Schema for kgXref
  Database: mm9    Primary Table: kgXref    Row Count: 55,419   Data last updated: 2011-03-02
Format description: Link together a Known Gene ID and a gene alias
On download server: MariaDB table dump directory
fieldexampleSQL type info description
kgID uc007afh.1varchar(40) values Known Gene ID
mRNA NM_008866varchar(40) values mRNA ID
spID P97823varchar(40) values UniProt protein Accession number
spDisplayID LYPA1_MOUSEvarchar(40) values UniProt display ID
geneSymbol Lypla1varchar(40) values Gene Symbol
refseq NM_008866varchar(40) values RefSeq ID
protAcc NP_032892varchar(40) values NCBI protein Accession number
description acyl-protein thioesterase 1longblob   Description

Connected Tables and Joining Fields
        mm9.cgapAlias.alias (via kgXref.geneSymbol)
      knownGeneV39.bioCycPathway.kgID (via kgXref.kgID)
      knownGeneV39.ceBlastTab.query (via kgXref.kgID)
      knownGeneV39.dmBlastTab.query (via kgXref.kgID)
      knownGeneV39.drBlastTab.query (via kgXref.kgID)
      knownGeneV39.foldUtr3.name (via kgXref.kgID)
      knownGeneV39.foldUtr5.name (via kgXref.kgID)
      knownGeneV39.gnfAtlas2Distance.query (via kgXref.kgID)
      knownGeneV39.gnfAtlas2Distance.target (via kgXref.kgID)
      knownGeneV39.kgAlias.kgID (via kgXref.kgID)
      knownGeneV39.kgColor.kgID (via kgXref.kgID)
      knownGeneV39.kgProtAlias.kgID (via kgXref.kgID)
      knownGeneV39.kgSpAlias.kgID (via kgXref.kgID)
      knownGeneV39.kgTargetAli.qName (via kgXref.kgID)
      knownGeneV39.kgXref.kgID (via kgXref.kgID)
      knownGeneV39.knownAttrs.kgID (via kgXref.kgID)
      knownGeneV39.knownBlastTab.query (via kgXref.kgID)
      knownGeneV39.knownBlastTab.target (via kgXref.kgID)
      knownGeneV39.knownCanonical.protein (via kgXref.kgID)
      knownGeneV39.knownCanonical.transcript (via kgXref.kgID)
      knownGeneV39.knownCds.name (via kgXref.kgID)
      knownGeneV39.knownGene.name (via kgXref.kgID)
      knownGeneV39.knownGeneMrna.name (via kgXref.kgID)
      knownGeneV39.knownGenePep.name (via kgXref.kgID)
      knownGeneV39.knownIsoforms.transcript (via kgXref.kgID)
      knownGeneV39.knownToEnsembl.name (via kgXref.kgID)
      knownGeneV39.knownToGnfAtlas2.name (via kgXref.kgID)
      knownGeneV39.knownToHprd.name (via kgXref.kgID)
      knownGeneV39.knownToLocusLink.name (via kgXref.kgID)
      knownGeneV39.knownToMrna.name (via kgXref.kgID)
      knownGeneV39.knownToMrnaSingle.name (via kgXref.kgID)
      knownGeneV39.knownToMupit.name (via kgXref.kgID)
      knownGeneV39.knownToPfam.name (via kgXref.kgID)
      knownGeneV39.knownToRefSeq.name (via kgXref.kgID)
      knownGeneV39.knownToSuper.gene (via kgXref.kgID)
      knownGeneV39.knownToTag.name (via kgXref.kgID)
      knownGeneV39.knownToU133.name (via kgXref.kgID)
      knownGeneV39.knownToU95.name (via kgXref.kgID)
      knownGeneV39.knownToVisiGene.name (via kgXref.kgID)
      knownGeneV39.knownToWikipedia.name (via kgXref.kgID)
      knownGeneV39.mmBlastTab.query (via kgXref.kgID)
      knownGeneV39.rnBlastTab.query (via kgXref.kgID)
      knownGeneV39.scBlastTab.query (via kgXref.kgID)
      knownGeneV39.ucscScop.ucscId (via kgXref.kgID)
      mm9.affyGnfU74ADistance.query (via kgXref.kgID)
      mm9.affyGnfU74ADistance.target (via kgXref.kgID)
      mm9.affyGnfU74BDistance.query (via kgXref.kgID)
      mm9.affyGnfU74BDistance.target (via kgXref.kgID)
      mm9.affyGnfU74CDistance.query (via kgXref.kgID)
      mm9.affyGnfU74CDistance.target (via kgXref.kgID)
      mm9.bioCycPathway.kgID (via kgXref.kgID)
      mm9.ccdsKgMap.geneId (via kgXref.kgID)
      mm9.ceBlastTab.query (via kgXref.kgID)
      mm9.dmBlastTab.query (via kgXref.kgID)
      mm9.drBlastTab.query (via kgXref.kgID)
      mm9.foldUtr3.name (via kgXref.kgID)
      mm9.foldUtr5.name (via kgXref.kgID)
      mm9.gnfAtlas2Distance.query (via kgXref.kgID)
      mm9.gnfAtlas2Distance.target (via kgXref.kgID)
      mm9.hgBlastTab.query (via kgXref.kgID)
      mm9.keggPathway.kgID (via kgXref.kgID)
      mm9.kgAlias.kgID (via kgXref.kgID)
      mm9.kgColor.kgID (via kgXref.kgID)
      mm9.kgProtAlias.kgID (via kgXref.kgID)
      mm9.kgProtMap2.qName (via kgXref.kgID)
      mm9.kgSpAlias.kgID (via kgXref.kgID)
      mm9.kgTargetAli.qName (via kgXref.kgID)
      mm9.kgTxInfo.name (via kgXref.kgID)
      mm9.knownBlastTab.query (via kgXref.kgID)
      mm9.knownBlastTab.target (via kgXref.kgID)
      mm9.knownCanonical.protein (via kgXref.kgID)
      mm9.knownCanonical.transcript (via kgXref.kgID)
      mm9.knownGene.name (via kgXref.kgID)
      mm9.knownGeneMrna.name (via kgXref.kgID)
      mm9.knownGenePep.name (via kgXref.kgID)
      mm9.knownIsoforms.transcript (via kgXref.kgID)
      mm9.knownToAllenBrain.name (via kgXref.kgID)
      mm9.knownToEnsembl.name (via kgXref.kgID)
      mm9.knownToGnfAtlas2.name (via kgXref.kgID)
      mm9.knownToKeggEntrez.name (via kgXref.kgID)
      mm9.knownToLocusLink.name (via kgXref.kgID)
      mm9.knownToPfam.name (via kgXref.kgID)
      mm9.knownToRefSeq.name (via kgXref.kgID)
      mm9.knownToSuper.gene (via kgXref.kgID)
      mm9.knownToVisiGene.name (via kgXref.kgID)
      mm9.rnBlastTab.query (via kgXref.kgID)
      mm9.scBlastTab.query (via kgXref.kgID)
      mm9.ucscScop.ucscId (via kgXref.kgID)
      hgFixed.refLink.protAcc (via kgXref.protAcc)
      knownGeneV39.kgProtAlias.alias (via kgXref.protAcc)
      knownGeneV39.kgSpAlias.alias (via kgXref.protAcc)
      knownGeneV39.kgXref.protAcc (via kgXref.protAcc)
      mm9.kgProtAlias.alias (via kgXref.protAcc)
      mm9.kgSpAlias.alias (via kgXref.protAcc)
      hgFixed.gbCdnaInfo.acc (via kgXref.refseq)
      hgFixed.gbSeq.acc (via kgXref.refseq)
      hgFixed.imageClone.acc (via kgXref.refseq)
      hgFixed.refLink.mrnaAcc (via kgXref.refseq)
      hgFixed.refSeqStatus.mrnaAcc (via kgXref.refseq)
      hgFixed.refSeqSummary.mrnaAcc (via kgXref.refseq)
      knownGeneV39.kgXref.refseq (via kgXref.refseq)
      knownGeneV39.knownToRefSeq.value (via kgXref.refseq)
      mm9.ccdsInfo.mrnaAcc (via kgXref.refseq)
      mm9.knownToRefSeq.value (via kgXref.refseq)
      mm9.mrnaOrientInfo.name (via kgXref.refseq)
      mm9.refFlat.name (via kgXref.refseq)
      mm9.refGene.name (via kgXref.refseq)
      mm9.refSeqAli.qName (via kgXref.refseq)
      go.goaPart.dbObjectSymbol (via kgXref.spDisplayID)
      knownGeneV39.kgProtAlias.displayID (via kgXref.spDisplayID)
      knownGeneV39.kgSpAlias.alias (via kgXref.spDisplayID)
      knownGeneV39.kgXref.spDisplayID (via kgXref.spDisplayID)
      knownGeneV39.knownCanonical.protein (via kgXref.spDisplayID)
      mm9.spMrna.spID (via kgXref.spDisplayID)
      proteome.spOldNew.newDisplayId (via kgXref.spDisplayID)
      proteome.spOldNew.oldDisplayId (via kgXref.spDisplayID)
      uniProt.displayId.val (via kgXref.spDisplayID)
      go.goaPart.dbObjectId (via kgXref.spID)
      knownGeneV39.kgProtAlias.alias (via kgXref.spID)
      knownGeneV39.kgSpAlias.spID (via kgXref.spID)
      knownGeneV39.kgXref.spID (via kgXref.spID)
      mm9.kgSpAlias.spID (via kgXref.spID)
      proteome.spOldNew.acc (via kgXref.spID)
      proteome.spReactomeEvent.spID (via kgXref.spID)
      proteome.spReactomeId.spID (via kgXref.spID)
      uniProt.accToKeyword.acc (via kgXref.spID)
      uniProt.accToTaxon.acc (via kgXref.spID)
      uniProt.citation.acc (via kgXref.spID)
      uniProt.comment.acc (via kgXref.spID)
      uniProt.description.acc (via kgXref.spID)
      uniProt.displayId.acc (via kgXref.spID)
      uniProt.extDbRef.acc (via kgXref.spID)
      uniProt.feature.acc (via kgXref.spID)
      uniProt.gene.acc (via kgXref.spID)
      uniProt.geneLogic.acc (via kgXref.spID)
      uniProt.info.acc (via kgXref.spID)
      uniProt.otherAcc.acc (via kgXref.spID)
      uniProt.protein.acc (via kgXref.spID)
      visiGene.gene.uniProt (via kgXref.spID)

Sample Rows
 
kgIDmRNAspIDspDisplayIDgeneSymbolrefseqprotAccdescription
uc007afh.1NM_008866P97823LYPA1_MOUSELypla1NM_008866NP_032892acyl-protein thioesterase 1
uc007afg.1AK050549P97823-2P97823-2Lypla1NM_008866NP_032892acyl-protein thioesterase 1
uc007afi.2NM_011541Q3UWX7Q3UWX7_MOUSETcea1NM_011541NP_035671transcription elongation factor A protein 1
uc011wht.1NM_001159750Q3UWX7Q3UWX7_MOUSETcea1NM_001159750NP_001153222transcription elongation factor A protein 1
uc011whu.1NM_001159751Q3UWX7Q3UWX7_MOUSETcea1NM_001159751NP_001153223transcription elongation factor A protein 1
uc007afn.1NM_133826Q8BVE3VATH_MOUSEAtp6v1hNM_133826NP_598587V-type proton ATPase subunit H
uc007afm.1AK081492Q3U9S9Q3U9S9_MOUSEAtp6v1hNM_133826NP_598587V-type proton ATPase subunit H
uc007afo.1NM_011011Q14AL5Q14AL5_MOUSEOprk1NM_011011NP_035141kappa-type opioid receptor
uc007afp.1S81111Q14AL5Q14AL5_MOUSEOprk1NM_011011NP_035141kappa-type opioid receptor
uc007afq.1AK138198Q14AL5Q14AL5_MOUSEOprk1NM_011011NP_035141kappa-type opioid receptor

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