Schema for knownGene
  Database: mm9    Primary Table: knownGene    Row Count: 55,419   Data last updated: 2011-03-02
Format description: Transcript from default gene set in UCSC browser
On download server: MariaDB table dump directory
fieldexampleSQL type info description
name uc007aet.1varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 3195984int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3205713int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3195984int(10) unsigned range Coding region start (or end position if for minus strand item)
cdsEnd 3195984int(10) unsigned range Coding region end (or start position if for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 3195984,3203519,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3197398,3205713,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 uc007aet.1varchar(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)
      mm9.affyGnfU74ADistance.query (via knownGene.name)
      mm9.affyGnfU74ADistance.target (via knownGene.name)
      mm9.affyGnfU74BDistance.query (via knownGene.name)
      mm9.affyGnfU74BDistance.target (via knownGene.name)
      mm9.affyGnfU74CDistance.query (via knownGene.name)
      mm9.affyGnfU74CDistance.target (via knownGene.name)
      mm9.bioCycPathway.kgID (via knownGene.name)
      mm9.ccdsKgMap.geneId (via knownGene.name)
      mm9.ceBlastTab.query (via knownGene.name)
      mm9.dmBlastTab.query (via knownGene.name)
      mm9.drBlastTab.query (via knownGene.name)
      mm9.foldUtr3.name (via knownGene.name)
      mm9.foldUtr5.name (via knownGene.name)
      mm9.gnfAtlas2Distance.query (via knownGene.name)
      mm9.gnfAtlas2Distance.target (via knownGene.name)
      mm9.hgBlastTab.query (via knownGene.name)
      mm9.keggPathway.kgID (via knownGene.name)
      mm9.kgAlias.kgID (via knownGene.name)
      mm9.kgColor.kgID (via knownGene.name)
      mm9.kgProtAlias.kgID (via knownGene.name)
      mm9.kgProtMap2.qName (via knownGene.name)
      mm9.kgSpAlias.kgID (via knownGene.name)
      mm9.kgTargetAli.qName (via knownGene.name)
      mm9.kgTxInfo.name (via knownGene.name)
      mm9.kgXref.kgID (via knownGene.name)
      mm9.knownBlastTab.query (via knownGene.name)
      mm9.knownBlastTab.target (via knownGene.name)
      mm9.knownCanonical.protein (via knownGene.name)
      mm9.knownCanonical.transcript (via knownGene.name)
      mm9.knownGeneMrna.name (via knownGene.name)
      mm9.knownGenePep.name (via knownGene.name)
      mm9.knownIsoforms.transcript (via knownGene.name)
      mm9.knownToAllenBrain.name (via knownGene.name)
      mm9.knownToEnsembl.name (via knownGene.name)
      mm9.knownToGnfAtlas2.name (via knownGene.name)
      mm9.knownToKeggEntrez.name (via knownGene.name)
      mm9.knownToLocusLink.name (via knownGene.name)
      mm9.knownToPfam.name (via knownGene.name)
      mm9.knownToRefSeq.name (via knownGene.name)
      mm9.knownToSuper.gene (via knownGene.name)
      mm9.knownToVisiGene.name (via knownGene.name)
      mm9.rnBlastTab.query (via knownGene.name)
      mm9.scBlastTab.query (via knownGene.name)
      mm9.ucscScop.ucscId (via knownGene.name)

Sample Rows
 
namechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsproteinIDalignID
uc007aet.1chr1-319598432057133195984319598423195984,3203519,3197398,3205713,uc007aet.1
uc007aeu.1chr1-320456236615793206102366142933204562,3411782,3660632,3207049,3411982,3661579,Q5GH67uc007aeu.1
uc007aev.1chr1-363839136489853638391363839123638391,3648927,3640590,3648985,uc007aev.1
uc007aew.1chr1-428092643993224283061439926844280926,4341990,4342282,4399250,4283093,4342162,4342918,4399322,NP_001182591uc007aew.1
uc007aex.2chr1-433358743503954334680434290644333587,4341990,4342282,4350280,4340172,4342162,4342918,4350395,Q548Q8uc007aex.2
uc007aey.1chr1-448100844838164481796448348724481008,4483180,4482749,4483816,Q61473uc007aey.1
uc007aez.1chr1-448100844864944481796448348754481008,4483180,4483852,4485216,4486371,4482749,4483547,4483944,4486023,4486494,Q61473uc007aez.1
uc007afa.1chr1-448100844864944481796448523644481008,4483852,4485216,4486371,4482749,4483944,4486023,4486494,Q61473uc007afa.1
uc007afb.1chr1-448100844864944481796448267234481008,4483852,4486371,4482749,4483944,4486494,Q61473-2uc007afb.1
uc007afc.1chr1-448100844864944481796448348744481008,4483180,4483852,4486371,4482749,4483571,4483944,4486494,Q61473uc007afc.1

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