ea653467d --- /dev/null +++ b/packages/jbrowse-plugin-apollo/test_data/so-2024-11-18.json @@ -0,0 +1 @@ +{"graphs":[{"nodes":[{"id":"http://purl.obolibrary.org/obo/SO_0005854","meta":{"definition":{"val":"An array of non-functional genes whose members, when captured by recombination form functional genes.","xrefs":["SO:ma"]},"comments":["This would include, for example, the arrays of non-functional VSG genes of Trypanosomes."],"synonyms":[{"pred":"hasExactSynonym","val":"gene cassette array","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"gene_cassette_array"},{"id":"http://purl.obolibrary.org/obo/SO_0001496","meta":{"definition":{"val":"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.","xrefs":["PMID:8720065"]},"comments":["The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739."],"synonyms":[{"pred":"hasExactSynonym","val":"telomeric repeat","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:telomeric_repeat","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:repeat_region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-11-09T06:00:42Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"telomeric_repeat"},{"id":"http://purl.obolibrary.org/obo/SO_0000165","meta":{"definition":{"val":"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.","xrefs":["http://www.insdc.org/files/feature_table.html"]},"comments":["An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Enhancer_(genetics)"}],"synonyms":[{"pred":"hasBroadSynonym","val":"INSDC_feature:regulatory","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:enhancer","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"enhancer"},{"id":"http://purl.obolibrary.org/obo/SO_0002344","meta":{"definition":{"val":"Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes.","xrefs":["PMID: 24572720","PMID:3044395"]},"comments":["Added as a request from EMBL. See GitHub Issue #493"],"synonyms":[{"pred":"hasExactSynonym","val":"mitochondrial small subunit rRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"MT SSU rRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"mitochondrial SSU rRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-06-10T16:45:30Z"}]},"type":"CLASS","lbl":"mt_SSU_rRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001012","meta":{"definition":{"val":"A DNA sequence with catalytic activity.","xrefs":["SO:cb"]},"comments":["Added by request from Colin Batchelor."],"synonyms":[{"pred":"hasRelatedSynonym","val":"deoxyribozyme","xrefs":[]},{"pred":"hasExactSynonym","val":"DNA enzyme","xrefs":[]},{"pred":"hasExactSynonym","val":"catalytic DNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"DNAzyme"},{"id":"http://purl.obolibrary.org/obo/SO_0001011","meta":{"definition":{"val":"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.","xrefs":["SO:ke"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/Peptide_nucleic_acid"}],"synonyms":[{"pred":"hasExactSynonym","val":"peptide nucleic acid","xrefs":[]},{"pred":"hasExactSynonym","val":"PNA oligo","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"PNA_oligo"},{"id":"http://purl.obolibrary.org/obo/SO_0005853","meta":{"definition":{"val":"A gene that can be substituted for a related gene at a different site in the genome.","xrefs":["SGD:se"]},"comments":["This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid."],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Gene_cassette"}],"synonyms":[{"pred":"hasExactSynonym","val":"gene cassette","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"gene_cassette"},{"id":"http://purl.obolibrary.org/obo/SO_0001495","meta":{"definition":{"val":"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.","xrefs":["PMID:11222754"]},"comments":["This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699."],"synonyms":[{"pred":"hasExactSynonym","val":"CDEIII","xrefs":[]},{"pred":"hasExactSynonym","val":"centromere DNA Element III","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-11-09T05:54:47Z"}]},"type":"CLASS","lbl":"centromere_DNA_Element_III"},{"id":"http://purl.obolibrary.org/obo/SO_0002345","meta":{"definition":{"val":"Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes.","xrefs":["PMID: 24572720","PMID:3044395"]},"comments":["Added as a request from EMBL. See GitHub Issue #493"],"synonyms":[{"pred":"hasExactSynonym","val":"mitochondrial LSU rRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"MT LSU rRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"mitochondrial large subunit rRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-06-10T16:45:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"mt_LSU_rRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0000164","meta":{"definition":{"val":"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.","xrefs":["SO:cjm","SO:ke","http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasRelatedSynonym","val":"acceptor","xrefs":[]},{"pred":"hasExactSynonym","val":"three prime splice site","xrefs":[]},{"pred":"hasExactSynonym","val":"splice acceptor site","xrefs":[]},{"pred":"hasExactSynonym","val":"acceptor splice site","xrefs":[]},{"pred":"hasRelatedSynonym","val":"3' splice site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"three_prime_cis_splice_site"},{"id":"http://purl.obolibrary.org/obo/SO_0002342","meta":{"definition":{"val":"A ncRNA_gene that encodes an ncRNA less than 200 nucleotides in length.","xrefs":["PMID:28449079","PMID:30069443","PMID:30937442"]},"comments":["Added as a request from FlyBase to make the ncRNA_gene branch in SO mirror the ncRNA branch. See GitHub Issue #514"],"synonyms":[{"pred":"hasExactSynonym","val":"sncRNA gene","xrefs":[]},{"pred":"hasExactSynonym","val":"small non-coding RNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-04-27T14:50:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"sncRNA_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0001498","meta":{"definition":{"val":"A region of sequence from the end of a YAC clone that may provide a highly specific marker.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"YAC end","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-11-19T11:07:18Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"YAC_end"},{"id":"http://purl.obolibrary.org/obo/SO_0000167","meta":{"definition":{"val":"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. 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Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Promoter"}],"synonyms":[{"pred":"hasBroadSynonym","val":"INSDC_feature:regulatory","xrefs":[]},{"pred":"hasExactSynonym","val":"promoter sequence","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:promoter","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"promoter"},{"id":"http://purl.obolibrary.org/obo/SO_0001014","meta":{"definition":{"val":"An intronic region that has an attribute.","xrefs":[]},"comments":["Requested by Colin Batchelor, Feb 2007."],"synonyms":[{"pred":"hasExactSynonym","val":"intron domain","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"intron_domain"},{"id":"http://purl.obolibrary.org/obo/SO_0005852","meta":{"definition":{"val":"A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.","xrefs":["SO:ma"]},"comments":["This would include, for example, a cluster of genes encoding different histones."],"synonyms":[{"pred":"hasExactSynonym","val":"gene subarray","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"gene_subarray"},{"id":"http://purl.obolibrary.org/obo/SO_0000166","meta":{"definition":{"val":"An enhancer bound by a factor.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"enhancer bound by factor","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"enhancer_bound_by_factor"},{"id":"http://purl.obolibrary.org/obo/SO_0005851","meta":{"definition":{"val":"An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.","xrefs":["SO:ma"]},"comments":["This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays."],"synonyms":[{"pred":"hasExactSynonym","val":"gene array","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"gene_array"},{"id":"http://purl.obolibrary.org/obo/SO_0002343","meta":{"definition":{"val":"Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes.","xrefs":["PMID:3044395"]},"comments":["Added as a request from EBI. See GitHub Issue #493"],"synonyms":[{"pred":"hasExactSynonym","val":"cytosolic ribosomal RNA","xrefs":[]},{"pred":"hasExactSynonym","val":"cytosolic rRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-06-10T16:45:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"cytosolic_rRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001497","meta":{"definition":{"val":"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.","xrefs":["PMID:7785338","PMID:8005434","http://www.yeastgenome.org/help/glossary.html#xelemcoresequence"]},"comments":["Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.\n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1."],"synonyms":[{"pred":"hasExactSynonym","val":"X element core sequence","xrefs":[]},{"pred":"hasRelatedSynonym","val":"X element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-11-10T10:56:54Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"X_element"},{"id":"http://purl.obolibrary.org/obo/SO_0001013","meta":{"definition":{"val":"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.","xrefs":["http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431"]},"synonyms":[{"pred":"hasRelatedSynonym","val":"multiple nucleotide polymorphism","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"MNP"},{"id":"http://purl.obolibrary.org/obo/SO_0000161","meta":{"definition":{"val":"A modified base in which adenine has been methylated.","xrefs":["SO:ke"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"methylated A","xrefs":[]},{"pred":"hasExactSynonym","val":"methylated_A","xrefs":[]},{"pred":"hasExactSynonym","val":"methylated adenine","xrefs":[]},{"pred":"hasExactSynonym","val":"methylated adenine base","xrefs":[]},{"pred":"hasExactSynonym","val":"methylated adenine residue","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"methylated_adenine"},{"id":"http://purl.obolibrary.org/obo/SO_0005850","meta":{"definition":{"val":"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.","xrefs":["http://www.insdc.org/files/feature_table.html"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/Primer_binding_site"}],"synonyms":[{"pred":"hasExactSynonym","val":"INSDC_feature:primer_bind","xrefs":[]},{"pred":"hasExactSynonym","val":"primer binding site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"primer_binding_site"},{"id":"http://purl.obolibrary.org/obo/SO_0002340","meta":{"definition":{"val":"An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length.","xrefs":["PMID:19246988","PMID:21853533","PMID:27369380"]},"comments":["Added as a request from FlyBase. See GitHub Issue #512"],"synonyms":[{"pred":"hasExactSynonym","val":"RNA 7SK","xrefs":[]},{"pred":"hasExactSynonym","val":"7SK RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-04-27T14:50:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"RNA_7SK"},{"id":"http://purl.obolibrary.org/obo/SO_0001492","meta":{"definition":{"val":"A regulatory region that is part of an intron.","xrefs":["SO:ke"]},"comments":["Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527."],"synonyms":[{"pred":"hasExactSynonym","val":"intronic regulatory region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-11-08T02:48:02Z"}]},"type":"CLASS","lbl":"intronic_regulatory_region"},{"id":"http://purl.obolibrary.org/obo/SO_0002341","meta":{"definition":{"val":"A gene encoding a 7SK RNA (SO:0002340).","xrefs":["PMID:19246988","PMID:21853533","PMID:27369380"]},"comments":["Added as a request from FlyBase. See GitHub Issue #512"],"synonyms":[{"pred":"hasExactSynonym","val":"RNA 7SK gene","xrefs":[]},{"pred":"hasExactSynonym","val":"7SK RNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-04-27T14:50:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"RNA_7SK_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0001491","meta":{"definition":{"val":"The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.","xrefs":["DOI:10.1126"]},"synonyms":[{"pred":"hasExactSynonym","val":"finished","xrefs":[]},{"pred":"hasExactSynonym","val":"finished genome","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-10-23T01:04:43Z"}]},"type":"CLASS","lbl":"finished_genome"},{"id":"http://purl.obolibrary.org/obo/SO_0000160","meta":{"definition":{"val":"A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.","xrefs":["ISBN:0-1767-2380-8"]},"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"lambda_clone"},{"id":"http://purl.obolibrary.org/obo/SO_0000163","meta":{"definition":{"val":"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.","xrefs":["SO:cjm","SO:ke","http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"5' splice site","xrefs":[]},{"pred":"hasExactSynonym","val":"donor splice site","xrefs":[]},{"pred":"hasExactSynonym","val":"five prime splice site","xrefs":[]},{"pred":"hasExactSynonym","val":"splice donor site","xrefs":[]},{"pred":"hasRelatedSynonym","val":"donor","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"five_prime_cis_splice_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001494","meta":{"definition":{"val":"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.","xrefs":["PMID:11222754"]},"comments":["This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699."],"synonyms":[{"pred":"hasExactSynonym","val":"CDEII","xrefs":[]},{"pred":"hasExactSynonym","val":"centromere DNA Element II","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-11-09T05:51:26Z"}]},"type":"CLASS","lbl":"centromere_DNA_Element_II"},{"id":"http://purl.obolibrary.org/obo/SO_0001010","meta":{"definition":{"val":"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.","xrefs":["PMID:9753739"]},"synonyms":[{"pred":"hasExactSynonym","val":"i motif","xrefs":[]},{"pred":"hasExactSynonym","val":"short intercalated motif","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"i_motif"},{"id":"http://purl.obolibrary.org/obo/SO_0001493","meta":{"definition":{"val":"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).","xrefs":["PMID:11222754"]},"comments":["This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699."],"synonyms":[{"pred":"hasExactSynonym","val":"Centromere DNA Element I","xrefs":[]},{"pred":"hasExactSynonym","val":"CDEI","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-11-09T05:47:23Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"centromere_DNA_Element_I"},{"id":"http://purl.obolibrary.org/obo/SO_0000162","meta":{"definition":{"val":"Consensus region of primary transcript bordering junction of splicing. 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See GitHub Issue #623."],"synonyms":[{"pred":"hasExactSynonym","val":"uSTOP_lost","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2024-11-18T22:39:25Z"}]},"type":"CLASS","lbl":"5_prime_UTR_uORF_stop_codon_loss_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0001055","meta":{"definition":{"val":"A regulatory_region that modulates the transcription of a gene or genes.","xrefs":["PMID:9679020","SO:regcreative"]},"comments":["Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"INSDC_qualifier:transcriptional_cis_regulatory_region","xrefs":[]},{"pred":"hasExactSynonym","val":"transcription-control region","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:regulatory","xrefs":[]},{"pred":"hasExactSynonym","val":"transcriptional cis regulatory region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"transcriptional_cis_regulatory_region"},{"id":"http://purl.obolibrary.org/obo/SO_0002386","meta":{"definition":{"val":"A 5' UTR variant where a stop codon in an upstream open reading frame is introduced, moved or lost.","xrefs":[]},"comments":["Added at the request of Sarah Hunt (EBI). See GitHub Issue #622."],"synonyms":[{"pred":"hasExactSynonym","val":"uFrameshift","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2024-11-18T22:33:06Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"5_prime_UTR_uORF_stop_codon_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0001058","meta":{"definition":{"val":"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.","xrefs":["SO:regcreative"]},"comments":["Obsoleted Jan 21, 2021 by Dave Sant. GREEKC consortium individuals pointed out that this did not fit with the other child terms of transcriptional_cis_regulatory_region (SO:0001055), which are currently promoter, CRM and promoter flanking region. No comments about when this term was created exist, no references are listed. GREEKC members assume that this was previously under enhansosome (SO:0001057), which was probably created along with this term but has since been obsoleted. This term can be resurrected as non-obsolete if we can find a reference publication and/or change the name to a term that is commonly used in the field."],"synonyms":[{"pred":"hasExactSynonym","val":"promoter targeting sequence","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"promoter_targeting_sequence"},{"id":"http://purl.obolibrary.org/obo/SO_0002387","meta":{"definition":{"val":"A 5' UTR variant which disrupts the translation of an upstream open reading frame because the number of nucleotides inserted or deleted is not a multiple of three.","xrefs":[]},"comments":["Added at the request of Sarah Hunt (EBI). See GitHub Issue #621."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2024-11-18T22:34:39Z"}]},"type":"CLASS","lbl":"5_prime_UTR_uORF_frameshift_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0001057","meta":{"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"enhanceosome"},{"id":"http://purl.obolibrary.org/obo/SO_0001052","meta":{"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"nested_repeat"},{"id":"http://purl.obolibrary.org/obo/SO_0002385","meta":{"definition":{"val":"A 5' UTR variant within an upstream open reading frame.","xrefs":["PMID:32461616","PMID:32926138"]},"comments":["Added at the request of Sarah Hunt (EBI). See GitHub Issue #647."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2024-11-18T22:30:12Z"}]},"type":"CLASS","lbl":"5_prime_UTR_uORF_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0001051","meta":{"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"nested_region"},{"id":"http://purl.obolibrary.org/obo/SO_0002382","meta":{"definition":{"val":"A conserved cis-acting element that confers extreme-distance regulatory activity to an enhancer.","xrefs":["https://doi.org/10.1101/2024.05.26.595809"]},"comments":["Added at the request of Chris Mungall (Berkeley Lab) on 6 June 2024. See GitHub Issue #649."],"synonyms":[{"pred":"hasExactSynonym","val":"REX","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://purl.org/dc/elements/1.1/date","val":"2024-06-06T16:53:56Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"range_extender_element"},{"id":"http://purl.obolibrary.org/obo/SO_0001054","meta":{"definition":{"val":"A portion of a transposon, interrupted by the insertion of another element.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"transposon fragment","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"transposon_fragment"},{"id":"http://purl.obolibrary.org/obo/SO_0002383","meta":{"definition":{"val":"A variant that has been found to be pathogenic in the context of a neoplastic disease.","xrefs":["PMID:35101336"]},"comments":["See GitHub Issue #643."],"basicPropertyValues":[{"pred":"http://purl.org/dc/elements/1.1/date","val":"2024-06-06T20:09:59Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"}]},"type":"CLASS","lbl":"oncogenic_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0001053","meta":{"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"nested_transposon"},{"id":"http://www.geneontology.org/formats/oboInOwl#hasSynonymType","type":"PROPERTY","lbl":"has_synonym_type"},{"id":"http://purl.obolibrary.org/obo/SO_0002380","meta":{"definition":{"val":"A gene that codes for pseudouridylation_guide_snoRNA. A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.","xrefs":["PMID:12457565"]},"comments":["Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)."],"synonyms":[{"pred":"hasExactSynonym","val":"pseudouridylation guide snoRNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-11-19T05:51:40Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"}]},"type":"CLASS","lbl":"pseudouridylation_guide_snoRNA_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002381","meta":{"definition":{"val":"A long non-coding RNA which is produced using the promoter of a protein-coding gene but with transcription occurring in the opposite direction.","xrefs":["PMID:30175284","PMID:34956340"]},"comments":["Created new term \"bidirectional_promoter_lncRNA\" (SO:0002381). See GitHub Issue #579."],"synonyms":[{"pred":"hasExactSynonym","val":"bidirectional_promoter_long_non-coding_RNA","xrefs":[]},{"pred":"hasExactSynonym","val":"bidirectional promoter lncRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"bidirectional promoter long non-coding RNA","xrefs":[]},{"pred":"hasExactSynonym","val":"bidirectional_lncRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"bidirectional lncRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2022-10-28T19:05:35Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"}]},"type":"CLASS","lbl":"bidirectional_promoter_lncRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001050","meta":{"definition":{"val":"A portion of a repeat, interrupted by the insertion of another element.","xrefs":["SO:ke"]},"comments":["Requested by Chris Smith, and others at Flybase to help annotate nested repeats."],"synonyms":[{"pred":"hasExactSynonym","val":"repeat fragment","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"repeat_fragment"},{"id":"http://purl.obolibrary.org/obo/SO_0001049","meta":{"definition":{"val":"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.","xrefs":["Phigo:ariane"]},"synonyms":[{"pred":"hasExactSynonym","val":"defective conjugative transposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"defective_conjugative_transposon"},{"id":"http://purl.obolibrary.org/obo/SO_0001048","meta":{"definition":{"val":"A region located within an inversion site.","xrefs":["SO:ke"]},"comments":["A term created to allow the parts of an inversion site have an is_a path back to the root."],"synonyms":[{"pred":"hasExactSynonym","val":"inversion site part","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"inversion_site_part"},{"id":"http://purl.obolibrary.org/obo/SO_0002379","meta":{"definition":{"val":"A gene that codes for methylation_guide_snoRNA. A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.","xrefs":["PMID:12457565"]},"comments":["Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)."],"synonyms":[{"pred":"hasExactSynonym","val":"methylation guide snoRNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-11-19T05:51:12Z"}]},"type":"CLASS","lbl":"methylation_guide_snoRNA_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002377","meta":{"definition":{"val":"A gene that codes for U14_snoRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.","xrefs":[]},"comments":["Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)."],"synonyms":[{"pred":"hasExactSynonym","val":"small nucleolar RNA U14 gene, snoRNA U14 gene, U14 small nucleolar RNA gene, U14 snoRNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-11-19T05:50:43Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"U14_snoRNA_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0000198","meta":{"definition":{"val":"An exon that does not contain any codons.","xrefs":["SO:ke"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"noncoding exon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"noncoding_exon"},{"id":"http://purl.obolibrary.org/obo/SO_0001045","meta":{"definition":{"val":"A MGE region consisting of two fused plasmids resulting from a replicative transposition event.","xrefs":["phigo:at"]},"synonyms":[{"pred":"hasExactSynonym","val":"cointegrated replicon","xrefs":[]},{"pred":"hasExactSynonym","val":"cointegrated plasmid","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"cointegrated_plasmid"},{"id":"http://purl.obolibrary.org/obo/SO_0000197","meta":{"definition":{"val":"The sequence of the three_prime_coding_exon that codes for protein.","xrefs":["SO:cjm"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"three prime exon coding region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"three_prime_coding_exon_coding_region"},{"id":"http://purl.obolibrary.org/obo/SO_0002378","meta":{"definition":{"val":"A gene that codes for U3_snoRNA. U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.","xrefs":[]},"comments":["Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)."],"synonyms":[{"pred":"hasExactSynonym","val":"small nucleolar RNA U3 gene, snoRNA U3 gene, U3 small nucleolar RNA gene, U3 snoRNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-11-19T05:50:57Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"}]},"type":"CLASS","lbl":"U3_snoRNA_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0001044","meta":{"definition":{"val":"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.","xrefs":["SO:xp"]},"comments":["Definition change requested by Val, 3172757."],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Numt"}],"synonyms":[{"pred":"hasExactSynonym","val":"nuclear mitochondrial pseudogene","xrefs":[]},{"pred":"hasExactSynonym","val":"NUMT","xrefs":[]},{"pred":"hasExactSynonym","val":"nuclear mt pseudogene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"nuclear_mt_pseudogene"},{"id":"http://purl.obolibrary.org/obo/SO_0002375","meta":{"definition":{"val":"A gene that codes a C_D_box_snoRNA. Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.","xrefs":["PMID:12457565","PMID:22065625"]},"comments":["Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565."],"synonyms":[{"pred":"hasExactSynonym","val":"box C/D snoRNA gene, C D box snoRNA gene, C/D box snoRNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-11-19T05:49:55Z"}]},"type":"CLASS","lbl":"C_D_box_snoRNA_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0001047","meta":{"definition":{"val":"Component of the inversion site located at the right of a region susceptible to site-specific inversion.","xrefs":["Phigo:at"]},"synonyms":[{"pred":"hasExactSynonym","val":"IRRinv site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"IRRinv_site"},{"id":"http://purl.obolibrary.org/obo/SO_0000199","meta":{"definition":{"val":"A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.","xrefs":["NCBI:th","SO:ke"]},"subsets":["http://purl.obolibrary.org/obo/so#DBVAR"],"synonyms":[{"pred":"hasExactSynonym","val":"translocated sequence","xrefs":[]},{"pred":"hasRelatedSynonym","val":"transchr","xrefs":["http://www.ncbi.nlm.nih.gov/dbvar/"]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"translocation"},{"id":"http://purl.obolibrary.org/obo/SO_0002376","meta":{"definition":{"val":"A gene that codes for H_ACA_box_snoRNA. Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.","xrefs":["PMID:12457565","PMID:22065625"]},"comments":["Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565."],"synonyms":[{"pred":"hasExactSynonym","val":"box H/ACA snoRNA gene, H ACA box snoRNA gene, H/ACA box snoRNA gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2021-11-19T05:50:14Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"evan"}]},"type":"CLASS","lbl":"H_ACA_box_snoRNA_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0001046","meta":{"definition":{"val":"Component of the inversion site located at the left of a region susceptible to site-specific inversion.","xrefs":["Phigo:at"]},"synonyms":[{"pred":"hasExactSynonym","val":"IRLinv site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"IRLinv_site"},{"id":"http://purl.obolibrary.org/obo/SO_0000194","meta":{"definition":{"val":"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.","xrefs":["http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html"]},"synonyms":[{"pred":"hasExactSynonym","val":"Long interspersed element","xrefs":[]},{"pred":"hasExactSynonym","val":"LINE","xrefs":[]},{"pred":"hasExactSynonym","val":"Long interspersed nuclear element","xrefs":[]},{"pred":"hasExactSynonym","val":"LINE element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"LINE_element"},{"id":"http://purl.obolibrary.org/obo/SO_0001041","meta":{"definition":{"val":"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.","xrefs":["SO:ke"]},"comments":["The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct."],"synonyms":[{"pred":"hasExactSynonym","val":"viral sequence","xrefs":[]},{"pred":"hasExactSynonym","val":"virus sequence","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"viral_sequence"},{"id":"http://purl.obolibrary.org/obo/SO_0002373","meta":{"definition":{"val":"A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs.","xrefs":["PMID:17099227","PMID:24659245"]},"comments":["Added at the request of Steven Marygold. 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(https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/478)"],"synonyms":[{"pred":"hasExactSynonym","val":"spurious protein","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-05-13T11:40:30Z"}]},"type":"CLASS","lbl":"spurious_protein"},{"id":"http://purl.obolibrary.org/obo/SO_0002289","meta":{"definition":{"val":"VIPER retrotransposons are members of the YR_retrotransposon (SO:0002286 superfamily with protein domains: RT, RH, YR. 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The thread for the discussion is available can be accessed via tracker ID:1917222."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"PROPERTY","lbl":"evidence_for_feature"},{"id":"http://purl.obolibrary.org/obo/so#derives_from","meta":{"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"PROPERTY","lbl":"derives_from"},{"id":"http://purl.obolibrary.org/obo/SO_0000099","meta":{"definition":{"val":"A gene from proviral sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"proviral gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"proviral_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002278","meta":{"definition":{"val":"Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. 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Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp.","xrefs":["PMID:17984973","PMID:8556864"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"Stowaway","xrefs":[]},{"pred":"hasExactSynonym","val":"TcMar-Stowaway transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"Tc1 transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"Mariner","xrefs":[]},{"pred":"hasExactSynonym","val":"DTT transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"Tc1 Mariner TIR transposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"}]},"type":"CLASS","lbl":"Tc1_Mariner_TIR_transposon"},{"id":"http://purl.obolibrary.org/obo/SO_0000098","meta":{"definition":{"val":"A gene from plasmid sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"plasmid gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"plasmid_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002279","meta":{"definition":{"val":"The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb.","xrefs":["PMID:11454746"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"Ac transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"hAT transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"Ds transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"hAT-Ac transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"hAT TIR transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"Ac/Ds transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"DTA transposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"hAT_TIR_transposon"},{"id":"http://purl.obolibrary.org/obo/SO_0002276","meta":{"definition":{"val":"Short interspersed elements that originated from 5S rRNAs.","xrefs":["PMID:21673742"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"5S SINE element","xrefs":[]},{"pred":"hasExactSynonym","val":"5S SINE retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"RSS retrotransposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"5S_SINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0002277","meta":{"definition":{"val":"Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules.","xrefs":["PMID:22011512"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"DYC transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"Crypton transposon","xrefs":[]},{"pred":"hasExactSynonym","val":"Crypton YR transposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"Crypton_YR_transposon"},{"id":"http://purl.obolibrary.org/obo/SO_0000095","meta":{"definition":{"val":"A plastid gene from leucoplast sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"leucoplast gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"leucoplast_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002274","meta":{"definition":{"val":"Short interspersed elements that originated from tRNAs.","xrefs":["PMID:21673742"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"tRNA SINE element","xrefs":[]},{"pred":"hasExactSynonym","val":"RST retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"tRNA SINE retrotransposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"tRNA_SINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0000094","meta":{"definition":{"val":"A gene from cyanelle sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"cyanelle gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"cyanelle_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002275","meta":{"definition":{"val":"Short interspersed elements that originated from 7SL RNAs.","xrefs":["PMID:21673742"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"7SL SINE element","xrefs":[]},{"pred":"hasExactSynonym","val":"RSL retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"7SL SINE retrotransposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"}]},"type":"CLASS","lbl":"7SL_SINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0002272","meta":{"definition":{"val":"Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs.","xrefs":["PMID:31709017"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"L1 LINE retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"L1 element","xrefs":[]},{"pred":"hasExactSynonym","val":"LINE-1 element","xrefs":[]},{"pred":"hasExactSynonym","val":"LINE 1 element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"L1_LINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0000097","meta":{"definition":{"val":"A gene from nucleomorph sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"nucleomorph gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"nucleomorph_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0000096","meta":{"definition":{"val":"A gene from proplastid sequence.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"proplastid gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"proplastid_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002273","meta":{"definition":{"val":"Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain.","xrefs":[]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"xrefs":[{"val":"https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-interspersed-nuclear-element"}],"synonyms":[{"pred":"hasExactSynonym","val":"I LINE retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"LINE I element","xrefs":[]},{"pred":"hasExactSynonym","val":"RII retrotransposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"}]},"type":"CLASS","lbl":"I_LINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0000091","meta":{"definition":{"val":"A gene from apicoplast sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"apicoplast gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"apicoplast_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002270","meta":{"definition":{"val":"RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain.","xrefs":["PMID:9729877"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"RIT retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"RTE LINE retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"RTE retrotransposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"RTE_LINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0000090","meta":{"definition":{"val":"A gene from plastid sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"plastid gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"plastid_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0002271","meta":{"definition":{"val":"Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT).","xrefs":["PMID:31709017"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"Jockey LINE retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"LINE Jockey element","xrefs":[]},{"pred":"hasExactSynonym","val":"RIJ retrotransposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"}]},"type":"CLASS","lbl":"Jockey_LINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0000093","meta":{"definition":{"val":"A gene from chromoplast_sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"chromoplast gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"chromoplast_gene"},{"id":"http://purl.obolibrary.org/obo/SO_0000092","meta":{"definition":{"val":"A gene from chloroplast sequence.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"chloroplast gene","xrefs":[]},{"pred":"hasExactSynonym","val":"ct gene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"ct_gene"},{"id":"http://purl.obolibrary.org/obo/so#dbvar","lbl":"DBVAR"},{"id":"http://purl.obolibrary.org/obo/SO_0002269","meta":{"definition":{"val":"R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes.","xrefs":["PMID:21734471"]},"comments":["Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)"],"synonyms":[{"pred":"hasExactSynonym","val":"RIR retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"R2 LINE retrotransposon","xrefs":[]},{"pred":"hasExactSynonym","val":"R2 retrotransposon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-06-25T14:00:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"R2_LINE_retrotransposon"},{"id":"http://purl.obolibrary.org/obo/SO_0002298","meta":{"definition":{"val":"An operon whose transcription is coordinated on a single transcription unit.","xrefs":["Bacterial_regulation_working_group:CMA","PMID:32665585"]},"comments":["Added as per Mejia-Almonte et.al PMID:32665585"],"synonyms":[{"pred":"hasExactSynonym","val":"simple operon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-08-05T11:49:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"simple_operon"},{"id":"http://purl.obolibrary.org/obo/SO_0002299","meta":{"definition":{"val":"An operon whose transcription is coordinated on several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.","xrefs":["Bacterial_regulation_working_group:CMA","PMID:32665585"]},"comments":["Added as per Mejia-Almonte et.al PMID:32665585"],"synonyms":[{"pred":"hasExactSynonym","val":"complex operon","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-08-05T11:49:30Z"}]},"type":"CLASS","lbl":"complex_operon"},{"id":"http://purl.obolibrary.org/obo/SO_0002296","meta":{"definition":{"val":"The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter. ","xrefs":["Bacterial_regulation_working_group:CMA","PMID:32665585"]},"comments":["Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527."],"synonyms":[{"pred":"hasExactSynonym","val":"transcription factor regulatory site phrase","xrefs":[]},{"pred":"hasExactSynonym","val":"transcription factor regulatory site module","xrefs":[]},{"pred":"hasExactSynonym","val":"TFRS phrase","xrefs":[]},{"pred":"hasExactSynonym","val":"TFRS module","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-08-05T11:49:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"TFRS_module"},{"id":"http://purl.obolibrary.org/obo/SO_0002297","meta":{"definition":{"val":"The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter.","xrefs":["Bacterial_regulation_working_group:CMA","PMID:32665585"]},"comments":["Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527."],"synonyms":[{"pred":"hasExactSynonym","val":"TFRS collection","xrefs":[]},{"pred":"hasExactSynonym","val":"transcription factor regulatory site collection","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-08-05T11:49:30Z"}]},"type":"CLASS","lbl":"TFRS_collection"},{"id":"http://purl.obolibrary.org/obo/SO_0002294","meta":{"definition":{"val":"Mitochondrial displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region.","xrefs":["http://www.insdc.org/files/feature_table.html"]},"comments":["Added as per request by Terence Murphy (INSDC) for GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/D_loop"}],"synonyms":[{"pred":"hasExactSynonym","val":"Mitochondrial D loop","xrefs":[]},{"pred":"hasExactSynonym","val":"Mitochondrial displacement loop","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-07-08T11:49:30Z"}]},"type":"CLASS","lbl":"mitochondrial_D_loop"},{"id":"http://purl.obolibrary.org/obo/SO_0002295","meta":{"definition":{"val":"A TF_binding_site that is involved in regulation of expression.","xrefs":["Bacterial_regulation_working_group:CMA","PMID:32665585"]},"comments":["Added as per Mejia-Almonte et.al PMID:32665585"],"synonyms":[{"pred":"hasExactSynonym","val":"transcription factor regulatory site","xrefs":[]},{"pred":"hasExactSynonym","val":"TFRS","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-08-05T11:49:30Z"}]},"type":"CLASS","lbl":"transcription_factor_regulatory_site"},{"id":"http://purl.obolibrary.org/obo/SO_0002292","meta":{"definition":{"val":"An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail.","xrefs":["PMID:29086764","PMID:29182528","PMID:29576969"]},"comments":["Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)"],"synonyms":[{"pred":"hasExactSynonym","val":"circular mRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"coding circRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-07-01T11:49:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"}]},"type":"CLASS","lbl":"circular_mRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0002293","meta":{"definition":{"val":"The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis.","xrefs":["PMID: 19407924","PMID:10968878"]},"comments":["Added as per GitHub Issue Request #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417) from INSDC"],"xrefs":[{"val":"https://en.wikipedia.org/wiki/MtDNA_control_region"}],"synonyms":[{"pred":"hasExactSynonym","val":"Mitochondrial noncoding region","xrefs":[]},{"pred":"hasExactSynonym","val":"MtDNA control region","xrefs":[]},{"pred":"hasExactSynonym","val":"Mitochondrial DNA control region","xrefs":[]},{"pred":"hasExactSynonym","val":"Mitochondrial NCR","xrefs":[]},{"pred":"hasExactSynonym","val":"MtDNA_control_region","xrefs":[]},{"pred":"hasExactSynonym","val":"Mitochondrial A+T region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2020-07-01T16:40:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"david"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"mitochondrial_control_region"},{"id":"http://purl.obolibrary.org/obo/SO_0002290","meta":{"definition":{"val":"Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). 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Do not obsolete without consulting MGED ontology."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"expressed sequence tag","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"EST"},{"id":"http://purl.obolibrary.org/obo/so#maximally_overlaps","meta":{"definition":{"val":"A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.","xrefs":["PMID:20226267"]},"comments":["Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2010-10-14T01:34:48Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"PROPERTY","lbl":"maximally_overlaps"},{"id":"http://purl.obolibrary.org/obo/SO_0001675","meta":{"definition":{"val":"An A box within an RNA polymerase III type 1 promoter.","xrefs":["SO:ke"]},"comments":["The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true."],"synonyms":[{"pred":"hasRelatedSynonym","val":"A box type 1","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2010-10-06T05:43:43Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"A_box_type_1"},{"id":"http://purl.obolibrary.org/obo/SO_0000344","meta":{"definition":{"val":"Region of a transcript that regulates splicing.","xrefs":["SO:ke"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"splice enhancer","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"splice_enhancer"},{"id":"http://purl.obolibrary.org/obo/SO_0000347","meta":{"definition":{"val":"A match against a nucleotide sequence.","xrefs":["SO:ke"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"nucleotide match","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"nucleotide_match"},{"id":"http://purl.obolibrary.org/obo/SO_0001678","meta":{"definition":{"val":"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.","xrefs":["PMID:12381659"]},"synonyms":[{"pred":"hasRelatedSynonym","val":"regulatory promoter element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2010-10-07T04:39:48Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"regulatory_promoter_element"},{"id":"http://purl.obolibrary.org/obo/SO_0000346","meta":{"definition":{"val":"Cre-Recombination target sequence.","xrefs":[]},"synonyms":[{"pred":"hasRelatedSynonym","val":"Cre-recombination target region","xrefs":[]},{"pred":"hasExactSynonym","val":"loxP site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"loxP_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001677","meta":{"definition":{"val":"A core promoter region of RNA polymerase III type 1 promoters.","xrefs":["PMID:12381659"]},"synonyms":[{"pred":"hasExactSynonym","val":"IE","xrefs":[]},{"pred":"hasRelatedSynonym","val":"intermediate element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2010-10-06T05:52:03Z"}]},"type":"CLASS","lbl":"intermediate_element"},{"id":"http://purl.obolibrary.org/obo/SO_0000385","meta":{"definition":{"val":"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.","xrefs":["http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030"]},"comments":["Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"INSDC_qualifier:RNase_MRP_RNA","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:ncRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"RNase MRP RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"RNase_MRP_RNA"},{"id":"http://purl.obolibrary.org/obo/SO_1000115","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."],"synonyms":[{"pred":"hasRelatedSynonym","val":"mutation causing complex 3D structural change","xrefs":[]},{"pred":"hasExactSynonym","val":"sequence variant causing complex 3D structural change","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0001600"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_causing_complex_3D_structural_change"},{"id":"http://purl.obolibrary.org/obo/SO_0001232","meta":{"definition":{"val":"A modified RNA base in which thymine is bound to the ribose ring.","xrefs":["RSC:cb"]},"comments":["The free molecule is CHEBI:30832."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"ribothymidine"},{"id":"http://purl.obolibrary.org/obo/SO_0000384","meta":{"definition":{"val":"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.","xrefs":["http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/OxyS_RNA"}],"synonyms":[{"pred":"hasExactSynonym","val":"OxyS RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"OxyS_RNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001231","meta":{"definition":{"val":"A modified RNA base in which guanine is methylated at the 7- position.","xrefs":["RSC:cb"]},"comments":["The free molecule is CHEBI:2274."],"synonyms":[{"pred":"hasExactSynonym","val":"seven methylguanine","xrefs":[]},{"pred":"hasExactSynonym","val":"7-methylguanine","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"seven_methylguanine"},{"id":"http://purl.obolibrary.org/obo/SO_1000114","meta":{"basicPropertyValues":[{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_1000111"},{"pred":"http://purl.obolibrary.org/obo/IAO_0000231","val":"http://purl.obolibrary.org/obo/IAO_0000227"}],"deprecated":true},"type":"CLASS"},{"id":"http://purl.obolibrary.org/obo/SO_1000113","meta":{"basicPropertyValues":[{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_1000111"},{"pred":"http://purl.obolibrary.org/obo/IAO_0000231","val":"http://purl.obolibrary.org/obo/IAO_0000227"}],"deprecated":true},"type":"CLASS"},{"id":"http://purl.obolibrary.org/obo/SO_0000387","meta":{"definition":{"val":"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.","xrefs":["http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/RprA_RNA"}],"synonyms":[{"pred":"hasExactSynonym","val":"RprA RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"RprA_RNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001234","meta":{"definition":{"val":"An attribute describing a feature that has either intra-genome or intracellular mobility.","xrefs":["RSC:cb"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/Mobile"}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"mobile"},{"id":"http://purl.obolibrary.org/obo/SO_1000112","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term."],"synonyms":[{"pred":"hasExactSynonym","val":"sequence variant causing no 3D structural change","xrefs":[]},{"pred":"hasRelatedSynonym","val":"mutation causing no 3D structural change","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_causing_no_3D_structural_change"},{"id":"http://purl.obolibrary.org/obo/SO_0000386","meta":{"definition":{"val":"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.","xrefs":["http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010"]},"comments":["Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasExactSynonym","val":"RNase P RNA","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:ncRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:RNase_P_RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"RNase_P_RNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001233","meta":{"definition":{"val":"A modified RNA base in which methylhypoxanthine is bound to the ribose ring.","xrefs":["RSC:cb"]},"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"methylinosine"},{"id":"http://purl.obolibrary.org/obo/SO_1000119","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."],"synonyms":[{"pred":"hasRelatedSynonym","val":"mutation causing inactive ligand binding site","xrefs":[]},{"pred":"hasExactSynonym","val":"sequence variant causing inactive ligand binding site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0001560"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_causing_inactive_ligand_binding_site"},{"id":"http://purl.obolibrary.org/obo/SO_0000381","meta":{"definition":{"val":"A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon.","xrefs":["PMID:20463000"]},"synonyms":[{"pred":"hasExactSynonym","val":"group IIA intron","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"group_IIA_intron"},{"id":"http://purl.obolibrary.org/obo/SO_0000380","meta":{"definition":{"val":"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.","xrefs":["PMID:2436805"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Hammerhead_ribozyme"}],"synonyms":[{"pred":"hasExactSynonym","val":"INSDC_qualifier:hammerhead_ribozyme","xrefs":[]},{"pred":"hasExactSynonym","val":"hammerhead ribozyme","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:ncRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"hammerhead_ribozyme"},{"id":"http://purl.obolibrary.org/obo/SO_1000118","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."],"synonyms":[{"pred":"hasRelatedSynonym","val":"mutation causing loss of function of polypeptide","xrefs":[]},{"pred":"hasRelatedSynonym","val":"loss of function of polypeptide","xrefs":[]},{"pred":"hasExactSynonym","val":"sequence variant causing loss of function of polypeptide","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0001559"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_causing_loss_of_function_of_polypeptide"},{"id":"http://purl.obolibrary.org/obo/SO_1000117","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."],"synonyms":[{"pred":"hasRelatedSynonym","val":"mutation affecting polypeptide function","xrefs":[]},{"pred":"hasExactSynonym","val":"sequence variant affecting polypeptide function","xrefs":[]}],"basicPropertyValues":[{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0001554"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_affecting_polypeptide_function"},{"id":"http://purl.obolibrary.org/obo/SO_0000383","meta":{"definition":{"val":"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.","xrefs":["http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/MicF_RNA"}],"synonyms":[{"pred":"hasExactSynonym","val":"MicF RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"MicF_RNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001230","meta":{"definition":{"val":"A modified RNA base in which hypoxanthine is bound to the ribose ring.","xrefs":["RSC:cb","http://library.med.utah.edu/RNAmods/"]},"comments":["The free molecule is CHEBI:17596."],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Inosine"}],"synonyms":[{"pred":"hasRelatedSynonym","val":"RNAMOD:017","xrefs":[]},{"pred":"hasRelatedSynonym","val":"I","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"inosine"},{"id":"http://purl.obolibrary.org/obo/SO_1000116","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."],"synonyms":[{"pred":"hasExactSynonym","val":"sequence variant causing conformational change","xrefs":[]},{"pred":"hasRelatedSynonym","val":"mutation causing conformational change","xrefs":[]}],"basicPropertyValues":[{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0001601"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_causing_conformational_change"},{"id":"http://purl.obolibrary.org/obo/SO_0000382","meta":{"definition":{"val":"A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon.","xrefs":["PMID:20463000"]},"synonyms":[{"pred":"hasExactSynonym","val":"group IIB intron","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"group_IIB_intron"},{"id":"http://purl.obolibrary.org/obo/SO_0001229","meta":{"definition":{"val":"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.","xrefs":["RSC:cb"]},"comments":["The free molecule is CHEBI:17802."],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Pseudouridine"},{"val":"RNAMOD:050"}],"synonyms":[{"pred":"hasExactSynonym","val":" Y","xrefs":[],"synonymType":"http://purl.obolibrary.org/obo/so#RNAMOD"}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"pseudouridine"},{"id":"http://purl.obolibrary.org/obo/SO_0001228","meta":{"definition":{"val":"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.","xrefs":["RSC:cb"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/Dihydrouridine"},{"val":"RNAMOD:051"}],"synonyms":[{"pred":"hasExactSynonym","val":" D","xrefs":[],"synonymType":"http://purl.obolibrary.org/obo/so#RNAMOD"}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"dihydrouridine"},{"id":"http://purl.obolibrary.org/obo/SO_1000122","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."],"synonyms":[{"pred":"hasExactSynonym","val":"sequence variant causing polypeptide post translational processing change","xrefs":[]},{"pred":"hasRelatedSynonym","val":"mutation causing polypeptide post translational processing change","xrefs":[]},{"pred":"hasExactSynonym","val":"polypeptide post-translational processing affected","xrefs":[]}],"basicPropertyValues":[{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0001562"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_causing_polypeptide_post_translational_processing_change"},{"id":"http://purl.obolibrary.org/obo/SO_0000378","meta":{"definition":{"val":"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.","xrefs":["http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/DsrA_RNA"}],"synonyms":[{"pred":"hasExactSynonym","val":"DsrA RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"DsrA_RNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001225","meta":{"definition":{"val":"A gene that is silenced by histone modification.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"gene silenced by histone modification","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"gene_silenced_by_histone_modification"},{"id":"http://purl.obolibrary.org/obo/SO_1000121","meta":{"comments":["OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."],"synonyms":[{"pred":"hasExactSynonym","val":"sequence variant causing polypeptide localization change","xrefs":[]},{"pred":"hasRelatedSynonym","val":"mutation causing polypeptide localization change","xrefs":[]}],"basicPropertyValues":[{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0001558"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"sequence_variant_causing_polypeptide_localization_change"},{"id":"http://purl.obolibrary.org/obo/SO_0000377","meta":{"definition":{"val":"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. 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negative.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"serine threonine staple motif","xrefs":[]},{"pred":"hasExactSynonym","val":"st_staple","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00230"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"serine_threonine_staple_motif"},{"id":"http://purl.obolibrary.org/obo/SO_0000275","meta":{"definition":{"val":"Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. 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They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing.\" to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"synonyms":[{"pred":"hasBroadSynonym","val":"INSDC_feature:ncRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"small nucleolar RNA","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:snoRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"snoRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001122","meta":{"definition":{"val":"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. 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Do not obsolete without consulting MGED ontology."],"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/SnRNA"}],"synonyms":[{"pred":"hasBroadSynonym","val":"INSDC_feature:ncRNA","xrefs":[]},{"pred":"hasExactSynonym","val":"small nuclear RNA","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:snRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"snRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0000277","meta":{"definition":{"val":"An attribute describing a sequence that is bound by another molecule.","xrefs":["SO:ke"]},"comments":["Formerly called transcript_by_bound_factor."],"synonyms":[{"pred":"hasExactSynonym","val":"bound by factor","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"bound_by_factor"},{"id":"http://purl.obolibrary.org/obo/SO_0001124","meta":{"definition":{"val":"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"schellmann loop seven","xrefs":[]},{"pred":"hasExactSynonym","val":"seven-residue schellmann loop","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00228"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"schellmann_loop_seven"},{"id":"http://purl.obolibrary.org/obo/SO_0001123","meta":{"definition":{"val":"A motif of six or seven consecutive residues that contains two H-bonds.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasRelatedSynonym","val":"paperclip","xrefs":[],"synonymType":"http://purl.obolibrary.org/obo/so#BS"},{"pred":"hasExactSynonym","val":"schellmann loop","xrefs":[]},{"pred":"hasRelatedSynonym","val":"paperclip loop","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00226"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"schellmann_loop"},{"id":"http://purl.obolibrary.org/obo/SO_0000276","meta":{"definition":{"val":"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes). 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Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.","xrefs":["PMID:2371257","SO:cb"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"type VIII turn","xrefs":[]},{"pred":"hasExactSynonym","val":"type VIII beta turn","xrefs":[]},{"pred":"hasExactSynonym","val":"beta turn type eight","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"beta_turn_type_eight"},{"id":"http://purl.obolibrary.org/obo/SO_0002004","meta":{"definition":{"val":"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS.","xrefs":["SGD:jd"]},"synonyms":[{"pred":"hasExactSynonym","val":"ARS consensus sequence","xrefs":[]},{"pred":"hasExactSynonym","val":"ACS","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2014-01-05T07:47:48Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"ARS_consensus_sequence"},{"id":"http://purl.obolibrary.org/obo/SO_0001154","meta":{"definition":{"val":"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.","xrefs":["PMID:2371257","SO:cb"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"type VIb turn","xrefs":[]},{"pred":"hasExactSynonym","val":"type VIb beta turn","xrefs":[]},{"pred":"hasExactSynonym","val":"beta turn type six b","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"beta_turn_type_six_b"},{"id":"http://purl.obolibrary.org/obo/SO_0001157","meta":{"definition":{"val":"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).","xrefs":["PMID:16827941:12537576"]},"synonyms":[{"pred":"hasExactSynonym","val":"promoter motif 1","xrefs":[]},{"pred":"hasNarrowSynonym","val":"YGGTCACATR","xrefs":[]},{"pred":"hasExactSynonym","val":"motif 1 element","xrefs":[]},{"pred":"hasExactSynonym","val":"directional motif v4","xrefs":[]},{"pred":"hasExactSynonym","val":"DMv4","xrefs":[]},{"pred":"hasExactSynonym","val":"DMv4 motif","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"DMv4_motif"},{"id":"http://purl.obolibrary.org/obo/SO_0002001","meta":{"definition":{"val":"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha).","xrefs":["SGD:jd"]},"comments":["Requested by Janos Demeter, SGD."],"synonyms":[{"pred":"hasExactSynonym","val":"Y-region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2014-01-05T07:33:30Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"Y_region"},{"id":"http://purl.obolibrary.org/obo/SO_0001156","meta":{"definition":{"val":"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.","xrefs":["PMID:12537576"]},"comments":["This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10."],"synonyms":[{"pred":"hasExactSynonym","val":"WATCGATW_motif","xrefs":[]},{"pred":"hasExactSynonym","val":"NDM4","xrefs":[]},{"pred":"hasExactSynonym","val":"DRE motif","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"DRE_motif"},{"id":"http://purl.obolibrary.org/obo/SO_0002002","meta":{"definition":{"val":"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR).","xrefs":["SGD:jd"]},"comments":["Requested by Janos Demeter, SGD."],"synonyms":[{"pred":"hasExactSynonym","val":"Z1-region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2014-01-05T07:34:59Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"Z1_region"},{"id":"http://purl.obolibrary.org/obo/SO_0001151","meta":{"definition":{"val":"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.","xrefs":["PMID:2371257","SO:cb"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"type VIa beta turn","xrefs":[]},{"pred":"hasExactSynonym","val":"type VIa turn","xrefs":[]},{"pred":"hasExactSynonym","val":"beta turn type six a","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"beta_turn_type_six_a"},{"id":"http://purl.obolibrary.org/obo/SO_0001150","meta":{"definition":{"val":"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.","xrefs":["SO:cb"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"type VI beta turn","xrefs":[]},{"pred":"hasExactSynonym","val":"cis-proline loop","xrefs":[]},{"pred":"hasExactSynonym","val":"beta turn type six","xrefs":[]},{"pred":"hasExactSynonym","val":"type VI turn","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"beta_turn_type_six"},{"id":"http://purl.obolibrary.org/obo/SO_0002000","meta":{"basicPropertyValues":[{"pred":"http://purl.obolibrary.org/obo/IAO_0100001","val":"http://purl.obolibrary.org/obo/SO_0002024"},{"pred":"http://purl.obolibrary.org/obo/IAO_0000231","val":"http://purl.obolibrary.org/obo/IAO_0000227"}],"deprecated":true},"type":"CLASS"},{"id":"http://purl.obolibrary.org/obo/SO_0001153","meta":{"definition":{"val":"A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees.","xrefs":["PMID:27428516"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"type VIa2 turn","xrefs":[]},{"pred":"hasExactSynonym","val":"beta turn type six a two","xrefs":[]},{"pred":"hasExactSynonym","val":"type VIa2 beta turn","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"beta_turn_type_six_a_two"},{"id":"http://purl.obolibrary.org/obo/SO_0001152","meta":{"definition":{"val":"A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees.","xrefs":["PMID:27428516"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"type VIa1 turn","xrefs":[]},{"pred":"hasExactSynonym","val":"beta turn type six a one","xrefs":[]},{"pred":"hasExactSynonym","val":"type VIa1 beta turn","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"beta_turn_type_six_a_one"},{"id":"http://purl.obolibrary.org/obo/so#lost","meta":{"definition":{"val":"X lost Y if X is a variant_of X' and Y part of X' but not X.","xrefs":["SO:ke"]},"comments":["A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2011-06-28T12:53:16Z"}]},"type":"PROPERTY","lbl":"lost"},{"id":"http://purl.obolibrary.org/obo/SO_0001148","meta":{"definition":{"val":"Site which has been experimentally altered.","xrefs":["EBIBS:GAR","UniProt:curation_manual"]},"comments":["Discrete."],"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"mutagen","xrefs":["uniprot:feature_type"],"synonymType":"http://purl.obolibrary.org/obo/so#BS"},{"pred":"hasExactSynonym","val":"mutated_site","xrefs":[]},{"pred":"hasExactSynonym","val":"mutagenesis","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00036"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"mutated_variant_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001147","meta":{"definition":{"val":"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.","xrefs":["EBIBS:GAR","UniProt:curation_manual"]},"comments":["Discrete."],"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasBroadSynonym","val":"natural_variant","xrefs":[]},{"pred":"hasBroadSynonym","val":"variant","xrefs":["uniprot:feature_type"]},{"pred":"hasBroadSynonym","val":"sequence variation","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00071"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"natural_variant_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001149","meta":{"definition":{"val":"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.","xrefs":["EBIBS:GAR","UniProt:curation_manual"]},"comments":["Discrete."],"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"alternative_sequence","xrefs":[]},{"pred":"hasNarrowSynonym","val":"isoform","xrefs":[]},{"pred":"hasExactSynonym","val":"var_seq","xrefs":["uniprot:feature_type"]},{"pred":"hasNarrowSynonym","val":"varsplic","xrefs":[]},{"pred":"hasNarrowSynonym","val":"sequence variation","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"SO:0001065"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00073"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"alternate_sequence_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001144","meta":{"definition":{"val":"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"st_turn_ir","xrefs":[]},{"pred":"hasExactSynonym","val":"st turn right handed type one","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00235"}]},"type":"CLASS","lbl":"st_turn_right_handed_type_one"},{"id":"http://purl.obolibrary.org/obo/SO_0000297","meta":{"definition":{"val":"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.","xrefs":["http://www.insdc.org/files/feature_table.html"]},"comments":["Moved from is_a: SO:0000296 origin_of_replication to is_a: SO:0001411 biological_region after Terrence Murphy (INSDC) pointed out that the D loop can also refer to a loop in DNA repair, which is not an origin of replication. See GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/D_loop"}],"synonyms":[{"pred":"hasExactSynonym","val":"D-loop","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_feature:D-loop","xrefs":[]},{"pred":"hasRelatedSynonym","val":"displacement loop","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"D_loop"},{"id":"http://purl.obolibrary.org/obo/SO_0001143","meta":{"definition":{"val":"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"st_turn_iil","xrefs":[]},{"pred":"hasExactSynonym","val":"st turn left handed type two","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00232"}]},"type":"CLASS","lbl":"st_turn_left_handed_type_two"},{"id":"http://purl.obolibrary.org/obo/SO_0000296","meta":{"definition":{"val":"A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites.","xrefs":["NCBI:cf","http://www.insdc.org/files/feature_table.html"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Origin_of_replication"}],"synonyms":[{"pred":"hasExactSynonym","val":"INSDC_feature:rep_origin","xrefs":[]},{"pred":"hasExactSynonym","val":"origin of replication","xrefs":[]},{"pred":"hasExactSynonym","val":"ori","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"origin_of_replication"},{"id":"http://purl.obolibrary.org/obo/SO_0000299","meta":{"definition":{"val":"A location where recombination or occurs during mitosis or meiosis.","xrefs":[]},"synonyms":[{"pred":"hasExactSynonym","val":"specific recombination site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"specific_recombination_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001146","meta":{"definition":{"val":"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.","xrefs":["EBIBS:GAR","SO:ke"]},"comments":["For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations."],"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"sequence_variations","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00336"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"polypeptide_variation_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001145","meta":{"definition":{"val":"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"st turn right handed type two","xrefs":[]},{"pred":"hasExactSynonym","val":"st_turn_iir","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00233"}]},"type":"CLASS","lbl":"st_turn_right_handed_type_two"},{"id":"http://purl.obolibrary.org/obo/SO_0000298","meta":{"definition":{"val":"A feature where there has been exchange of genetic material in the event of mitosis or meiosis","xrefs":[]},"synonyms":[{"pred":"hasExactSynonym","val":"INSDC_qualifier:other","xrefs":[]},{"pred":"hasExactSynonym","val":"recombination feature","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:misc_recomb","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"recombination_feature"},{"id":"http://purl.obolibrary.org/obo/SO_0000293","meta":{"definition":{"val":"A repetitive element that is engineered and foreign.","xrefs":["SO:xp"]},"synonyms":[{"pred":"hasExactSynonym","val":"engineered foreign repetitive element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"engineered_foreign_repetitive_element"},{"id":"http://purl.obolibrary.org/obo/SO_0001140","meta":{"definition":{"val":"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"gamma turn inverse","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00221"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"gamma_turn_inverse"},{"id":"http://purl.obolibrary.org/obo/SO_0000292","meta":{"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}],"deprecated":true},"type":"CLASS","lbl":"repetitive_element"},{"id":"http://purl.obolibrary.org/obo/SO_0000295","meta":{"definition":{"val":"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.","xrefs":["PMID:9428511"]},"comments":["May have either GT-AC or AT-AC 5' and 3' boundaries."],"synonyms":[{"pred":"hasExactSynonym","val":"U12 intron","xrefs":[]},{"pred":"hasExactSynonym","val":"U12-dependent intron","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"U12_intron"},{"id":"http://purl.obolibrary.org/obo/SO_0001142","meta":{"definition":{"val":"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"st_turn_il","xrefs":[]},{"pred":"hasExactSynonym","val":"st turn left handed type one","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00234"}]},"type":"CLASS","lbl":"st_turn_left_handed_type_one"},{"id":"http://purl.obolibrary.org/obo/SO_0001141","meta":{"definition":{"val":"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"serine/threonine turn","xrefs":[]},{"pred":"hasExactSynonym","val":"st_turn","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasAlternativeId","val":"BS:00231"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"serine_threonine_turn"},{"id":"http://purl.obolibrary.org/obo/SO_0000294","meta":{"definition":{"val":"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.","xrefs":["SO:ke"]},"subsets":["http://purl.obolibrary.org/obo/so#SOFA"],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Inverted_repeat"}],"synonyms":[{"pred":"hasExactSynonym","val":"inverted repeat sequence","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:inverted","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:repeat_region","xrefs":[]},{"pred":"hasExactSynonym","val":"inverted repeat","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"inverted_repeat"},{"id":"http://purl.obolibrary.org/obo/SO_0000291","meta":{"definition":{"val":"A region of a repeating trinucleotide sequence (three bases).","xrefs":[]},"synonyms":[{"pred":"hasExactSynonym","val":"trinucleotide repeat microsatellite feature","xrefs":[]},{"pred":"hasExactSynonym","val":"rinucleotide repeat microsatellite","xrefs":[]},{"pred":"hasExactSynonym","val":"trinucleotide repeat microsatellite locus","xrefs":[]},{"pred":"hasRelatedSynonym","val":"dinucleotide repeat microsatellite marker","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"trinucleotide_repeat_microsatellite_feature"},{"id":"http://purl.obolibrary.org/obo/SO_0000290","meta":{"definition":{"val":"A region of a repeating dinucleotide sequence (two bases).","xrefs":[]},"synonyms":[{"pred":"hasExactSynonym","val":"dinucleotide repeat microsatellite marker","xrefs":[]},{"pred":"hasExactSynonym","val":"dinucleotide repeat microsatellite","xrefs":[]},{"pred":"hasExactSynonym","val":"dinucleotide repeat microsatellite locus","xrefs":[]},{"pred":"hasExactSynonym","val":"dinucleotide repeat microsatellite feature","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"dinucleotide_repeat_microsatellite_feature"},{"id":"http://purl.obolibrary.org/obo/SO_0001137","meta":{"definition":{"val":"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. 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This term was Requested by Val Wood, PomBase."],"synonyms":[{"pred":"hasExactSynonym","val":"cis-acting homologous chromosome pairing region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2014-07-14T11:40:34Z"}]},"type":"CLASS","lbl":"cis_acting_homologous_chromosome_pairing_region"},{"id":"http://purl.obolibrary.org/obo/SO_0001177","meta":{"definition":{"val":"Non-base-paired sequence of three nucleotide bases in tRNA. 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See GitHub Issue #527."],"synonyms":[{"pred":"hasExactSynonym","val":"transcription pause site","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-02-09T15:32:52Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"transcription_pause_site"},{"id":"http://purl.obolibrary.org/obo/SO_0001198","meta":{"definition":{"val":"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"double stranded DNA virus","xrefs":[]},{"pred":"hasExactSynonym","val":"ds DNA viral sequence","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"ds_DNA_viral_sequence"},{"id":"http://purl.obolibrary.org/obo/SO_0002048","meta":{"definition":{"val":"A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).","xrefs":["SGD:se"]},"synonyms":[{"pred":"hasExactSynonym","val":"dORF","xrefs":[]},{"pred":"hasRelatedSynonym","val":"disabled_reading frame","xrefs":[]},{"pred":"hasExactSynonym","val":"disabled ORF","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-02-09T16:15:46Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"disabled_reading_frame"},{"id":"http://purl.obolibrary.org/obo/SO_0002045","meta":{"definition":{"val":"A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].","xrefs":["PMID:1489142","SO:ke"]},"comments":["Requested by Rama, SGD."],"synonyms":[{"pred":"hasExactSynonym","val":"pheromone response element","xrefs":[]},{"pred":"hasExactSynonym","val":"PRE","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-02-09T15:05:43Z"}]},"type":"CLASS","lbl":"pheromone_response_element"},{"id":"http://purl.obolibrary.org/obo/SO_0002046","meta":{"definition":{"val":"A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae.","xrefs":["PMID:1489142","SO:ke"]},"comments":["Requested by Rama, SGD."],"synonyms":[{"pred":"hasExactSynonym","val":"filamentation and invasion response element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-02-09T15:09:47Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"FRE"},{"id":"http://purl.obolibrary.org/obo/SO_0001195","meta":{"definition":{"val":"An oligo composed of (R)-GNA residues.","xrefs":["RSC:cb"]},"synonyms":[{"pred":"hasExactSynonym","val":"(R)-glycerol nucleic acid","xrefs":[]},{"pred":"hasExactSynonym","val":"R GNA oligo","xrefs":[]},{"pred":"hasExactSynonym","val":"(R)-glycol nucleic acid","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"R_GNA_oligo"},{"id":"http://purl.obolibrary.org/obo/SO_0002043","meta":{"definition":{"val":"A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"miR encoding Y-RNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:37:46Z"}]},"type":"CLASS","lbl":"miR_encoding_Y_RNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0001194","meta":{"definition":{"val":"An attribute describing a GNA sequence in the (R)-GNA enantiomer.","xrefs":["CHEBI:48016"]},"comments":["Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead."],"synonyms":[{"pred":"hasExactSynonym","val":"R GNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"R_GNA"},{"id":"http://purl.obolibrary.org/obo/SO_0002044","meta":{"definition":{"val":"A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT.","xrefs":["PMID:1489142","PMID:20118212","SO:ke"]},"comments":["Requested by Rama - SGD."],"synonyms":[{"pred":"hasExactSynonym","val":"TEA Consensus Sequence ","xrefs":[]},{"pred":"hasExactSynonym","val":"TCS element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-02-09T15:02:53Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"TCS_element"},{"id":"http://purl.obolibrary.org/obo/SO_0001197","meta":{"definition":{"val":"An oligo composed of (S)-GNA residues.","xrefs":["RSC:cb"]},"synonyms":[{"pred":"hasExactSynonym","val":"S GNA oligo","xrefs":[]},{"pred":"hasExactSynonym","val":"(S)-glycol nucleic acid","xrefs":[]},{"pred":"hasExactSynonym","val":"(S)-glycerol nucleic acid","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"S_GNA_oligo"},{"id":"http://purl.obolibrary.org/obo/SO_0002041","meta":{"definition":{"val":"A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"miR encoding vaultRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:34:32Z"}]},"type":"CLASS","lbl":"miR_encoding_vaultRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0001196","meta":{"definition":{"val":"An attribute describing a GNA sequence in the (S)-GNA enantiomer.","xrefs":["CHEBI:48017"]},"comments":["Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead."],"synonyms":[{"pred":"hasExactSynonym","val":"S GNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"S_GNA"},{"id":"http://purl.obolibrary.org/obo/SO_0002042","meta":{"definition":{"val":"A primary transcript encoding a Y-RNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"Y-RNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:36:51Z"}]},"type":"CLASS","lbl":"Y_RNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0001191","meta":{"definition":{"val":"An oligo composed of TNA residues.","xrefs":["RSC:cb"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/Threose_nucleic_acid"}],"synonyms":[{"pred":"hasExactSynonym","val":"threose nucleic acid","xrefs":[]},{"pred":"hasExactSynonym","val":"TNA oligo","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"TNA_oligo"},{"id":"http://purl.obolibrary.org/obo/SO_0002040","meta":{"definition":{"val":"A primary transcript encoding a vaultRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"vaultRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:33:33Z"}]},"type":"CLASS","lbl":"vaultRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0001190","meta":{"definition":{"val":"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.","xrefs":["CHEBI:48019"]},"comments":["Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"TNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001193","meta":{"definition":{"val":"An oligo composed of GNA residues.","xrefs":["RSC:cb"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/Glycerol_nucleic_acid"}],"synonyms":[{"pred":"hasExactSynonym","val":"glycol nucleic acid","xrefs":[]},{"pred":"hasExactSynonym","val":"GNA oligo","xrefs":[]},{"pred":"hasExactSynonym","val":"glycerol nucleic acid","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"GNA_oligo"},{"id":"http://purl.obolibrary.org/obo/SO_0001192","meta":{"definition":{"val":"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.","xrefs":["CHEBI:48015"]},"comments":["Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"GNA"},{"id":"http://purl.obolibrary.org/obo/so#edited_to","meta":{"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2009-08-19T02:19:11Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"PROPERTY","lbl":"edited_to"},{"id":"http://purl.obolibrary.org/obo/SO_0002038","meta":{"definition":{"val":"A primary transcript encoding an shRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"shRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:30:43Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"shRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0002039","meta":{"definition":{"val":"A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"miR encoding shRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:32:00Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"miR_encoding_shRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0002036","meta":{"definition":{"val":"A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"miR encoding lncRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:23:48Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"miR_encoding_lncRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0001188","meta":{"definition":{"val":"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.","xrefs":["CHEBI:48010"]},"comments":["Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"LNA"},{"id":"http://purl.obolibrary.org/obo/SO_0002037","meta":{"definition":{"val":"A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"miR encoding tRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:28:23Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"miR_encoding_tRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0001187","meta":{"definition":{"val":"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.","xrefs":["GOC:mah","PMID:12457565"]},"comments":["Has RNA pseudouridylation guide activity (GO:0030558)."],"synonyms":[{"pred":"hasExactSynonym","val":"pseudouridylation guide snoRNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"pseudouridylation_guide_snoRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0002034","meta":{"definition":{"val":"A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"miR encoding snoRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:02:13Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"miR_encoding_snoRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0002035","meta":{"definition":{"val":"A primary transcript encoding a lncRNA.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"lncRNA primary transcript","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T15:23:03Z"}]},"type":"CLASS","lbl":"lncRNA_primary_transcript"},{"id":"http://purl.obolibrary.org/obo/SO_0001189","meta":{"definition":{"val":"An oligo composed of LNA residues.","xrefs":["RSC:cb"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/Locked_nucleic_acid"}],"synonyms":[{"pred":"hasExactSynonym","val":"LNA oligo","xrefs":[]},{"pred":"hasExactSynonym","val":"locked nucleic acid","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"LNA_oligo"},{"id":"http://purl.obolibrary.org/obo/SO_0002032","meta":{"definition":{"val":"A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA.","xrefs":["SO:ke"]},"comments":["MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015."],"synonyms":[{"pred":"hasExactSynonym","val":"microRNA-offset RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T13:57:43Z"}]},"type":"CLASS","lbl":"moR"},{"id":"http://purl.obolibrary.org/obo/SO_0001184","meta":{"definition":{"val":"An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.","xrefs":["RSC:cb"]},"comments":["Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead."],"synonyms":[{"pred":"hasRelatedSynonym","val":"peptide nucleic acid","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"PNA"},{"id":"http://purl.obolibrary.org/obo/SO_0002033","meta":{"definition":{"val":"A short, non coding transcript of loop-derived sequences encoded in precursor miRNA.","xrefs":["SO:ke"]},"comments":["MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015."],"synonyms":[{"pred":"hasExactSynonym","val":"loop-origin miRs","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2015-01-09T14:02:02Z"}]},"type":"CLASS","lbl":"loR"},{"id":"http://purl.obolibrary.org/obo/SO_0001183","meta":{"definition":{"val":"An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.","xrefs":["RSC:cb"]},"comments":["Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead."],"xrefs":[{"val":"http://en.wikipedia.org/wiki/Morpholino"}],"synonyms":[{"pred":"hasExactSynonym","val":"morpholino backbone","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"morpholino_backbone"},{"id":"http://purl.obolibrary.org/obo/SO_0002030","meta":{"definition":{"val":"One of two segments of homology found at all three mating loci (HML, MAT and HMR).","xrefs":["SGD:jd"]},"synonyms":[{"pred":"hasExactSynonym","val":"x-region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2014-07-14T18:43:21Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"X_region"},{"id":"http://purl.obolibrary.org/obo/SO_0001186","meta":{"definition":{"val":"An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.","xrefs":["RSC:cb"]},"comments":["Do not use this for feature annotation. Use ribozyme (SO:0000374) instead."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"ribozymic"},{"id":"http://purl.obolibrary.org/obo/SO_0002031","meta":{"definition":{"val":"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference.","xrefs":["PMID:6699500","SO:ke"]},"xrefs":[{"val":"http:http:en.wikipedia.org/wiki/Small_hairpin_RNA"}],"synonyms":[{"pred":"hasExactSynonym","val":"small hairpin RNA","xrefs":[]},{"pred":"hasExactSynonym","val":"short hairpin RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2014-10-23T09:16:29Z"}]},"type":"CLASS","lbl":"shRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0001185","meta":{"definition":{"val":"An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.","xrefs":["RSC:cb"]},"comments":["Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"enzymatic"},{"id":"http://purl.obolibrary.org/obo/SO_0001180","meta":{"definition":{"val":"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.","xrefs":["PMID:7892223"]},"xrefs":[{"val":"http://en.wikipedia.org/wiki/AU-rich_element"}],"synonyms":[{"pred":"hasRelatedSynonym","val":"ARE","xrefs":[]},{"pred":"hasExactSynonym","val":"AU-rich element","xrefs":[]},{"pred":"hasExactSynonym","val":"AU rich element","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"AU_rich_element"},{"id":"http://purl.obolibrary.org/obo/SO_0001182","meta":{"definition":{"val":"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. 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protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).","xrefs":["EBIBS:GAR"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"peptide coil","xrefs":[]},{"pred":"hasRelatedSynonym","val":"random coil","xrefs":[],"synonymType":"http://purl.obolibrary.org/obo/so#BS"},{"pred":"hasRelatedSynonym","val":"coil","xrefs":[],"synonymType":"http://purl.obolibrary.org/obo/so#BS"}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"peptide_coil"},{"id":"http://purl.obolibrary.org/obo/SO_0100006","meta":{"definition":{"val":"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"catmat-3r","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"catmat_right_handed_three"},{"id":"http://purl.obolibrary.org/obo/SO_0100007","meta":{"definition":{"val":"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"catmat-4r","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"catmat_right_handed_four"},{"id":"http://purl.obolibrary.org/obo/SO_0100004","meta":{"definition":{"val":"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"catmat-3l","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"catmat_left_handed_three"},{"id":"http://purl.obolibrary.org/obo/SO_0100005","meta":{"definition":{"val":"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"catmat-4l","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"catmat_left_handed_four"},{"id":"http://www.geneontology.org/formats/oboInOwl#inSubset","type":"PROPERTY","lbl":"in_subset"},{"id":"http://purl.obolibrary.org/obo/SO_0100008","meta":{"definition":{"val":"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.","xrefs":["EBIBS:GAR","http://www.ebi.ac.uk/msd-srv/msdmotif/"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"alpha beta motif","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"alpha_beta_motif"},{"id":"http://purl.obolibrary.org/obo/SO_0100009","meta":{"definition":{"val":"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.","xrefs":["EBIBS:GAR"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"prokaryotic membrane lipoprotein lipid attachment site","xrefs":[]},{"pred":"hasExactSynonym","val":"lipoprotein signal peptide","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"lipoprotein_signal_peptide"},{"id":"http://purl.obolibrary.org/obo/SO_0002098","meta":{"definition":{"val":"A pseudogene derived from an immunoglobulin gene.","xrefs":["SO:ke"]},"comments":["These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."],"synonyms":[{"pred":"hasExactSynonym","val":"immunoglobulin pseudogene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-07-15T16:01:47Z"}]},"type":"CLASS","lbl":"immunoglobulin_pseudogene"},{"id":"http://purl.obolibrary.org/obo/SO_0002099","meta":{"definition":{"val":"A pseudogene derived from a T-cell receptor gene.","xrefs":["SO:ke"]},"comments":["These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-07-15T16:02:18Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"T_cell_receptor_pseudogene"},{"id":"http://purl.obolibrary.org/obo/SO_0002096","meta":{"definition":{"val":"A variation that expands or contracts a tandem repeat with regard to a reference.","xrefs":["SO:ke"]},"synonyms":[{"pred":"hasExactSynonym","val":"short tandem repeat variation","xrefs":[]},{"pred":"hasExactSynonym","val":"str variation","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-07-14T16:04:40Z"}]},"type":"CLASS","lbl":"short_tandem_repeat_variation"},{"id":"http://purl.obolibrary.org/obo/SO_0002097","meta":{"definition":{"val":"A pseudogene derived from a vertebrate immune system gene.","xrefs":["SO:ke"]},"comments":["These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."],"synonyms":[{"pred":"hasExactSynonym","val":"vertebrate immune system pseudogene","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-07-15T16:00:22Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"vertebrate_immune_system_pseudogene"},{"id":"http://purl.obolibrary.org/obo/SO_0002094","meta":{"definition":{"val":"A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination.","xrefs":[]},"synonyms":[{"pred":"hasExactSynonym","val":"INSDC_qualifier:non_allelic_homologous","xrefs":[]},{"pred":"hasBroadSynonym","val":"INSDC_feature:misc_recomb","xrefs":[]},{"pred":"hasExactSynonym","val":"NAHRR","xrefs":[]},{"pred":"hasExactSynonym","val":"INSDC_qualifier:non_allelic_homologous_recombination","xrefs":[]},{"pred":"hasExactSynonym","val":"non allelic homologous recombination region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-05-17T13:34:12Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"nicole"}]},"type":"CLASS","lbl":"non_allelic_homologous_recombination_region"},{"id":"http://purl.obolibrary.org/obo/SO_0002095","meta":{"definition":{"val":"A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs).","xrefs":["PMC:126017","PMID:27775477","PMID:28869095","SO:nrs"]},"comments":["Moved from is_a ncRNA (SO:0000655) to is_a snoRNA (SO:0000275) as per request from FlyBase by Dave Sant 24 April 2021. See GitHub Issue #509."],"xrefs":[{"val":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/"}],"synonyms":[{"pred":"hasExactSynonym","val":"small Cajal body specific RNA","xrefs":[]},{"pred":"hasExactSynonym","val":"small Cajal body-specific RNA","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-05-19T13:42:45Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"nicole"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"scaRNA"},{"id":"http://purl.obolibrary.org/obo/SO_0002092","meta":{"definition":{"val":"A UTR variant of exonic sequence of the 5' UTR.","xrefs":["SO:ke"]},"comments":["Requested by visze github tracker ID 346."],"synonyms":[{"pred":"hasExactSynonym","val":"5 prime UTR exon variant","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-03-07T10:38:26Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"5_prime_UTR_exon_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0002093","meta":{"definition":{"val":"A variant that impacts the internal interactions of the resulting polypeptide structure.","xrefs":["SO:ke"]},"comments":["Requested by Pablo Cingolani. The way I calculate this is simply by looking at the PDB entry of one protein and then marking those AA that are within 3 Angstrom of each other (and far away in the AA sequence, e.g. over 20 AA distance). The assumption is that, since they are very close in distance, they must be \"interacting\" and thus important for protein structure."],"synonyms":[{"pred":"hasExactSynonym","val":"structural interaction variant","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-03-07T11:43:55Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"structural_interaction_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0100002","meta":{"definition":{"val":"A region that is involved a contact with another molecule.","xrefs":["EBIBS:GAR"]},"comments":["Range."],"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasRelatedSynonym","val":"molecular contact region","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"molecular_contact_region"},{"id":"http://purl.obolibrary.org/obo/SO_0002090","meta":{"definition":{"val":"A UTR variant of intronic sequence of the 3' UTR.","xrefs":["SO:ke"]},"comments":["Requested by visze github tracker ID 346."],"synonyms":[{"pred":"hasExactSynonym","val":"3 prime UTR intron variant","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-03-07T10:37:41Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"3_prime_UTR_intron_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0002091","meta":{"definition":{"val":"A UTR variant of intronic sequence of the 5' UTR.","xrefs":["SO:ke"]},"comments":["Requested by visze github tracker ID 346."],"synonyms":[{"pred":"hasExactSynonym","val":"5 prime UTR intron variant","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2016-03-07T10:38:04Z"}]},"type":"CLASS","lbl":"5_prime_UTR_intron_variant"},{"id":"http://purl.obolibrary.org/obo/SO_0100003","meta":{"definition":{"val":"A region of polypeptide chain with high conformational flexibility.","xrefs":["EBIBS:GAR"]},"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasExactSynonym","val":"intrinsically unstructured polypeptide region","xrefs":[]},{"pred":"hasRelatedSynonym","val":"disordered region","xrefs":[],"synonymType":"http://purl.obolibrary.org/obo/so#BS"}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"intrinsically_unstructured_polypeptide_region"},{"id":"http://purl.obolibrary.org/obo/SO_0100001","meta":{"definition":{"val":"A region of a peptide that is involved in a biochemical function.","xrefs":["EBIBS:GAR"]},"comments":["Range."],"subsets":["http://purl.obolibrary.org/obo/so#biosapiens"],"synonyms":[{"pred":"hasRelatedSynonym","val":"biochemical_region","xrefs":[]},{"pred":"hasExactSynonym","val":"biochemical motif","xrefs":[]},{"pred":"hasExactSynonym","val":"biochemical region of peptide","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"biochemical_region_of_peptide"},{"id":"http://purl.obolibrary.org/obo/SO_0001929","meta":{"definition":{"val":"A sequencer read of a mitochondrial DNA sample.","xrefs":["GMOD:ea"]},"comments":["Requested by Bayer Cropscience, October, 2012."],"synonyms":[{"pred":"hasExactSynonym","val":"mitochondrial DNA read","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2012-11-14T04:39:56Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"},{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"}]},"type":"CLASS","lbl":"mitochondrial_DNA_read"},{"id":"http://purl.obolibrary.org/obo/SO_0001926","meta":{"definition":{"val":"A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts.","xrefs":["PMID:22139915"]},"comments":["Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012."],"synonyms":[{"pred":"hasExactSynonym","val":"anti-ARRET","xrefs":[]}],"basicPropertyValues":[{"pred":"http://www.geneontology.org/formats/oboInOwl#hasOBONamespace","val":"sequence"},{"pred":"http://www.geneontology.org/formats/oboInOwl#creation_date","val":"2012-10-31T01:40:22Z"},{"pred":"http://www.geneontology.org/formats/oboInOwl#created_by","val":"kareneilbeck"}]},"type":"CLASS","lbl":"anti_ARRET"},{"id":"http://purl.obolibrary.org/obo/SO_0001925","meta":{"definition":{"val":"A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats.","xrefs":["PMID:22139915"]},"comments":["Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. 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The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.", - "xrefs" : [ "SO:xp" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "recoded codon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000146", - "lbl" : "capped", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.", - "xrefs" : [ "SO:ke" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000147", - "lbl" : "exon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:exon" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Exon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000148", - "lbl" : "supercontig", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.", - "xrefs" : [ "SO:ls" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "scaffold" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000149", - "lbl" : "contig", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.", - "xrefs" : [ "SO:ls" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Contig" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000150", - "lbl" : "read", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.", - "xrefs" : [ "SO:rd" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000151", - "lbl" : "clone", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "xrefs" : [ { - "val" : "http:http://en.wikipedia.org/wiki/Clone_(genetics)" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000152", - "lbl" : "YAC", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.", - "xrefs" : [ "SO:ma" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "yeast artificial chromosome" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000153", - "lbl" : "BAC", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.", - "xrefs" : [ "SO:ma" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "bacterial artificial chromosome" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000154", - "lbl" : "PAC", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.", - "xrefs" : [ "http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "P1" - }, { - "pred" : "hasExactSynonym", - "val" : "P1 artificial chromosome" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000155", - "lbl" : "plasmid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.", - "xrefs" : [ "SO:ma" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "plasmid sequence" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000156", - "lbl" : "cosmid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.", - "xrefs" : [ "SO:ma" ] - }, - "comments" : [ "Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cosmid vector" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Cosmid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000157", - "lbl" : "phagemid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.", - "xrefs" : [ "SO:ma" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "phagemid vector" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Phagemid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000158", - "lbl" : "fosmid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cloning vector that utilizes the E. coli F factor.", - "xrefs" : [ "SO:ma" ] - }, - "comments" : [ "Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "fosmid vector" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Fosmid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000159", - "lbl" : "deletion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The point at which one or more contiguous nucleotides were excised.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "deleted_sequence" - }, { - "pred" : "hasExactSynonym", - "val" : "nucleotide deletion" - }, { - "pred" : "hasExactSynonym", - "val" : "nucleotide_deletion" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Nucleotide_deletion" - }, { - "val" : "loinc:LA6692-3" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "SO:1000033" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000160", - "lbl" : "lambda_clone", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. 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A splice_site that is upstream_adjacent_to exon and finishes intron.", - "xrefs" : [ "SO:cjm", "SO:ke", "http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "acceptor splice site" - }, { - "pred" : "hasExactSynonym", - "val" : "splice acceptor site" - }, { - "pred" : "hasExactSynonym", - "val" : "three prime splice site" - }, { - "pred" : "hasRelatedSynonym", - "val" : "3' splice site" - }, { - "pred" : "hasRelatedSynonym", - "val" : "acceptor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000165", - "lbl" : "enhancer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "comments" : [ "An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:enhancer" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Enhancer_(genetics)" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000166", - "lbl" : "enhancer_bound_by_factor", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An enhancer bound by a factor.", - "xrefs" : [ "SO:xp" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "enhancer bound by factor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000167", - "lbl" : "promoter", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.", - "xrefs" : [ "SO:regcreative" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "promoter sequence" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Promoter" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000168", - "lbl" : "restriction_enzyme_cut_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.", - "xrefs" : [ "SO:ma" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000169", - "lbl" : "RNApol_I_promoter", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RNA polymerase A promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "RNApol I promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "pol I promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "polymerase I promoter" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000170", - "lbl" : "RNApol_II_promoter", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RNA polymerase B promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "RNApol II promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "polymerase II promoter" - }, { - "pred" : "hasRelatedSynonym", - "val" : "pol II promoter" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000171", - "lbl" : "RNApol_III_promoter", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RNA polymerase C promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "RNApol III promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "pol III promoter" - }, { - "pred" : "hasExactSynonym", - "val" : "polymerase III promoter" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000172", - "lbl" : "CAAT_signal", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "CAAT box" - }, { - "pred" : "hasExactSynonym", - "val" : "CAAT signal" - }, { - "pred" : "hasExactSynonym", - "val" : "CAAT-box" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:CAAT_signal" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/CAAT_box" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000173", - "lbl" : "GC_rich_promoter_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "GC rich promoter region" - }, { - "pred" : "hasExactSynonym", - "val" : "GC-rich region" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:GC_rich_promoter_region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000174", - "lbl" : "TATA_box", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).", - "xrefs" : [ "PMID:16858867", "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "comments" : [ "Binds TBP." ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "Goldstein-Hogness box" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:TATA_box" - }, { - "pred" : "hasExactSynonym", - "val" : "TATA box" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/TATA_box" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000175", - "lbl" : "minus_10_signal", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "-10 signal" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:minus_10_signal" - }, { - "pred" : "hasExactSynonym", - "val" : "Pribnow Schaller box" - }, { - "pred" : "hasExactSynonym", - "val" : "Pribnow box" - }, { - "pred" : "hasExactSynonym", - "val" : "Pribnow-Schaller box" - }, { - "pred" : "hasExactSynonym", - "val" : "minus 10 signal" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Pribnow_box" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000176", - "lbl" : "minus_35_signal", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "-35 signal" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:minus_35_signal" - }, { - "pred" : "hasExactSynonym", - "val" : "minus 35 signal" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000177", - "lbl" : "cross_genome_match", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A nucleotide match against a sequence from another organism.", - "xrefs" : [ "SO:ma" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cross genome match" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000178", - "lbl" : "operon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.", - "xrefs" : [ "SO:ma" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:operon" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Operon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000179", - "lbl" : "clone_insert_start", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The start of the clone insert.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "clone insert start" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000180", - "lbl" : "retrotransposon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.", - "xrefs" : [ "http://www.dddmag.com/Glossary.aspx#r" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "class I transposon" - }, { - "pred" : "hasExactSynonym", - "val" : "retrotransposon element" - }, { - "pred" : "hasRelatedSynonym", - "val" : "class I" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Retrotransposon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000181", - "lbl" : "translated_nucleotide_match", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A match against a translated sequence.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "translated nucleotide match" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000182", - "lbl" : "DNA_transposon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transposon where the mechanism of transposition is via a DNA intermediate.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA transposon" - }, { - "pred" : "hasExactSynonym", - "val" : "class II transposon" - }, { - "pred" : "hasRelatedSynonym", - "val" : "class II" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000183", - "lbl" : "non_transcribed_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of the gene which is not transcribed.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "non transcribed region" - }, { - "pred" : "hasExactSynonym", - "val" : "non-transcribed sequence" - }, { - "pred" : "hasExactSynonym", - "val" : "nontranscribed region" - }, { - "pred" : "hasExactSynonym", - "val" : "nontranscribed sequence" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000184", - "lbl" : "U2_intron", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.", - "xrefs" : [ "PMID:9428511" ] - }, - "comments" : [ "May have either GT-AG or AT-AG 5' and 3' boundaries." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "U2 intron" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000185", - "lbl" : "primary_transcript", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transcript that in its initial state requires modification to be functional.", - "xrefs" : [ "SO:ma" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:precursor_RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:prim_transcript" - }, { - "pred" : "hasExactSynonym", - "val" : "precursor RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "primary transcript" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Primary_transcript" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000186", - "lbl" : "LTR_retrotransposon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A retrotransposon flanked by long terminal repeat sequences.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "LTR retrotransposon" - }, { - "pred" : "hasExactSynonym", - "val" : "long terminal repeat retrotransposon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000187", - "lbl" : "repeat_family", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A group of characterized repeat sequences.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000188", - "lbl" : "intron", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "comments" : [ "This term is mapped to MGED. 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Do not obsolete without consulting MGED ontology." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Chromosome" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000341", - "lbl" : "chromosome_band", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.", - "xrefs" : [ "SO:ma" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chromosome band" - }, { - "pred" : "hasExactSynonym", - "val" : "cytoband" - }, { - "pred" : "hasExactSynonym", - "val" : "cytological band" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Cytological_band" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000342", - "lbl" : "site_specific_recombination_target_region", - "type" : "CLASS", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "site specific recombination target region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000343", - "lbl" : "match", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000344", - "lbl" : "splice_enhancer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Region of a transcript that regulates splicing.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "splice enhancer" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000345", - "lbl" : "EST", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "expressed sequence tag" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000346", - "lbl" : "loxP_site", - "type" : "CLASS", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "loxP site" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Cre-recombination target region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000347", - "lbl" : "nucleotide_match", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A match against a nucleotide sequence.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "nucleotide match" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000348", - "lbl" : "nucleic_acid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.", - "xrefs" : [ "CHEBI:33696", "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "nucleic acid" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Nucleic_acid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000349", - "lbl" : "protein_match", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A match against a protein sequence.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "protein match" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000350", - "lbl" : "FRT_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.", - "xrefs" : [ "SO:ma" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "FLP recombination target region" - }, { - "pred" : "hasExactSynonym", - "val" : "FRT site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000351", - "lbl" : "synthetic_sequence", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.", - "xrefs" : [ "SO:ma" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "synthetic sequence" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000352", - "lbl" : "DNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.", - "xrefs" : [ "RSC:cb" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000353", - "lbl" : "sequence_assembly", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.", - "xrefs" : [ "SO:ma" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "sequence assembly" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Sequence_assembly" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000354", - "lbl" : "group_1_intron_homing_endonuclease_target_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of intronic nucleotide sequence targeted by a nuclease enzyme.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "group 1 intron homing endonuclease target region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000355", - "lbl" : "haplotype_block", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of the genome which is co-inherited as the result of the lack of historic recombination within it.", - "xrefs" : [ "SO:ma" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "haplotype block" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000356", - "lbl" : "RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.", - "xrefs" : [ "RSC:cb" ] - }, - "comments" : [ "This term is mapped to MGED. 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Usually an experimental artifact.", - "xrefs" : [ "SO:ma" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "invalidated by chimeric cDNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000363", - "lbl" : "floxed_gene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transgene that is floxed.", - "xrefs" : [ "SO:xp" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "floxed gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000364", - "lbl" : "transposable_element_flanking_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The region of sequence surrounding a transposable element.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "transposable element flanking region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000365", - "lbl" : "integron", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.", - "xrefs" : [ "SO:as" ] - }, - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Integron" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000366", - "lbl" : "insertion_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The junction where an insertion occurred.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "insertion site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000367", - "lbl" : "attI_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.", - "xrefs" : [ "SO:as" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "attI site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000368", - "lbl" : "transposable_element_insertion_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The junction in a genome where a transposable_element has inserted.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "transposable element insertion site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000369", - "lbl" : "integrase_coding_region", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000370", - "lbl" : "small_regulatory_ncRNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others).", - "xrefs" : [ "PMID:28541282", "PomBase:al", "SO:ma" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "small regulatory ncRNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000371", - "lbl" : "conjugative_transposon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transposon that encodes function required for conjugation.", - "xrefs" : [ "http://www.sci.sdsu.edu/~smaloy/Glossary/C.html" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "conjugative transposon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000372", - "lbl" : "enzymatic_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.", - "xrefs" : [ "RSC:cb" ] - }, - "comments" : [ "This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "enzymatic RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000373", - "lbl" : "recombinationally_inverted_gene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A recombinationally rearranged gene by inversion.", - "xrefs" : [ "SO:xp" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "recombinationally inverted gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000374", - "lbl" : "ribozyme", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An RNA with catalytic activity.", - "xrefs" : [ "SO:ma" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:ncRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:ribozyme" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Ribozyme" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000375", - "lbl" : "rRNA_5_8S", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "5.8S LSU rRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "5.8S rRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "5.8S ribosomal RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "rRNA 5 8S" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000376", - "lbl" : "RNA_6S", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "6S RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "RNA 6S" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/6S_RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000377", - "lbl" : "CsrB_RsmB_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "CsrB RsmB RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "CsrB-RsmB RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000378", - "lbl" : "DsrA_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DsrA RNA" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/DsrA_RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000379", - "lbl" : "GcvB_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "GcvB RNA" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/GcvB_RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000380", - "lbl" : "hammerhead_ribozyme", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.", - "xrefs" : [ "PMID:2436805" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:ncRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:hammerhead_ribozyme" - }, { - "pred" : "hasExactSynonym", - "val" : "hammerhead ribozyme" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Hammerhead_ribozyme" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000381", - "lbl" : "group_IIA_intron", - "type" : "CLASS", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "group IIA intron" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000382", - "lbl" : "group_IIB_intron", - "type" : "CLASS", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "group IIB intron" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000383", - "lbl" : "MicF_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "MicF RNA" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/MicF_RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000384", - "lbl" : "OxyS_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "OxyS RNA" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/OxyS_RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000385", - "lbl" : "RNase_MRP_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:ncRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:RNase_MRP_RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "RNase MRP RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000386", - "lbl" : "RNase_P_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:ncRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:RNase_P_RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "RNase P RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000387", - "lbl" : "RprA_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RprA RNA" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/RprA_RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000388", - "lbl" : "RRE_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RRE RNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000389", - "lbl" : "spot_42_RNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. 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"xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:misc_difference" - }, { - "pred" : "hasExactSynonym", - "val" : "sequence difference" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000414", - "lbl" : "invalidated_by_genomic_contamination", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute to describe a feature that is invalidated due to genomic contamination.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "invalidated by genomic contamination" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000415", - "lbl" : "invalidated_by_genomic_polyA_primed_cDNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute to describe a feature that is invalidated due to polyA priming.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "invalidated by genomic polyA primed cDNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000416", - "lbl" : "invalidated_by_partial_processing", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute to describe a feature that is invalidated due to partial processing.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "invalidated by partial processing" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000417", - "lbl" : "polypeptide_domain", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A structurally or functionally defined protein region. 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This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.", - "xrefs" : [ "PMID:12177293" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Hoogsteen base pair" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Hoogsteen_base_pair" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000501", - "lbl" : "reverse_Hoogsteen_base_pair", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A type of non-canonical base-pairing.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "reverse Hoogsteen base pair" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000502", - "lbl" : "transcribed_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of sequence that is transcribed. 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We are going with 'associated_with' for the time being." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000503", - "lbl" : "alternately_spliced_gene_encodeing_one_transcript", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000504", - "lbl" : "D_DJ_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "D DJ C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "D-(DJ)-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000505", - "lbl" : "D_DJ_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "D DJ cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "D-(DJ)-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000506", - "lbl" : "D_DJ_J_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "D DJ J C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "D-(DJ)-J-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000507", - "lbl" : "pseudogenic_exon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non functional descendant of an exon, part of a pseudogene.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pseudogenic exon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000508", - "lbl" : "D_DJ_J_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "D DJ J cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "D-(DJ)-J-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000509", - "lbl" : "D_J_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "D J C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "D-J-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000510", - "lbl" : "VD_gene_segment", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "VD gene" - }, { - "pred" : "hasExactSynonym", - "val" : "V_D_GENE" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000511", - "lbl" : "J_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "J C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "J-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000512", - "lbl" : "inversion_derived_deficiency_plus_aneuploid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.", - "xrefs" : [ "FB:km" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "inversion derived deficiency plus aneuploid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000513", - "lbl" : "J_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "J cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "J-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000514", - "lbl" : "J_nonamer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "J nonamer" - }, { - "pred" : "hasExactSynonym", - "val" : "J-NONAMER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000515", - "lbl" : "J_heptamer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "J heptamer" - }, { - "pred" : "hasExactSynonym", - "val" : "J-HEPTAMER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000516", - "lbl" : "pseudogenic_transcript", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non functional descendant of a transcript, part of a pseudogene.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations." ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:misc_RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:pseudo" - }, { - "pred" : "hasExactSynonym", - "val" : "pseudogenic transcript" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000517", - "lbl" : "J_spacer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "J spacer" - }, { - "pred" : "hasExactSynonym", - "val" : "J-SPACER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000518", - "lbl" : "V_DJ_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V DJ cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-(DJ)-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000519", - "lbl" : "V_DJ_J_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V DJ J cluster" - }, { - "pred" : "hasRelatedSynonym", - "val" : "V-(DJ)-J-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000520", - "lbl" : "V_VDJ_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V VDJ C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-(VDJ)-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000521", - "lbl" : "V_VDJ_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V VDJ cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-(VDJ)-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000522", - "lbl" : "V_VDJ_J_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V VDJ J cluster" - }, { - "pred" : "hasRelatedSynonym", - "val" : "V-(VDJ)-J-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000523", - "lbl" : "V_VJ_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V VJ C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-(VJ)-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000524", - "lbl" : "V_VJ_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V VJ cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-(VJ)-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000525", - "lbl" : "V_VJ_J_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V VJ J cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-(VJ)-J-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000526", - "lbl" : "V_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000527", - "lbl" : "V_D_DJ_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V D DJ C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-D-(DJ)-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000528", - "lbl" : "V_D_DJ_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V D DJ cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-D-(DJ)-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000529", - "lbl" : "V_D_DJ_J_C_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "V D DJ J C cluster" - }, { - "pred" : "hasExactSynonym", - "val" : "V-D-(DJ)-J-C-CLUSTER" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000530", - "lbl" : "V_D_DJ_J_cluster", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.", - "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ] - 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These chromosomes are described as translocation elements. 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A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.", - "xrefs" : [ "SO:immuno_workshop" ] - }, - "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:gene" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000705", - "lbl" : "tandem_repeat", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Two or more adjacent copies of a region (of length greater than 1).", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:repeat_region" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:tandem" - }, { - "pred" : "hasExactSynonym", - "val" : "tandem repeat" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Tandem_repeat" - }, { - "val" : "http://www.sci.sdsu.edu/~smaloy/Glossary/T.html" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000706", - "lbl" : "trans_splice_acceptor_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The 3' splice site of the acceptor primary transcript.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trans splice acceptor site" - }, { - "pred" : "hasRelatedSynonym", - "val" : "3' trans splice site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000707", - "lbl" : "trans_splice_donor_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The 5' five prime splice site region of the donor RNA.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "SL RNA contains a donor site." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trans splice donor site" - }, { - "pred" : "hasExactSynonym", - "val" : "trans-splice donor site" - }, { - "pred" : "hasRelatedSynonym", - "val" : "5 prime trans splice site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000708", - "lbl" : "SL1_acceptor_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.", - "xrefs" : [ "SO:nlw" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "SL1 acceptor site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000709", - "lbl" : "SL2_acceptor_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.", - "xrefs" : [ "SO:nlw" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "SL2 acceptor site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000710", - "lbl" : "gene_with_stop_codon_redefined_as_selenocysteine", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene encoding an mRNA that has the stop codon redefined as selenocysteine.", - "xrefs" : [ "SO:xp" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gene with stop codon redefined as selenocysteine" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000711", - "lbl" : "gene_with_mRNA_recoded_by_translational_bypass", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene with mRNA recoded by translational bypass.", - "xrefs" : [ "SO:xp" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gene with mRNA recoded by translational bypass" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000712", - "lbl" : "gene_with_transcript_with_translational_frameshift", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene encoding a transcript that has a translational frameshift.", - "xrefs" : [ "SO:xp" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gene with transcript with translational frameshift" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000713", - "lbl" : "DNA_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A motif that is active in the DNA form of the sequence.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA motif" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/DNA_motif" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000714", - "lbl" : "nucleotide_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of nucleotide sequence corresponding to a known motif.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:misc_feature" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_note:nucleotide_motif" - }, { - "pred" : "hasExactSynonym", - "val" : "nucleotide motif" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000715", - "lbl" : "RNA_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A motif that is active in RNA sequence.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RNA motif" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000716", - "lbl" : "dicistronic_mRNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An mRNA that has the quality dicistronic.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "dicistronic mRNA" - }, { - "pred" : "hasRelatedSynonym", - "val" : "dicistronic processed transcript" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000717", - "lbl" : "reading_frame", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.", - "xrefs" : [ "SGD:rb" ] - }, - "comments" : [ "This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "reading frame" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Reading_frame" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000718", - "lbl" : "blocked_reading_frame", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons.", - "xrefs" : [ "SGD:rb" ] - }, - "comments" : [ "Term requested by Rama from SGD." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blocked reading frame" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000719", - "lbl" : "ultracontig", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.", - "xrefs" : [ "FB:WG" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "superscaffold" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000720", - "lbl" : "foreign_transposable_element", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transposable element that is foreign.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "requested by Michael on 19 Nov 2004." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "foreign transposable element" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000721", - "lbl" : "gene_with_dicistronic_primary_transcript", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene that encodes a dicistronic primary transcript.", - "xrefs" : [ "SO:xp" ] - }, - "comments" : [ "Requested by Michael, 19 nov 2004." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gene with dicistronic primary transcript" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000722", - "lbl" : "gene_with_dicistronic_mRNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene that encodes a polycistronic mRNA.", - "xrefs" : [ "SO:xp" ] - }, - "comments" : [ "Requested by MA nov 19 2004." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gene with dicistronic mRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "gene with dicistronic processed transcript" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000723", - "lbl" : "iDNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Genomic sequence removed from the genome, as a normal event, by a process of recombination.", - "xrefs" : [ "SO:ma" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:iDNA" - }, { - "pred" : "hasExactSynonym", - "val" : "intervening DNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000724", - "lbl" : "oriT", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:oriT" - }, { - "pred" : "hasExactSynonym", - "val" : "origin of transfer" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Origin_of_transfer" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000725", - "lbl" : "transit_peptide", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).", - "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] - }, - "comments" : [ "Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:transit_peptide" - }, { - "pred" : "hasExactSynonym", - "val" : "transit peptide" - }, { - "pred" : "hasRelatedSynonym", - "val" : "signal" - }, { - "pred" : "hasRelatedSynonym", - "val" : "transit", - "xrefs" : [ "uniprot:feature_type" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00055" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000726", - "lbl" : "repeat_unit", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The simplest repeated component of a repeat region. A single repeat.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "Added to comply with the feature table. A single repeat." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "repeat unit" - } ], - "xrefs" : [ { - "val" : "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000727", - "lbl" : "CRM", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.", - "xrefs" : [ "PMID:19660565", "SO:SG" ] - }, - "comments" : [ "Requested by Stephen Grossmann Dec 2004." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "TF module" - }, { - "pred" : "hasExactSynonym", - "val" : "cis regulatory module" - }, { - "pred" : "hasExactSynonym", - "val" : "transcription factor module" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000728", - "lbl" : "intein", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "Intein-mediated protein splicing occurs after mRNA has been translated into a protein." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "protein intron" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Intein" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000729", - "lbl" : "intein_containing", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute of protein-coding genes where the initial protein product contains an intein.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "intein containing" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000730", - "lbl" : "gap", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gap in the sequence of known length. The unknown bases are filled in with N's.", - "xrefs" : [ "SO:ke" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "INSDC_feature:gap" - }, { - "pred" : "hasNarrowSynonym", - "val" : "INSDC_feature:assembly_gap" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000731", - "lbl" : "fragmentary", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute to describe a feature that is incomplete.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "Term added because of request by MO people." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "fragment" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000732", - "lbl" : "predicted", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing an unverified region.", - "xrefs" : [ "SO:ke" ] - }, - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Predicted" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000733", - "lbl" : "feature_attribute", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a located_sequence_feature.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "feature attribute" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0000734", - "lbl" : "exemplar_mRNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An exemplar is a representative cDNA sequence for each gene. 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Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "asx turn left handed type two" - }, { - "pred" : "hasExactSynonym", - "val" : "asx_turn_iil" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00204" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001131", - "lbl" : "asx_turn_right_handed_type_two", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "asx turn right handed type two" - }, { - "pred" : "hasExactSynonym", - "val" : "asx_turn_iir" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001132", - "lbl" : "asx_turn_right_handed_type_one", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. 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It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn left handed type one" - }, { - "pred" : "hasExactSynonym", - "val" : "beta_turn_il" - }, { - "pred" : "hasExactSynonym", - "val" : "type I' beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type I' turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00215" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001135", - "lbl" : "beta_turn_left_handed_type_two", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. 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It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. 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It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn right handed type two" - }, { - "pred" : "hasExactSynonym", - "val" : "beta_turn_iir" - }, { - "pred" : "hasExactSynonym", - "val" : "type II beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type II turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00214" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001138", - "lbl" : "gamma_turn", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gamma turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00219" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001139", - "lbl" : "gamma_turn_classic", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "classic gamma turn" - }, { - "pred" : "hasExactSynonym", - "val" : "gamma turn classic" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00220" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001140", - "lbl" : "gamma_turn_inverse", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gamma turn inverse" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00221" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001141", - "lbl" : "serine_threonine_turn", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "serine/threonine turn" - }, { - "pred" : "hasExactSynonym", - "val" : "st_turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00231" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001142", - "lbl" : "st_turn_left_handed_type_one", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The peptide twists in an anticlockwise, left handed manner. 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The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "st turn left handed type two" - }, { - "pred" : "hasExactSynonym", - "val" : "st_turn_iil" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00232" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001144", - "lbl" : "st_turn_right_handed_type_one", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "st turn right handed type one" - }, { - "pred" : "hasExactSynonym", - "val" : "st_turn_ir" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001145", - "lbl" : "st_turn_right_handed_type_two", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.", - "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "st turn right handed type two" - }, { - "pred" : "hasExactSynonym", - "val" : "st_turn_iir" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00233" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001146", - "lbl" : "polypeptide_variation_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.", - "xrefs" : [ "EBIBS:GAR", "SO:ke" ] - }, - "comments" : [ "For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "sequence_variations" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00336" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001147", - "lbl" : "natural_variant_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.", - "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ] - }, - "comments" : [ "Discrete." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "natural_variant" - }, { - "pred" : "hasBroadSynonym", - "val" : "sequence variation" - }, { - "pred" : "hasBroadSynonym", - "val" : "variant", - "xrefs" : [ "uniprot:feature_type" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00071" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001148", - "lbl" : "mutated_variant_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Site which has been experimentally altered.", - "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ] - }, - "comments" : [ "Discrete." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/so#BS", - "pred" : "hasExactSynonym", - "val" : "mutagen", - "xrefs" : [ "uniprot:feature_type" ] - }, { - "pred" : "hasExactSynonym", - "val" : "mutagenesis" - }, { - "pred" : "hasExactSynonym", - "val" : "mutated_site" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00036" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001149", - "lbl" : "alternate_sequence_site", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.", - "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ] - }, - "comments" : [ "Discrete." ], - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "alternative_sequence" - }, { - "pred" : "hasExactSynonym", - "val" : "var_seq", - "xrefs" : [ "uniprot:feature_type" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "isoform" - }, { - "pred" : "hasNarrowSynonym", - "val" : "sequence variation" - }, { - "pred" : "hasNarrowSynonym", - "val" : "varsplic" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "BS:00073" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "SO:0001065" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001150", - "lbl" : "beta_turn_type_six", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.", - "xrefs" : [ "SO:cb" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn type six" - }, { - "pred" : "hasExactSynonym", - "val" : "cis-proline loop" - }, { - "pred" : "hasExactSynonym", - "val" : "type VI beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type VI turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001151", - "lbl" : "beta_turn_type_six_a", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.", - "xrefs" : [ "PMID:2371257", "SO:cb" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn type six a" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIa beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIa turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001152", - "lbl" : "beta_turn_type_six_a_one", - "type" : "CLASS", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn type six a one" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIa1 beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIa1 turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001153", - "lbl" : "beta_turn_type_six_a_two", - "type" : "CLASS", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn type six a two" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIa2 beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIa2 turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001154", - "lbl" : "beta_turn_type_six_b", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.", - "xrefs" : [ "PMID:2371257", "SO:cb" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn type six b" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIb beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIb turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001155", - "lbl" : "beta_turn_type_eight", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.", - "xrefs" : [ "PMID:2371257", "SO:cb" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "beta turn type eight" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIII beta turn" - }, { - "pred" : "hasExactSynonym", - "val" : "type VIII turn" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001156", - "lbl" : "DRE_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.", - "xrefs" : [ "PMID:12537576" ] - }, - "comments" : [ "This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DRE motif" - }, { - "pred" : "hasExactSynonym", - "val" : "NDM4" - }, { - "pred" : "hasExactSynonym", - "val" : "WATCGATW_motif" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001157", - "lbl" : "DMv4_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).", - "xrefs" : [ "PMID:16827941:12537576" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DMv4" - }, { - "pred" : "hasExactSynonym", - "val" : "DMv4 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "directional motif v4" - }, { - "pred" : "hasExactSynonym", - "val" : "motif 1 element" - }, { - "pred" : "hasExactSynonym", - "val" : "promoter motif 1" - }, { - "pred" : "hasNarrowSynonym", - "val" : "YGGTCACATR" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001158", - "lbl" : "E_box_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).", - "xrefs" : [ "PMID:12537576:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "E box motif" - }, { - "pred" : "hasExactSynonym", - "val" : "generic E box motif" - }, { - "pred" : "hasNarrowSynonym", - "val" : "AWCAGCTGWT" - }, { - "pred" : "hasRelatedSynonym", - "val" : "NDM5" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001159", - "lbl" : "DMv5_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).", - "xrefs" : [ "PMID:12537576:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DMv5" - }, { - "pred" : "hasExactSynonym", - "val" : "DMv5 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "directional motif v5" - }, { - "pred" : "hasNarrowSynonym", - "val" : "KTYRGTATWTTT" - }, { - "pred" : "hasRelatedSynonym", - "val" : "promoter motif 6" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001160", - "lbl" : "DMv3_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).", - "xrefs" : [ "PMID:12537576:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DMv3" - }, { - "pred" : "hasExactSynonym", - "val" : "DMv3 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "directional motif v3" - }, { - "pred" : "hasExactSynonym", - "val" : "promoter motif 7" - }, { - "pred" : "hasNarrowSynonym", - "val" : "KNNCAKCNCTRNY" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001161", - "lbl" : "DMv2_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).", - "xrefs" : [ "PMID:12537576:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DMv2" - }, { - "pred" : "hasExactSynonym", - "val" : "DMv2 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "directional motif v2" - }, { - "pred" : "hasExactSynonym", - "val" : "promoter motif 8" - }, { - "pred" : "hasNarrowSynonym", - "val" : "MKSYGGCARCGSYSS" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001162", - "lbl" : "MTE", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).", - "xrefs" : [ "PMID:12537576:15231738", "PMID:16858867" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "motif ten element" - }, { - "pred" : "hasExactSynonym", - "val" : "motif_ten_element" - }, { - "pred" : "hasNarrowSynonym", - "val" : "CSARCSSAACGS" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001163", - "lbl" : "INR1_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A promoter motif with consensus sequence TCATTCG.", - "xrefs" : [ "PMID:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DMp3" - }, { - "pred" : "hasExactSynonym", - "val" : "INR1 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "directional motif p3" - }, { - "pred" : "hasExactSynonym", - "val" : "directional promoter motif 3" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001164", - "lbl" : "DPE1_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A promoter motif with consensus sequence CGGACGT.", - "xrefs" : [ "PMID:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DMp5" - }, { - "pred" : "hasExactSynonym", - "val" : "DPE1 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "directional motif 5" - }, { - "pred" : "hasRelatedSynonym", - "val" : "directional promoter motif 5" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001165", - "lbl" : "DMv1_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A promoter motif with consensus sequence CARCCCT.", - "xrefs" : [ "PMID:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DMv1 motif" - }, { - "pred" : "hasRelatedSynonym", - "val" : "DMv1" - }, { - "pred" : "hasRelatedSynonym", - "val" : "directional promoter motif v1" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001166", - "lbl" : "GAGA_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non directional promoter motif with consensus sequence GAGAGCG.", - "xrefs" : [ "PMID:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "GAGA" - }, { - "pred" : "hasExactSynonym", - "val" : "GAGA motif" - }, { - "pred" : "hasExactSynonym", - "val" : "NDM1" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001167", - "lbl" : "NDM2_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non directional promoter motif with consensus CGMYGYCR.", - "xrefs" : [ "PMID:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "NDM2" - }, { - "pred" : "hasExactSynonym", - "val" : "NDM2 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "non directional promoter motif 2" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001168", - "lbl" : "NDM3_motif", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non directional promoter motif with consensus sequence GAAAGCT.", - "xrefs" : [ "PMID:16827941" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "NDM3" - }, { - "pred" : "hasExactSynonym", - "val" : "NDM3 motif" - }, { - "pred" : "hasExactSynonym", - "val" : "non directional motif 3" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001169", - "lbl" : "ds_RNA_viral_sequence", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "double stranded RNA virus sequence" - }, { - "pred" : "hasExactSynonym", - "val" : "ds RNA viral sequence" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001170", - "lbl" : "polinton", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.", - "xrefs" : [ "PMID:16537396" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "maverick element" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001171", - "lbl" : "rRNA_21S", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A component of the large ribosomal subunit in mitochondrial rRNA.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "21S LSU rRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "21S rRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "21S ribosomal RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "rRNA 21S" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001172", - "lbl" : "tRNA_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of a tRNA.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "tRNA region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001173", - "lbl" : "anticodon_loop", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.", - "xrefs" : [ "ISBN:0716719207" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "anti-codon loop" - }, { - "pred" : "hasExactSynonym", - "val" : "anticodon loop" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001174", - "lbl" : "anticodon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "anti-codon" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Anticodon" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001175", - "lbl" : "CCA_tail", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.", - "xrefs" : [ "ISBN:0716719207" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "CCA sequence" - }, { - "pred" : "hasExactSynonym", - "val" : "CCA tail" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001176", - "lbl" : "DHU_loop", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.", - "xrefs" : [ "ISBN:071671920" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DHU loop" - }, { - "pred" : "hasRelatedSynonym", - "val" : "D loop" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001177", - "lbl" : "T_loop", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.", - "xrefs" : [ "ISBN:0716719207" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "T loop" - }, { - "pred" : "hasExactSynonym", - "val" : "TpsiC loop" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001178", - "lbl" : "pyrrolysine_tRNA_primary_transcript", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A primary transcript encoding pyrrolysyl tRNA (SO:0000766).", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pyrrolysine tRNA primary transcript" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001179", - "lbl" : "U3_snoRNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.", - "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012" ] - }, - "comments" : [ "The definition is most of the old definition for snoRNA (SO:0000275)." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "U3 small nucleolar RNA" - }, { - "pred" : "hasExactSynonym", - "val" : "U3 snoRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "small nucleolar RNA U3" - }, { - "pred" : "hasExactSynonym", - "val" : "snoRNA U3" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001180", - "lbl" : "AU_rich_element", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.", - "xrefs" : [ "PMID:7892223" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "AU rich element" - }, { - "pred" : "hasExactSynonym", - "val" : "AU-rich element" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ARE" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/AU-rich_element" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001181", - "lbl" : "Bruno_response_element", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.", - "xrefs" : [ "PMID:10893231" ] - }, - "comments" : [ "Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Bruno response element" - }, { - "pred" : "hasRelatedSynonym", - "val" : "BRE" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001182", - "lbl" : "iron_responsive_element", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.", - "xrefs" : [ "PMID:3198610", "PMID:8710843" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "IRE" - }, { - "pred" : "hasExactSynonym", - "val" : "iron responsive element" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Iron_responsive_element" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001183", - "lbl" : "morpholino_backbone", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.", - "xrefs" : [ "RSC:cb" ] - }, - "comments" : [ "Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "morpholino backbone" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Morpholino" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001184", - "lbl" : "PNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.", - "xrefs" : [ "RSC:cb" ] - }, - "comments" : [ "Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "peptide nucleic acid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001185", - "lbl" : "enzymatic", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.", - "xrefs" : [ "RSC:cb" ] - }, - "comments" : [ "Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001186", - "lbl" : "ribozymic", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.", - "xrefs" : [ "RSC:cb" ] - }, - "comments" : [ "Do not use this for feature annotation. Use ribozyme (SO:0000374) instead." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001187", - "lbl" : "pseudouridylation_guide_snoRNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.", - "xrefs" : [ "GOC:mah", "PMID:12457565" ] - }, - "comments" : [ "Has RNA pseudouridylation guide activity (GO:0030558)." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pseudouridylation guide snoRNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001188", - "lbl" : "LNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.", - "xrefs" : [ "CHEBI:48010" ] - }, - "comments" : [ "Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001189", - "lbl" : "LNA_oligo", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An oligo composed of LNA residues.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "LNA oligo" - }, { - "pred" : "hasExactSynonym", - "val" : "locked nucleic acid" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Locked_nucleic_acid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001190", - "lbl" : "TNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.", - "xrefs" : [ "CHEBI:48019" ] - }, - "comments" : [ "Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001191", - "lbl" : "TNA_oligo", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An oligo composed of TNA residues.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "TNA oligo" - }, { - "pred" : "hasExactSynonym", - "val" : "threose nucleic acid" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Threose_nucleic_acid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001192", - "lbl" : "GNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.", - "xrefs" : [ "CHEBI:48015" ] - }, - "comments" : [ "Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001193", - "lbl" : "GNA_oligo", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An oligo composed of GNA residues.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "GNA oligo" - }, { - "pred" : "hasExactSynonym", - "val" : "glycerol nucleic acid" - }, { - "pred" : "hasExactSynonym", - "val" : "glycol nucleic acid" - } ], - "xrefs" : [ { - "val" : "http://en.wikipedia.org/wiki/Glycerol_nucleic_acid" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001194", - "lbl" : "R_GNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a GNA sequence in the (R)-GNA enantiomer.", - "xrefs" : [ "CHEBI:48016" ] - }, - "comments" : [ "Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "R GNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001195", - "lbl" : "R_GNA_oligo", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An oligo composed of (R)-GNA residues.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "(R)-glycerol nucleic acid" - }, { - "pred" : "hasExactSynonym", - "val" : "(R)-glycol nucleic acid" - }, { - "pred" : "hasExactSynonym", - "val" : "R GNA oligo" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001196", - "lbl" : "S_GNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attribute describing a GNA sequence in the (S)-GNA enantiomer.", - "xrefs" : [ "CHEBI:48017" ] - }, - "comments" : [ "Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "S GNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001197", - "lbl" : "S_GNA_oligo", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An oligo composed of (S)-GNA residues.", - "xrefs" : [ "RSC:cb" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "(S)-glycerol nucleic acid" - }, { - "pred" : "hasExactSynonym", - "val" : "(S)-glycol nucleic acid" - }, { - "pred" : "hasExactSynonym", - "val" : "S GNA oligo" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001198", - "lbl" : "ds_DNA_viral_sequence", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "double stranded DNA virus" - }, { - "pred" : "hasExactSynonym", - "val" : "ds DNA viral sequence" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001199", - "lbl" : "ss_RNA_viral_sequence", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "single strand RNA virus" - }, { - "pred" : "hasExactSynonym", - "val" : "ss RNA viral sequence" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001200", - "lbl" : "negative_sense_ssRNA_viral_sequence", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "negative sense ssRNA viral sequence" - }, { - "pred" : "hasRelatedSynonym", - "val" : "negative sense single stranded RNA virus" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001201", - "lbl" : "positive_sense_ssRNA_viral_sequence", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.", - "xrefs" : [ "SO:ke" ] - 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These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). 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Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete.", - "xrefs" : [ "DOI:10.1126" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "standard draft" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-10-23T12:48:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001487", - "lbl" : "high_quality_draft", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.", - "xrefs" : [ "DOI:10.1126" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "high quality draft" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - 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"val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001489", - "lbl" : "annotation_directed_improved_draft", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.", - "xrefs" : [ "DOI:10.1126" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "annotation directed improvement" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-10-23T12:57:10Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001490", - "lbl" : "noncontiguous_finished", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.", - "xrefs" : [ "DOI:10.1126" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "non contiguous finished" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-10-23T01:01:07Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001491", - "lbl" : "finished_genome", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.", - "xrefs" : [ "DOI:10.1126" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "finished" - }, { - "pred" : "hasExactSynonym", - "val" : "finished genome" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-10-23T01:04:43Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001492", - "lbl" : "intronic_regulatory_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A regulatory region that is part of an intron.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "intronic regulatory region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-11-08T02:48:02Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001493", - "lbl" : "centromere_DNA_Element_I", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).", - "xrefs" : [ "PMID:11222754" ] - }, - "comments" : [ "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "CDEI" - }, { - "pred" : "hasExactSynonym", - "val" : "Centromere DNA Element I" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-11-09T05:47:23Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001494", - "lbl" : "centromere_DNA_Element_II", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.", - "xrefs" : [ "PMID:11222754" ] - }, - "comments" : [ "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "CDEII" - }, { - "pred" : "hasExactSynonym", - "val" : "centromere DNA Element II" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-11-09T05:51:26Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001495", - "lbl" : "centromere_DNA_Element_III", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.", - "xrefs" : [ "PMID:11222754" ] - }, - "comments" : [ "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "CDEIII" - }, { - "pred" : "hasExactSynonym", - "val" : "centromere DNA Element III" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-11-09T05:54:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001496", - "lbl" : "telomeric_repeat", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.", - "xrefs" : [ "PMID:8720065" ] - }, - "comments" : [ "The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739." ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:repeat_region" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:telomeric_repeat" - }, { - "pred" : "hasExactSynonym", - "val" : "telomeric repeat" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-11-09T06:00:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001497", - "lbl" : "X_element", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.", - "xrefs" : [ "PMID:7785338", "PMID:8005434", "http://www.yeastgenome.org/help/glossary.html#xelemcoresequence" ] - }, - "comments" : [ "Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. \n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "X element core sequence" - }, { - "pred" : "hasRelatedSynonym", - "val" : "X element" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-11-10T10:56:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001498", - "lbl" : "YAC_end", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of sequence from the end of a YAC clone that may provide a highly specific marker.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "YAC end" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-11-19T11:07:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001499", - "lbl" : "whole_genome_sequence_status", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The status of whole genome sequence.", - "xrefs" : [ "DOI:10.1126" ] - }, - "comments" : [ "This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "whole genome sequence status" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-10-23T12:47:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001500", - "lbl" : "heritable_phenotypic_marker", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.", - "xrefs" : [ "JAX:hdene" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heritable phenotypic marker" - }, { - "pred" : "hasExactSynonym", - "val" : "phenotypic marker" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-07T01:50:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001501", - "lbl" : "peptide_collection", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A collection of peptide sequences.", - "xrefs" : [ "BBOP:nlw" ] - }, - "comments" : [ "Term requested via tracker ID: 2910829." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "peptide collection" - }, { - "pred" : "hasExactSynonym", - "val" : "peptide set" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-11T10:58:58Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001502", - "lbl" : "high_identity_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An experimental feature with high sequence identity to another sequence.", - "xrefs" : [ "SO:ke" ] - }, - "comments" : [ "Requested by tracker ID: 2902685." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "high identity region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-11T11:06:05Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001503", - "lbl" : "processed_transcript", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transcript for which no open reading frame has been identified and for which no other function has been determined.", - "xrefs" : [ "MGI:hdeen" ] - }, - "comments" : [ "Ensembl and Vega also use this term name. Requested by Howard Deen of MGI." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "processed transcript" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-12-21T05:37:14Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0001504", - "lbl" : "assortment_derived_variation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A chromosome variation derived from an event during meiosis.", - "xrefs" : [ "SO:ke" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "assortment derived variation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kareneilbeck" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - 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The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA.", - "xrefs" : [ "PMID:26453491" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RefSeq miRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "RefSeq-miRNA" - }, { - "pred" : "hasExactSynonym", - "val" : "ref miRNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-06-22T11:05:49Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002167", - "lbl" : "isomiR", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA.", - "xrefs" : [ "PMID:26453491" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-06-22T11:09:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002168", - "lbl" : "RNA_thermometer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression.", - "xrefs" : [ "PMID:22421878" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "RNA thermometer" - }, { - "pred" : "hasExactSynonym", - "val" : "RNA thermoregulator" - }, { - "pred" : "hasExactSynonym", - "val" : "RNAT" - }, { - "pred" : "hasExactSynonym", - "val" : "thermoregulator" - } ], - "xrefs" : [ { - "val" : "https://en.wikipedia.org/wiki/RNA_thermometer" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-07-17T10:07:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002169", - "lbl" : "splice_polypyrimidine_tract_variant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17)." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "splice polypyrimidine tract variant" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-07-31T13:40:13Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002170", - "lbl" : "splice_donor_region_variant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron)." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "splice donor region variant" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-07-31T13:48:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002171", - 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} ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002172", - "lbl" : "sequence_alteration_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "sequence alteration artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T13:43:26Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002173", - "lbl" : "indel_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An indel that is the result of base-calling or assembly error." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "indel artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T15:16:20Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002174", - "lbl" : "deletion_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deletion that is the result of base-calling or assembly error." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "deletion artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T15:17:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002175", - "lbl" : "insertion_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An insertion that is the result of base-calling or assembly error." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "insertion artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T15:17:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002176", - "lbl" : "substitution_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A substitution that is the result of base-calling or assembly error." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "substitution artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T15:18:12Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002177", - "lbl" : "duplication_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A duplication that is the result of base-calling or assembly error." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "duplication artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T15:26:00Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002178", - "lbl" : "SNV_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An SNV that is the result of base-calling or assembly error." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "SNV artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T15:26:49Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002179", - "lbl" : "MNV_artifact", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An MNV that is the result of base-calling or assembly error." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "MNV artifact" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-08-18T15:27:21Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002180", - "lbl" : "enzymatic_RNA_gene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene that encodes an enzymatic RNA." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "enzymatic RNA gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-27T10:30:27Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002181", - "lbl" : "ribozyme_gene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene that encodes a ribozyme." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ribozyme gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-27T10:31:09Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002182", - "lbl" : "antisense_lncRNA_gene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene that encodes an antisense long, non-coding RNA." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "antisense lncRNA gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-27T10:44:00Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002183", - "lbl" : "sense_overlap_ncRNA_gene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene that encodes a sense overlap long non-coding RNA." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "sense overlap lncRNA gene" - }, { - "pred" : "hasExactSynonym", - "val" : "sense overlap ncRNA gene" - }, { - "pred" : "hasExactSynonym", - "val" : "sense_overlap_lncRNA_gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-27T10:48:05Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002184", - "lbl" : "sense_intronic_ncRNA_gene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene that encodes a sense intronic long non-coding RNA." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "sense intronic lncRNA gene" - }, { - "pred" : "hasExactSynonym", - "val" : "sense intronic ncRNA gene" - }, { - "pred" : "hasExactSynonym", - "val" : "sense_intronic_lncRNA_gene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-27T11:03:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002185", - "lbl" : "bidirectional_promoter_lncRNA", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand.", - "xrefs" : [ "https://www.gencodegenes.org/gencode_biotypes.html" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "bidirectional promoter lncRNA" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-10-03T11:43:48Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002186", - "lbl" : "mutational_hotspot", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mutational hotspot" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-07T12:27:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002187", - "lbl" : "HERV_insertion", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An insertion of sequence from the HERV family of mobile elements with respect to a reference.", - "xrefs" : [ "NCBI:th" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "HERV insertion" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-20T11:52:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002188", - "lbl" : "functional_gene_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product.", - "xrefs" : [ "Clingen:mb" ] - }, - "comments" : [ "A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "functional gene region" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-15T11:08:43Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002189", - "lbl" : "allelic_pseudogene", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes." - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:gene" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:allelic" - }, { - "pred" : "hasExactSynonym", - "val" : "allelic pseudogene" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-03T15:47:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002190", - "lbl" : "enhancer_blocking_element", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator.", - "xrefs" : [ "NCBI:cf" ] - }, - "comments" : [ "Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf)." ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "INSDC_feature:regulatory" - }, { - "pred" : "hasExactSynonym", - "val" : "INSDC_qualifier:enhancer_blocking_element" - }, { - "pred" : "hasExactSynonym", - "val" : "enhancer blocking element" - }, { - "pred" : "hasRelatedSynonym", - "val" : "insulator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "nicole" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-04T17:28:52Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "sequence" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/SO_0002191", - "lbl" : "imprinting_control_region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. 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