Schema for knownCanonical

Database: hg19 Primary Table: knownCanonical Row Count: 80,274 Data last updated: 2025-09-29
Format description: Describes the canonical splice variant of a gene
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`chrom`	chrX	`varchar(255)`	values	Chromosome
`chromStart`	99882104	`int(11)`	range	Start position (0 based). Represents transcription start for + strand genes, end for - strand genes
`chromEnd`	99891803	`int(11)`	range	End position (non-inclusive). Represents transcription end for + strand genes, start for - strand genes
`clusterId`	1	`int(11)`	range	Which cluster of transcripts this belongs to in knownIsoforms
`transcript`	ENST00000373020.9_7	`varchar(255)`	values	Corresponds to knownGene name field.
`protein`	ENSG00000000003.17_11	`varchar(255)`	values	Accession of the associated protein, or UCSC ID in newer tables.

Connected Tables and Joining Fields


	hg19.knownIsoforms.clusterId (via knownCanonical.clusterId) knownGeneV39.knownCanonical.clusterId (via knownCanonical.clusterId) knownGeneV39.knownIsoforms.clusterId (via knownCanonical.clusterId) hg19.bioCycPathway.kgID (via knownCanonical.transcript) hg19.ceBlastTab.query (via knownCanonical.transcript) hg19.dmBlastTab.query (via knownCanonical.transcript) hg19.drBlastTab.query (via knownCanonical.transcript) hg19.foldUtr3.name (via knownCanonical.transcript) hg19.foldUtr5.name (via knownCanonical.transcript) hg19.gnfAtlas2Distance.query (via knownCanonical.transcript) hg19.gnfAtlas2Distance.target (via knownCanonical.transcript) hg19.gnfU95Distance.query (via knownCanonical.transcript) hg19.gnfU95Distance.target (via knownCanonical.transcript) hg19.humanHprdP2P.query (via knownCanonical.transcript) hg19.humanHprdP2P.target (via knownCanonical.transcript) hg19.humanVidalP2P.query (via knownCanonical.transcript) hg19.humanVidalP2P.target (via knownCanonical.transcript) hg19.humanWankerP2P.query (via knownCanonical.transcript) hg19.humanWankerP2P.target (via knownCanonical.transcript) hg19.keggPathway.kgID (via knownCanonical.transcript) hg19.kgAlias.kgID (via knownCanonical.transcript) hg19.kgColor.kgID (via knownCanonical.transcript) hg19.kgProtAlias.kgID (via knownCanonical.transcript) hg19.kgProtMap2.qName (via knownCanonical.transcript) hg19.kgSpAlias.kgID (via knownCanonical.transcript) hg19.kgTargetAli.qName (via knownCanonical.transcript) hg19.kgTxInfo.name (via knownCanonical.transcript) hg19.kgXref.kgID (via knownCanonical.transcript) hg19.knownAttrs.kgID (via knownCanonical.transcript) hg19.knownBlastTab.query (via knownCanonical.transcript) hg19.knownBlastTab.target (via knownCanonical.transcript) hg19.knownCds.name (via knownCanonical.transcript) hg19.knownGene.name (via knownCanonical.transcript) hg19.knownGeneMrna.name (via knownCanonical.transcript) hg19.knownGenePep.name (via knownCanonical.transcript) hg19.knownGeneTxMrna.name (via knownCanonical.transcript) hg19.knownGeneTxPep.name (via knownCanonical.transcript) hg19.knownIsoforms.transcript (via knownCanonical.transcript) hg19.knownToAllenBrain.name (via knownCanonical.transcript) hg19.knownToEnsembl.name (via knownCanonical.transcript) hg19.knownToGnfAtlas2.name (via knownCanonical.transcript) hg19.knownToHInv.name (via knownCanonical.transcript) hg19.knownToHprd.name (via knownCanonical.transcript) hg19.knownToKeggEntrez.name (via knownCanonical.transcript) hg19.knownToLocusLink.name (via knownCanonical.transcript) hg19.knownToLynx.name (via knownCanonical.transcript) hg19.knownToMrna.name (via knownCanonical.transcript) hg19.knownToMrnaSingle.name (via knownCanonical.transcript) hg19.knownToMupit.name (via knownCanonical.transcript) hg19.knownToNextProt.name (via knownCanonical.transcript) hg19.knownToPfam.name (via knownCanonical.transcript) hg19.knownToRefSeq.name (via knownCanonical.transcript) hg19.knownToSuper.gene (via knownCanonical.transcript) hg19.knownToTag.name (via knownCanonical.transcript) hg19.knownToTreefam.name (via knownCanonical.transcript) hg19.knownToU133.name (via knownCanonical.transcript) hg19.knownToU133Plus2.name (via knownCanonical.transcript) hg19.knownToU95.name (via knownCanonical.transcript) hg19.knownToVisiGene.name (via knownCanonical.transcript) hg19.knownToWikipedia.name (via knownCanonical.transcript) hg19.mmBlastTab.query (via knownCanonical.transcript) hg19.rnBlastTab.query (via knownCanonical.transcript) hg19.scBlastTab.query (via knownCanonical.transcript) hg19.ucscScop.ucscId (via knownCanonical.transcript) knownGeneV39.bioCycPathway.kgID (via knownCanonical.transcript) knownGeneV39.ceBlastTab.query (via knownCanonical.transcript) knownGeneV39.dmBlastTab.query (via knownCanonical.transcript) knownGeneV39.drBlastTab.query (via knownCanonical.transcript) knownGeneV39.foldUtr3.name (via knownCanonical.transcript) knownGeneV39.foldUtr5.name (via knownCanonical.transcript) knownGeneV39.gnfAtlas2Distance.query (via knownCanonical.transcript) knownGeneV39.gnfAtlas2Distance.target (via knownCanonical.transcript) knownGeneV39.kgAlias.kgID (via knownCanonical.transcript) knownGeneV39.kgColor.kgID (via knownCanonical.transcript) knownGeneV39.kgProtAlias.kgID (via knownCanonical.transcript) knownGeneV39.kgSpAlias.kgID (via knownCanonical.transcript) knownGeneV39.kgTargetAli.qName (via knownCanonical.transcript) knownGeneV39.kgXref.kgID (via knownCanonical.transcript) knownGeneV39.knownAttrs.kgID (via knownCanonical.transcript) knownGeneV39.knownBlastTab.query (via knownCanonical.transcript) knownGeneV39.knownBlastTab.target (via knownCanonical.transcript) knownGeneV39.knownCanonical.protein (via knownCanonical.transcript) knownGeneV39.knownCanonical.transcript (via knownCanonical.transcript) knownGeneV39.knownCds.name (via knownCanonical.transcript) knownGeneV39.knownGene.name (via knownCanonical.transcript) knownGeneV39.knownGeneMrna.name (via knownCanonical.transcript) knownGeneV39.knownGenePep.name (via knownCanonical.transcript) knownGeneV39.knownIsoforms.transcript (via knownCanonical.transcript) knownGeneV39.knownToEnsembl.name (via knownCanonical.transcript) knownGeneV39.knownToGnfAtlas2.name (via knownCanonical.transcript) knownGeneV39.knownToHprd.name (via knownCanonical.transcript) knownGeneV39.knownToLocusLink.name (via knownCanonical.transcript) knownGeneV39.knownToMrna.name (via knownCanonical.transcript) knownGeneV39.knownToMrnaSingle.name (via knownCanonical.transcript) knownGeneV39.knownToMupit.name (via knownCanonical.transcript) knownGeneV39.knownToPfam.name (via knownCanonical.transcript) knownGeneV39.knownToRefSeq.name (via knownCanonical.transcript) knownGeneV39.knownToSuper.gene (via knownCanonical.transcript) knownGeneV39.knownToTag.name (via knownCanonical.transcript) knownGeneV39.knownToU133.name (via knownCanonical.transcript) knownGeneV39.knownToU95.name (via knownCanonical.transcript) knownGeneV39.knownToVisiGene.name (via knownCanonical.transcript) knownGeneV39.knownToWikipedia.name (via knownCanonical.transcript) knownGeneV39.mmBlastTab.query (via knownCanonical.transcript) knownGeneV39.rnBlastTab.query (via knownCanonical.transcript) knownGeneV39.scBlastTab.query (via knownCanonical.transcript) knownGeneV39.ucscScop.ucscId (via knownCanonical.transcript)

Sample Rows

chrom	chromStart	chromEnd	clusterId	transcript	protein
chrX	99882104	99891803	1	ENST00000373020.9_7	ENSG00000000003.17_11
chrX	99839932	99854882	2	ENST00000373031.5_4	ENSG00000000005.6_7
chr20	49551406	49575069	3	ENST00000371588.10_6	ENSG00000000419.15_14
chr1	169818771	169863037	4	ENST00000367771.11_11	ENSG00000000457.15_15
chr1	169764180	169823221	5	ENST00000359326.9_7	ENSG00000000460.18_12
chr1	27938574	27961696	6	ENST00000374005.8_8	ENSG00000000938.14_16
chr1	196621172	196716634	7	ENST00000367429.9_5	ENSG00000000971.18_13
chr6	143815948	143832857	8	ENST00000002165.11_8	ENSG00000001036.15_11
chr6	53362138	53409899	9	ENST00000650454.1_8	ENSG00000001084.14_22
chr6	41040712	41070142	10	ENST00000341376.11_6	ENSG00000001167.16_8

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.