Schema for knownGene
  Database: mm39    Primary Table: knownGene    Row Count: 278,375   Data last updated: 2024-08-15
Format description: Transcript from default gene set in UCSC browser
On download server: MariaDB table dump directory
fieldexampleSQL type info description
name ENSMUST00000193812.2varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 3143475int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3144545int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3143475int(10) unsigned range Coding region start (or end position if for minus strand item)
cdsEnd 3143475int(10) unsigned range Coding region end (or start position if for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 3143475,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3144545,longblob   Exon end positions (or start positions for minus strand item)
proteinID  varchar(40) values UniProt display ID, UniProt accession, or RefSeq protein ID
alignID uc287gdb.2varchar(255) values Unique identifier (GENCODE transcript ID for GENCODE Basic)

Connected Tables and Joining Fields
        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)
      mm39.bioCycPathway.kgID (via knownGene.name)
      mm39.ceBlastTab.query (via knownGene.name)
      mm39.dmBlastTab.query (via knownGene.name)
      mm39.drBlastTab.query (via knownGene.name)
      mm39.foldUtr3.name (via knownGene.name)
      mm39.foldUtr5.name (via knownGene.name)
      mm39.hgBlastTab.query (via knownGene.name)
      mm39.kgAlias.kgID (via knownGene.name)
      mm39.kgColor.kgID (via knownGene.name)
      mm39.kgProtAlias.kgID (via knownGene.name)
      mm39.kgSpAlias.kgID (via knownGene.name)
      mm39.kgTargetAli.qName (via knownGene.name)
      mm39.kgXref.kgID (via knownGene.name)
      mm39.knownAttrs.kgID (via knownGene.name)
      mm39.knownBlastTab.query (via knownGene.name)
      mm39.knownBlastTab.target (via knownGene.name)
      mm39.knownCanonical.transcript (via knownGene.name)
      mm39.knownCds.name (via knownGene.name)
      mm39.knownGeneMrna.name (via knownGene.name)
      mm39.knownIsoforms.transcript (via knownGene.name)
      mm39.knownToEnsembl.name (via knownGene.name)
      mm39.knownToLocusLink.name (via knownGene.name)
      mm39.knownToMrna.name (via knownGene.name)
      mm39.knownToMrnaSingle.name (via knownGene.name)
      mm39.knownToMupit.name (via knownGene.name)
      mm39.knownToNextProt.name (via knownGene.name)
      mm39.knownToPfam.name (via knownGene.name)
      mm39.knownToRefSeq.name (via knownGene.name)
      mm39.knownToSuper.gene (via knownGene.name)
      mm39.knownToTag.name (via knownGene.name)
      mm39.knownToVisiGene.name (via knownGene.name)
      mm39.knownToWikipedia.name (via knownGene.name)
      mm39.rnBlastTab.query (via knownGene.name)
      mm39.scBlastTab.query (via knownGene.name)
      mm39.ucscScop.ucscId (via knownGene.name)

Sample Rows
 
namechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsproteinIDalignID
ENSMUST00000193812.2chr1+314347531445453143475314347513143475,3144545,uc287gdb.2
ENSMUST00000082908.3chr1+317223831723483172238317223813172238,3172348,uc287gdc.2
ENSMUST00000162897.2chr1-327612332865673276123327612323276123,3283831,3277540,3286567,uc287gdd.2
ENSMUST00000159265.2chr1-327674532858553276745327674523276745,3283661,3277540,3285855,uc007aet.3
ENSMUST00000070533.5chr1-328470437417213286244374157133284704,3491924,3740774,3287191,3492124,3741721,Q5GH67uc007aeu.2
ENSMUST00000195335.2chr1-343595334387723435953343595313435953,3438772,uc287gdf.2
ENSMUST00000192336.2chr1-344577834480113445778344577813445778,3448011,uc287gdg.2
ENSMUST00000194099.2chr1-353519935375083535199353519913535199,3537508,uc287gdh.2
ENSMUST00000161581.3chr1+353679335837763536793353679323536793,3583627,3536910,3583776,uc287gdi.3
ENSMUST00000192973.2chr1-358267335847303582673358267313582673,3584730,uc287gdj.2

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