Schema for knownGene
  Database: rn3    Primary Table: knownGene    Row Count: 8,348   Data last updated: 2004-03-23
Format description: Transcript from default gene set in UCSC browser
On download server: MariaDB table dump directory
fieldexampleSQL type info description
name AY389467varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1306645int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1307637int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1307285int(10) unsigned range Coding region start (or end position if for minus strand item)
cdsEnd 1307637int(10) unsigned range Coding region end (or start position if for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 1306645,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1307637,longblob   Exon end positions (or start positions for minus strand item)
proteinID AAR26470varchar(40) values UniProt display ID, UniProt accession, or RefSeq protein ID
alignID 1192varchar(8) 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)
      rn3.dmBlastTab.query (via knownGene.name)
      rn3.drBlastTab.query (via knownGene.name)
      rn3.dupSpMrna.mrnaID (via knownGene.name)
      rn3.gnfAtlas2Distance.query (via knownGene.name)
      rn3.gnfAtlas2Distance.target (via knownGene.name)
      rn3.hgBlastTab.query (via knownGene.name)
      rn3.keggPathway.kgID (via knownGene.name)
      rn3.kgAlias.kgID (via knownGene.name)
      rn3.kgProtAlias.kgID (via knownGene.name)
      rn3.kgSpAlias.kgID (via knownGene.name)
      rn3.kgXref.kgID (via knownGene.name)
      rn3.knownBlastTab.query (via knownGene.name)
      rn3.knownBlastTab.target (via knownGene.name)
      rn3.knownCanonical.transcript (via knownGene.name)
      rn3.knownGeneLink.name (via knownGene.name)
      rn3.knownGeneMrna.name (via knownGene.name)
      rn3.knownGenePep.name (via knownGene.name)
      rn3.knownIsoforms.transcript (via knownGene.name)
      rn3.knownToEnsembl.name (via knownGene.name)
      rn3.knownToGnfAtlas2.name (via knownGene.name)
      rn3.knownToLocusLink.name (via knownGene.name)
      rn3.knownToPfam.name (via knownGene.name)
      rn3.knownToRefSeq.name (via knownGene.name)
      rn3.knownToSuper.gene (via knownGene.name)
      rn3.scBlastTab.query (via knownGene.name)

Sample Rows
 
namechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsproteinIDalignID
AY389467chr1+130664513076371307285130763711306645,1307637,AAR264701192
X61294chr1-167159620796541671596207965421671596,2078043,1672039,2079654,Q632884741
X61295chr1-184228618438281842286184382711842286,1843828,Q632895019
M26686chr1-228914423046382293873230463872289144,2293836,2295667,2296340,2300387,2303332,2304533,2289554,2294053,2295753,2296461,2300492,2303364,2304638,PIMT_RAT4282
U92072chr1-4428181457937344283194579023274428181,4430152,4434880,4436531,4437024,4438219,4445380,4457096,4466636,4468700,4468767,4474843,4475459,4481106,4481378,4481665, ...4428361,4430373,4434992,4436697,4437394,4438459,4445431,4457162,4466788,4468717,4468800,4475022,4475680,4481147,4481446,4481813, ...Q9Z1528668
AF118889chr1-4428319457902344283194579023294428319,4430152,4434880,4436531,4437024,4438219,4445380,4452472,4452623,4457096,4466636,4468700,4468767,4474843,4475459,4481106, ...4428361,4430373,4434992,4436697,4437394,4438459,4445431,4452520,4452683,4457162,4466788,4468717,4468800,4475022,4475680,4481147, ...Q9WU708567
AF118890chr1-4428319457902344283194579023264428319,4430152,4434880,4436531,4437024,4438219,4457096,4466636,4468700,4468767,4474843,4475459,4481106,4481378,4481665,4485520, ...4428361,4430373,4434992,4436697,4437394,4438459,4457162,4466788,4468717,4468800,4475022,4475680,4481147,4481446,4481813,4485593, ...Q9WU718568
M61099chr1-531861657445905321454574287295318616,5351305,5367198,5375506,5380906,5417295,5615098,5742172,5744535,5322394,5352236,5367325,5375675,5381153,5417531,5615348,5743190,5744590,MGR1_RAT3147
Y18809chr1-532230253514685322302535146825322302,5351305,5322359,5351468,Q9WUY18602
Y18810chr1-532230253514685330228535146835322302,5330204,5351305,5322394,5330289,5351468,Q9WTJ18532

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