Schema for knownGene

Database: hg38 Primary Table: knownGene Row Count: 670,670 Data last updated: 2026-07-16
Format description: Transcript from default gene set in UCSC browser
On download server: MariaDB table dump directory

field	example	SQL type	description
`name`	ENST00000832824.1	`varchar(255)`	Name of gene
`chrom`	chr1	`varchar(255)`	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	+ or - for strand
`txStart`	11120	`int(10) unsigned`	Transcription start position (or end position for minus strand item)
`txEnd`	14413	`int(10) unsigned`	Transcription end position (or start position for minus strand item)
`cdsStart`	11120	`int(10) unsigned`	Coding region start (or end position if for minus strand item)
`cdsEnd`	11120	`int(10) unsigned`	Coding region end (or start position if for minus strand item)
`exonCount`	4	`int(10) unsigned`	Number of exons
`exonStarts`	11120,12009,12612,13452,	`longblob`	Exon start positions (or end positions for minus strand item)
`exonEnds`	11211,12227,12721,14413,	`longblob`	Exon end positions (or start positions for minus strand item)
`proteinID`		`varchar(40)`	UniProt display ID, UniProt accession, or RefSeq protein ID
`alignID`	uc345qln.1	`varchar(255)`	Unique identifier (GENCODE transcript ID for GENCODE Basic)

Connected Tables and Joining Fields


	hg38.bioCycPathway.kgID (via knownGene.name) hg38.ccdsKgMap.geneId (via knownGene.name) hg38.ceBlastTab.query (via knownGene.name) hg38.dmBlastTab.query (via knownGene.name) hg38.drBlastTab.query (via knownGene.name) hg38.foldUtr3.name (via knownGene.name) hg38.foldUtr5.name (via knownGene.name) hg38.gnfAtlas2Distance.query (via knownGene.name) hg38.gnfAtlas2Distance.target (via knownGene.name) hg38.gnfU95Distance.query (via knownGene.name) hg38.gnfU95Distance.target (via knownGene.name) hg38.humanHprdP2P.query (via knownGene.name) hg38.humanHprdP2P.target (via knownGene.name) hg38.humanVidalP2P.query (via knownGene.name) hg38.humanVidalP2P.target (via knownGene.name) hg38.humanWankerP2P.query (via knownGene.name) hg38.humanWankerP2P.target (via knownGene.name) hg38.keggPathway.kgID (via knownGene.name) hg38.kgAlias.kgID (via knownGene.name) hg38.kgColor.kgID (via knownGene.name) hg38.kgProtAlias.kgID (via knownGene.name) hg38.kgSpAlias.kgID (via knownGene.name) hg38.kgTargetAli.qName (via knownGene.name) hg38.kgXref.kgID (via knownGene.name) hg38.knownAttrs.kgID (via knownGene.name) hg38.knownBlastTab.query (via knownGene.name) hg38.knownBlastTab.target (via knownGene.name) hg38.knownCanonical.transcript (via knownGene.name) hg38.knownCds.name (via knownGene.name) hg38.knownGeneMrna.name (via knownGene.name) hg38.knownGenePep.name (via knownGene.name) hg38.knownIsoforms.transcript (via knownGene.name) hg38.knownToEnsembl.name (via knownGene.name) hg38.knownToGnfAtlas2.name (via knownGene.name) hg38.knownToHprd.name (via knownGene.name) hg38.knownToKeggEntrez.name (via knownGene.name) hg38.knownToLocusLink.name (via knownGene.name) hg38.knownToLynx.name (via knownGene.name) hg38.knownToMrna.name (via knownGene.name) hg38.knownToMrnaSingle.name (via knownGene.name) hg38.knownToMupit.name (via knownGene.name) hg38.knownToNextProt.name (via knownGene.name) hg38.knownToPfam.name (via knownGene.name) hg38.knownToRefSeq.name (via knownGene.name) hg38.knownToSuper.gene (via knownGene.name) hg38.knownToTag.name (via knownGene.name) hg38.knownToU133.name (via knownGene.name) hg38.knownToU95.name (via knownGene.name) hg38.knownToVisiGene.name (via knownGene.name) hg38.knownToWikipedia.name (via knownGene.name) hg38.mmBlastTab.query (via knownGene.name) hg38.rnBlastTab.query (via knownGene.name) hg38.scBlastTab.query (via knownGene.name) hg38.ucscRetroInfo9.kgName (via knownGene.name) hg38.ucscScop.ucscId (via knownGene.name) knownGeneV39.bioCycPathway.kgID (via knownGene.name) knownGeneV39.ceBlastTab.query (via knownGene.name) knownGeneV39.dmBlastTab.query (via knownGene.name) knownGeneV39.drBlastTab.query (via knownGene.name) knownGeneV39.foldUtr3.name (via knownGene.name) knownGeneV39.foldUtr5.name (via knownGene.name) knownGeneV39.gnfAtlas2Distance.query (via knownGene.name) knownGeneV39.gnfAtlas2Distance.target (via knownGene.name) knownGeneV39.kgAlias.kgID (via knownGene.name) knownGeneV39.kgColor.kgID (via knownGene.name) knownGeneV39.kgProtAlias.kgID (via knownGene.name) knownGeneV39.kgSpAlias.kgID (via knownGene.name) knownGeneV39.kgTargetAli.qName (via knownGene.name) knownGeneV39.kgXref.kgID (via knownGene.name) knownGeneV39.knownAttrs.kgID (via knownGene.name) knownGeneV39.knownBlastTab.query (via knownGene.name) knownGeneV39.knownBlastTab.target (via knownGene.name) knownGeneV39.knownCanonical.protein (via knownGene.name) knownGeneV39.knownCanonical.transcript (via knownGene.name) knownGeneV39.knownCds.name (via knownGene.name) knownGeneV39.knownGene.name (via knownGene.name) knownGeneV39.knownGeneMrna.name (via knownGene.name) knownGeneV39.knownGenePep.name (via knownGene.name) knownGeneV39.knownIsoforms.transcript (via knownGene.name) knownGeneV39.knownToEnsembl.name (via knownGene.name) knownGeneV39.knownToGnfAtlas2.name (via knownGene.name) knownGeneV39.knownToHprd.name (via knownGene.name) knownGeneV39.knownToLocusLink.name (via knownGene.name) knownGeneV39.knownToMrna.name (via knownGene.name) knownGeneV39.knownToMrnaSingle.name (via knownGene.name) knownGeneV39.knownToMupit.name (via knownGene.name) knownGeneV39.knownToPfam.name (via knownGene.name) knownGeneV39.knownToRefSeq.name (via knownGene.name) knownGeneV39.knownToSuper.gene (via knownGene.name) knownGeneV39.knownToTag.name (via knownGene.name) knownGeneV39.knownToU133.name (via knownGene.name) knownGeneV39.knownToU95.name (via knownGene.name) knownGeneV39.knownToVisiGene.name (via knownGene.name) knownGeneV39.knownToWikipedia.name (via knownGene.name) knownGeneV39.mmBlastTab.query (via knownGene.name) knownGeneV39.rnBlastTab.query (via knownGene.name) knownGeneV39.scBlastTab.query (via knownGene.name) knownGeneV39.ucscScop.ucscId (via knownGene.name)

Sample Rows

name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	alignID
ENST00000832824.1	chr1	+	11120	14413	11120	11120	4	11120,12009,12612,13452,	11211,12227,12721,14413,	uc345qln.1
ENST00000832825.1	chr1	+	11124	14405	11124	11124	4	11124,12009,12612,13402,	11211,12227,12721,14405,	uc345qlo.1
ENST00000832826.1	chr1	+	11409	14413	11409	11409	4	11409,12009,12594,13482,	11671,12227,12721,14413,	uc345qlp.1
ENST00000832827.1	chr1	+	11410	14413	11410	11410	4	11410,12009,12612,13482,	11671,12227,12721,14413,	uc345qlq.1
ENST00000832828.1	chr1	+	11425	14409	11425	11425	4	11425,12009,12612,13220,	11671,12227,12721,14409,	uc345qlr.1
ENST00000832829.1	chr1	+	11769	14416	11769	11769	4	11769,12009,12612,13482,	11844,12227,12721,14416,	uc345qls.1
ENST00000832830.1	chr1	+	11818	14413	11818	11818	4	11818,12009,12612,13482,	11844,12227,12697,14413,	uc345qlt.1
ENST00000832837.1	chr1	+	11822	14406	11822	11822	4	11822,12009,12594,13220,	11844,12227,12721,14406,	uc345qma.1
ENST00000832836.1	chr1	+	11823	14409	11823	11823	3	11823,12009,13482,	11844,12697,14409,	uc345qlz.1
ENST00000832832.1	chr1	+	11823	14413	11823	11823	4	11823,12009,12612,13486,	11844,12227,12721,14413,	uc345qlv.1

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