Schema for kgXref
  Database: rn3    Primary Table: kgXref    Row Count: 7,528   Data last updated: 2004-03-23
Format description: Link together a Known Gene ID and a gene alias
On download server: MariaDB table dump directory
fieldexampleSQL type info description
kgID AB000098varchar(40) values Known Gene ID
mRNA AB000098varchar(40) values mRNA ID
spID O54755varchar(40) values UniProt protein Accession number
spDisplayID O54755varchar(40) values UniProt display ID
geneSymbol Mipp65varchar(40) values Gene Symbol
refseq NM_022607varchar(40) values RefSeq ID
protAcc NP_072129varchar(40) values NCBI protein Accession number
description MIPP65.varchar(255) values Description

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)
      rn3.dmBlastTab.query (via kgXref.kgID)
      rn3.drBlastTab.query (via kgXref.kgID)
      rn3.dupSpMrna.mrnaID (via kgXref.kgID)
      rn3.gnfAtlas2Distance.query (via kgXref.kgID)
      rn3.gnfAtlas2Distance.target (via kgXref.kgID)
      rn3.hgBlastTab.query (via kgXref.kgID)
      rn3.keggPathway.kgID (via kgXref.kgID)
      rn3.kgAlias.kgID (via kgXref.kgID)
      rn3.kgProtAlias.kgID (via kgXref.kgID)
      rn3.kgSpAlias.kgID (via kgXref.kgID)
      rn3.knownBlastTab.query (via kgXref.kgID)
      rn3.knownBlastTab.target (via kgXref.kgID)
      rn3.knownCanonical.transcript (via kgXref.kgID)
      rn3.knownGene.name (via kgXref.kgID)
      rn3.knownGeneLink.name (via kgXref.kgID)
      rn3.knownGeneMrna.name (via kgXref.kgID)
      rn3.knownGenePep.name (via kgXref.kgID)
      rn3.knownIsoforms.transcript (via kgXref.kgID)
      rn3.knownToEnsembl.name (via kgXref.kgID)
      rn3.knownToGnfAtlas2.name (via kgXref.kgID)
      rn3.knownToLocusLink.name (via kgXref.kgID)
      rn3.knownToPfam.name (via kgXref.kgID)
      rn3.knownToRefSeq.name (via kgXref.kgID)
      rn3.knownToSuper.gene (via kgXref.kgID)
      rn3.scBlastTab.query (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)
      rn3.kgProtAlias.alias (via kgXref.protAcc)
      rn3.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)
      rn3.knownToRefSeq.value (via kgXref.refseq)
      rn3.mrnaOrientInfo.name (via kgXref.refseq)
      rn3.mrnaRefseq.refseq (via kgXref.refseq)
      rn3.refFlat.name (via kgXref.refseq)
      rn3.refGene.name (via kgXref.refseq)
      rn3.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)
      proteome.spOldNew.newDisplayId (via kgXref.spDisplayID)
      proteome.spOldNew.oldDisplayId (via kgXref.spDisplayID)
      rn3.dupSpMrna.dupProteinID (via kgXref.spDisplayID)
      rn3.dupSpMrna.proteinID (via kgXref.spDisplayID)
      rn3.kgProtAlias.displayID (via kgXref.spDisplayID)
      rn3.kgSpAlias.alias (via kgXref.spDisplayID)
      rn3.knownCanonical.protein (via kgXref.spDisplayID)
      rn3.spMrna.spID (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)
      proteome.spOldNew.acc (via kgXref.spID)
      proteome.spReactomeEvent.spID (via kgXref.spID)
      proteome.spReactomeId.spID (via kgXref.spID)
      rn3.kgProtAlias.alias (via kgXref.spID)
      rn3.kgProtMap.qName (via kgXref.spID)
      rn3.kgSpAlias.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
AB000098AB000098O54755O54755Mipp65NM_022607NP_072129MIPP65.
AB000107AB000107P97786P97786PrlpdNM_022537NP_071982Prolactin-like protein D.
AB000113AB000113O08812CTR3_RATSlc7a3NM_017217NP_058913Cationic amino acid transporter 3 (CAT-3) (Solute carrier family 7 member 3) (Cationic amino acid transporter y+).
AB000199AB000199O35048O35048Cca2NM_139329NP_647545CCA2 protein.
AB000215AB000215O35049O35049Smpd3NM_053605NP_446057CCA1 protein.
AB000216AB000216O08764O08764Cca3NM_134403NP_599230CCA3.
AB000280AB000280O09014O09014LOC246280NM_144758NP_653359Peptide/histidine transporter.
AB000362AB000362Q61413CIRP_MOUSECirbpNM_031147NP_112409Cold-inducible RNA-binding protein (Glycine-rich RNA-binding protein CIRP) (A18 hnRNP).
AB000489AB000489Q9JJP0Q9JJP0Slc20a1NM_031148NP_112410RPHO-1.
AB000491AB000491P47210PRS8_HUMANPSMC5NM_031149NP_112411proteasome (prosome, macropain) 26S subunit, ATPase, 5

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