Schema for knownIsoforms

Database: hg19 Primary Table: knownIsoforms Row Count: 639,904 Data last updated: 2026-07-16
Format description: Links together various transcripts of a gene into a cluster
On download server: MariaDB table dump directory

field	example	SQL type	description
`clusterId`	1	`int(11)`	Unique id for transcript cluster (aka gene)
`transcript`	ENST00000373020.9_7	`varchar(255)`	Corresponds to name in knownGene table, transcript in knownCanonical

Connected Tables and Joining Fields


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

Sample Rows

clusterId	transcript
1	ENST00000373020.9_7
1	ENST00000494424.1_3
1	ENST00000496771.5_3
1	ENST00000612152.4_4
1	ENST00000867886.2_2
1	ENST00000867887.1_2
1	ENST00000867888.2_2
1	ENST00000867889.2_2
1	ENST00000867890.2_2
1	ENST00000867891.2_2

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