Schema for kgXref
  Database: hg16    Primary Table: kgXref    Row Count: 42,026   Data last updated: 2004-03-27
Format description: Link together a Known Gene ID and a gene alias
On download server: MariaDB table dump directory
fieldexampleSQL type info description
kgID AB000099varchar(40) values Known Gene ID
mRNA AB000099varchar(40) values mRNA ID
spID P56555varchar(40) values UniProt protein Accession number
spDisplayID DSR4_HUMANvarchar(40) values UniProt display ID
geneSymbol DSCR4varchar(40) values Gene Symbol
refseq NM_005867varchar(40) values RefSeq ID
protAcc NP_005858varchar(40) values NCBI protein Accession number
description Down syndrome critical regi...varchar(255) values Description

Connected Tables and Joining Fields
        hg16.atlasOncoGene.locusSymbol (via kgXref.geneSymbol)
      hg16.jaxOrtholog.humanSymbol (via kgXref.geneSymbol)
      hg16.kgAlias.alias (via kgXref.geneSymbol)
      hg16.refFlat.geneName (via kgXref.geneSymbol)
      hgFixed.ctdSorted.GeneSymbol (via kgXref.geneSymbol)
      hgFixed.ggGeneClass.gene (via kgXref.geneSymbol)
      hgFixed.ggGeneName.gene (via kgXref.geneSymbol)
      hgFixed.ggLink.gene1 (via kgXref.geneSymbol)
      hgFixed.ggLink.gene2 (via kgXref.geneSymbol)
      hgFixed.refLink.name (via kgXref.geneSymbol)
      visiGene.gene.name (via kgXref.geneSymbol)
      hg16.bioCycPathway.kgID (via kgXref.kgID)
      hg16.dmBlastTab.query (via kgXref.kgID)
      hg16.drBlastTab.query (via kgXref.kgID)
      hg16.dupSpMrna.mrnaID (via kgXref.kgID)
      hg16.foldUtr3.name (via kgXref.kgID)
      hg16.foldUtr5.name (via kgXref.kgID)
      hg16.gnfAtlas2Distance.query (via kgXref.kgID)
      hg16.gnfAtlas2Distance.target (via kgXref.kgID)
      hg16.gnfU95Distance.query (via kgXref.kgID)
      hg16.gnfU95Distance.target (via kgXref.kgID)
      hg16.hg17Kg.name (via kgXref.kgID)
      hg16.keggPathway.kgID (via kgXref.kgID)
      hg16.kgAlias.kgID (via kgXref.kgID)
      hg16.kgProtAlias.kgID (via kgXref.kgID)
      hg16.knownBlastTab.query (via kgXref.kgID)
      hg16.knownBlastTab.target (via kgXref.kgID)
      hg16.knownCanonical.transcript (via kgXref.kgID)
      hg16.knownGene.name (via kgXref.kgID)
      hg16.knownGeneLink.name (via kgXref.kgID)
      hg16.knownGeneMrna.name (via kgXref.kgID)
      hg16.knownGenePep.name (via kgXref.kgID)
      hg16.knownIsoforms.transcript (via kgXref.kgID)
      hg16.knownToEnsembl.name (via kgXref.kgID)
      hg16.knownToGnfAtlas2.name (via kgXref.kgID)
      hg16.knownToHInv.name (via kgXref.kgID)
      hg16.knownToLocusLink.name (via kgXref.kgID)
      hg16.knownToPfam.name (via kgXref.kgID)
      hg16.knownToRefSeq.name (via kgXref.kgID)
      hg16.knownToSuper.gene (via kgXref.kgID)
      hg16.knownToU133.name (via kgXref.kgID)
      hg16.knownToU95.name (via kgXref.kgID)
      hg16.scBlastTab.query (via kgXref.kgID)
      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)
      hg16.kgProtAlias.alias (via kgXref.protAcc)
      hgFixed.refLink.protAcc (via kgXref.protAcc)
      knownGeneV39.kgProtAlias.alias (via kgXref.protAcc)
      knownGeneV39.kgSpAlias.alias (via kgXref.protAcc)
      knownGeneV39.kgXref.protAcc (via kgXref.protAcc)
      hg16.altGraphX.mrnaRefs (via kgXref.refseq)
      hg16.knownToRefSeq.value (via kgXref.refseq)
      hg16.mrnaOrientInfo.name (via kgXref.refseq)
      hg16.mrnaRefseq.refseq (via kgXref.refseq)
      hg16.refFlat.name (via kgXref.refseq)
      hg16.refGene.name (via kgXref.refseq)
      hg16.refSeqAli.qName (via kgXref.refseq)
      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)
      go.goaPart.dbObjectSymbol (via kgXref.spDisplayID)
      hg16.dupSpMrna.dupProteinID (via kgXref.spDisplayID)
      hg16.dupSpMrna.proteinID (via kgXref.spDisplayID)
      hg16.kgProtAlias.displayID (via kgXref.spDisplayID)
      hg16.knownCanonical.protein (via kgXref.spDisplayID)
      hg16.spMrna.spID (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)
      proteome.spOldNew.newDisplayId (via kgXref.spDisplayID)
      proteome.spOldNew.oldDisplayId (via kgXref.spDisplayID)
      uniProt.displayId.val (via kgXref.spDisplayID)
      go.goaPart.dbObjectId (via kgXref.spID)
      hg16.kgProtAlias.alias (via kgXref.spID)
      hg16.kgProtMap.qName (via kgXref.spID)
      knownGeneV39.kgProtAlias.alias (via kgXref.spID)
      knownGeneV39.kgSpAlias.spID (via kgXref.spID)
      knownGeneV39.kgXref.spID (via kgXref.spID)
      proteome.hgncXref.uniProt (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
AB000099AB000099P56555DSR4_HUMANDSCR4NM_005867NP_005858Down syndrome critical region gene 4
AB000114AB000114Q99983OMD_HUMANOMDNM_005014NP_005005osteomodulin
AB000115AB000115Q99984Q99984C1orf29NM_006820NP_006811mRNA expressed in osteoblast.
AB000220AB000220Q99985SM3C_HUMANSEMA3CNM_006379NP_006370sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C
AB000277AB000277O14490DLP1_HUMANDLGAP1NM_004746NP_004737discs, large (Drosophila) homolog-associated protein 1
AB000449AB000449Q99986VRK1_HUMANVRK1NM_003384NP_003375vaccinia related kinase 1
AB000459AB000459P78311P78311C4orf8NM_003704NP_003695mRNA, complete cds, clone:RES4-22A,.
AB000460AB000460P78312P78312C4orf8NM_003704NP_003695chromosome 4 open reading frame 8
AB000461AB000461P78313P78313C4orf8NM_003704NP_003695mRNA, complete cds, clone:RES4-22C.
AB000462AB000462P783143BP2_HUMANSH3BP2NM_003023NP_003014SH3-domain binding protein 2

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