Schema for kgXref
  Database: mm39    Primary Table: kgXref    Row Count: 149,547   Data last updated: 2023-08-17
Format description: Link together a Known Gene ID and a gene alias
On download server: MariaDB table dump directory
fieldexampleSQL type info description
kgID ENSMUST00000000001.5varchar(255) values Known Gene ID
mRNA NM_010306varchar(255) values mRNA ID
spID Q9DC51varchar(255) values UniProt protein Accession number
spDisplayID GNAI3_MOUSEvarchar(255) values UniProt display ID
geneSymbol Gnai3varchar(255) values Gene Symbol
refseq NM_010306varchar(255) values RefSeq ID
protAcc NM_010306varchar(255) values NCBI protein Accession number
description Mus musculus guanine nucleo...longblob   Description
rfamAcc  varchar(255) values Rfam accession number
tRnaName  varchar(255) values Name from the tRNA track

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

Sample Rows
 
kgIDmRNAspIDspDisplayIDgeneSymbolrefseqprotAccdescriptionrfamAcctRnaName
ENSMUST00000000001.5NM_010306Q9DC51GNAI3_MOUSEGnai3NM_010306NM_010306Mus musculus guanine nucleotide binding protein (G protein), alpha inhibiting 3 (Gnai3), mRNA. (from RefSeq NM_010306)
ENSMUST00000000003.14NM_017471Q3UV89Q3UV89_MOUSEPbsnNM_017471NM_017471Mus musculus probasin (Pbsn), mRNA. (from RefSeq NM_017471)
ENSMUST00000000010.9NM_008270P20615HXB9_MOUSEHoxb9NM_008270NM_008270Mus musculus homeobox B9 (Hoxb9), mRNA. (from RefSeq NM_008270)
ENSMUST00000000028.14NM_009862Q9Z1X9CDC45_MOUSECdc45NM_009862NM_009862Mus musculus cell division cycle 45 (Cdc45), transcript variant 1, mRNA. (from RefSeq NM_009862)
ENSMUST00000000033.12NM_001315489P09535IGF2_MOUSEIgf2NM_001315489NM_001315489Mus musculus insulin-like growth factor 2 (Igf2), transcript variant 5, mRNA. (from RefSeq NM_001315489)
ENSMUST00000000049.6NM_013475Q01339APOH_MOUSEApohNM_013475NM_013475Mus musculus apolipoprotein H (Apoh), mRNA. (from RefSeq NM_013475)
ENSMUST00000000058.7NM_016900Q9WVC3CAV2_MOUSECav2NM_016900NM_016900Mus musculus caveolin 2 (Cav2), transcript variant 1, mRNA. (from RefSeq NM_016900)
ENSMUST00000000080.8NM_011803Q8BPQ2Q8BPQ2_MOUSEKlf6NM_011803NM_011803Mus musculus Kruppel-like factor 6 (Klf6), mRNA. (from RefSeq NM_011803)
ENSMUST00000000087.13NM_013883Q8K214SCMH1_MOUSEScmh1NM_013883NM_013883Mus musculus sex comb on midleg homolog 1 (Scmh1), transcript variant 1, mRNA. (from RefSeq NM_013883)
ENSMUST00000000090.8NM_007747P12787COX5A_MOUSECox5aNM_007747NM_007747Mus musculus cytochrome c oxidase subunit 5A (Cox5a), mRNA; nuclear gene for mitochondrial product. (from RefSeq NM_007747)

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