Schema for knownIsoforms

Database: hg38 Primary Table: knownIsoforms Row Count: 533,740 Data last updated: 2025-09-26
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	`varchar(255)`	Corresponds to name in knownGene table, transcript in knownCanonical

Connected Tables and Joining Fields


	hg38.knownCanonical.clusterId (via knownIsoforms.clusterId) knownGeneV39.knownCanonical.clusterId (via knownIsoforms.clusterId) knownGeneV39.knownIsoforms.clusterId (via knownIsoforms.clusterId) hg38.bioCycPathway.kgID (via knownIsoforms.transcript) hg38.ccdsKgMap.geneId (via knownIsoforms.transcript) hg38.ceBlastTab.query (via knownIsoforms.transcript) hg38.dmBlastTab.query (via knownIsoforms.transcript) hg38.drBlastTab.query (via knownIsoforms.transcript) hg38.foldUtr3.name (via knownIsoforms.transcript) hg38.foldUtr5.name (via knownIsoforms.transcript) hg38.gnfAtlas2Distance.query (via knownIsoforms.transcript) hg38.gnfAtlas2Distance.target (via knownIsoforms.transcript) hg38.gnfU95Distance.query (via knownIsoforms.transcript) hg38.gnfU95Distance.target (via knownIsoforms.transcript) hg38.humanHprdP2P.query (via knownIsoforms.transcript) hg38.humanHprdP2P.target (via knownIsoforms.transcript) hg38.humanVidalP2P.query (via knownIsoforms.transcript) hg38.humanVidalP2P.target (via knownIsoforms.transcript) hg38.humanWankerP2P.query (via knownIsoforms.transcript) hg38.humanWankerP2P.target (via knownIsoforms.transcript) hg38.keggPathway.kgID (via knownIsoforms.transcript) hg38.kgAlias.kgID (via knownIsoforms.transcript) hg38.kgColor.kgID (via knownIsoforms.transcript) hg38.kgProtAlias.kgID (via knownIsoforms.transcript) hg38.kgSpAlias.kgID (via knownIsoforms.transcript) hg38.kgTargetAli.qName (via knownIsoforms.transcript) hg38.kgXref.kgID (via knownIsoforms.transcript) hg38.knownAttrs.kgID (via knownIsoforms.transcript) hg38.knownBlastTab.query (via knownIsoforms.transcript) hg38.knownBlastTab.target (via knownIsoforms.transcript) hg38.knownCanonical.transcript (via knownIsoforms.transcript) hg38.knownCds.name (via knownIsoforms.transcript) hg38.knownGene.name (via knownIsoforms.transcript) hg38.knownGeneMrna.name (via knownIsoforms.transcript) hg38.knownGenePep.name (via knownIsoforms.transcript) hg38.knownToEnsembl.name (via knownIsoforms.transcript) hg38.knownToGnfAtlas2.name (via knownIsoforms.transcript) hg38.knownToHprd.name (via knownIsoforms.transcript) hg38.knownToKeggEntrez.name (via knownIsoforms.transcript) hg38.knownToLocusLink.name (via knownIsoforms.transcript) hg38.knownToLynx.name (via knownIsoforms.transcript) hg38.knownToMrna.name (via knownIsoforms.transcript) hg38.knownToMrnaSingle.name (via knownIsoforms.transcript) hg38.knownToMupit.name (via knownIsoforms.transcript) hg38.knownToNextProt.name (via knownIsoforms.transcript) hg38.knownToPfam.name (via knownIsoforms.transcript) hg38.knownToRefSeq.name (via knownIsoforms.transcript) hg38.knownToSuper.gene (via knownIsoforms.transcript) hg38.knownToTag.name (via knownIsoforms.transcript) hg38.knownToU133.name (via knownIsoforms.transcript) hg38.knownToU95.name (via knownIsoforms.transcript) hg38.knownToVisiGene.name (via knownIsoforms.transcript) hg38.knownToWikipedia.name (via knownIsoforms.transcript) hg38.mmBlastTab.query (via knownIsoforms.transcript) hg38.rnBlastTab.query (via knownIsoforms.transcript) hg38.scBlastTab.query (via knownIsoforms.transcript) hg38.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
1	ENST00000494424.1
1	ENST00000496771.5
1	ENST00000612152.4
1	ENST00000867886.1
1	ENST00000867887.1
1	ENST00000867888.1
1	ENST00000867889.1
1	ENST00000867890.1
1	ENST00000867891.1

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