Schema for kgXref
  Database: hg38    Primary Table: kgXref    Row Count: 412,034   Data last updated: 2024-08-19
Format description: Link together a Known Gene ID and a gene alias
On download server: MariaDB table dump directory
fieldexampleSQL type info description
kgID ENST00000000233.10varchar(255) values Known Gene ID
mRNA NM_001662varchar(255) values mRNA ID
spID P84085varchar(255) values UniProt protein Accession number
spDisplayID ARF5_HUMANvarchar(255) values UniProt display ID
geneSymbol ARF5varchar(255) values Gene Symbol
refseq NM_001662varchar(255) values RefSeq ID
protAcc NM_001662varchar(255) values NCBI protein Accession number
description ADP ribosylation factor 5 (...longblob   Description
rfamAcc  varchar(255) values Rfam accession number
tRnaName  varchar(255) values Name from the tRNA track

Connected Tables and Joining Fields
        hg38.cgapAlias.alias (via kgXref.geneSymbol)
      hg38.geneReviews.name (via kgXref.geneSymbol)
      hg38.geneReviewsDetail.geneSymbol (via kgXref.geneSymbol)
      hg38.kgAlias.alias (via kgXref.geneSymbol)
      hg38.kgSpAlias.alias (via kgXref.geneSymbol)
      hg38.omimGeneMap.geneSymbol (via kgXref.geneSymbol) Note: genome-wide queries are not available for this table.
      hg38.omimGeneMap2.geneSymbol (via kgXref.geneSymbol) Note: genome-wide queries are not available for this table.
      hg38.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)
      hg38.bioCycPathway.kgID (via kgXref.kgID)
      hg38.ccdsKgMap.geneId (via kgXref.kgID)
      hg38.ceBlastTab.query (via kgXref.kgID)
      hg38.dmBlastTab.query (via kgXref.kgID)
      hg38.drBlastTab.query (via kgXref.kgID)
      hg38.foldUtr3.name (via kgXref.kgID)
      hg38.foldUtr5.name (via kgXref.kgID)
      hg38.gnfAtlas2Distance.query (via kgXref.kgID)
      hg38.gnfAtlas2Distance.target (via kgXref.kgID)
      hg38.gnfU95Distance.query (via kgXref.kgID)
      hg38.gnfU95Distance.target (via kgXref.kgID)
      hg38.humanHprdP2P.query (via kgXref.kgID)
      hg38.humanHprdP2P.target (via kgXref.kgID)
      hg38.humanVidalP2P.query (via kgXref.kgID)
      hg38.humanVidalP2P.target (via kgXref.kgID)
      hg38.humanWankerP2P.query (via kgXref.kgID)
      hg38.humanWankerP2P.target (via kgXref.kgID)
      hg38.keggPathway.kgID (via kgXref.kgID)
      hg38.kgAlias.kgID (via kgXref.kgID)
      hg38.kgColor.kgID (via kgXref.kgID)
      hg38.kgProtAlias.kgID (via kgXref.kgID)
      hg38.kgSpAlias.kgID (via kgXref.kgID)
      hg38.kgTargetAli.qName (via kgXref.kgID)
      hg38.knownAttrs.kgID (via kgXref.kgID)
      hg38.knownBlastTab.query (via kgXref.kgID)
      hg38.knownBlastTab.target (via kgXref.kgID)
      hg38.knownCanonical.transcript (via kgXref.kgID)
      hg38.knownCds.name (via kgXref.kgID)
      hg38.knownGene.name (via kgXref.kgID)
      hg38.knownGeneMrna.name (via kgXref.kgID)
      hg38.knownGenePep.name (via kgXref.kgID)
      hg38.knownIsoforms.transcript (via kgXref.kgID)
      hg38.knownToEnsembl.name (via kgXref.kgID)
      hg38.knownToGnfAtlas2.name (via kgXref.kgID)
      hg38.knownToHprd.name (via kgXref.kgID)
      hg38.knownToKeggEntrez.name (via kgXref.kgID)
      hg38.knownToLocusLink.name (via kgXref.kgID)
      hg38.knownToLynx.name (via kgXref.kgID)
      hg38.knownToMrna.name (via kgXref.kgID)
      hg38.knownToMrnaSingle.name (via kgXref.kgID)
      hg38.knownToMupit.name (via kgXref.kgID)
      hg38.knownToNextProt.name (via kgXref.kgID)
      hg38.knownToPfam.name (via kgXref.kgID)
      hg38.knownToRefSeq.name (via kgXref.kgID)
      hg38.knownToSuper.gene (via kgXref.kgID)
      hg38.knownToTag.name (via kgXref.kgID)
      hg38.knownToU133.name (via kgXref.kgID)
      hg38.knownToU95.name (via kgXref.kgID)
      hg38.knownToVisiGene.name (via kgXref.kgID)
      hg38.knownToWikipedia.name (via kgXref.kgID)
      hg38.mmBlastTab.query (via kgXref.kgID)
      hg38.rnBlastTab.query (via kgXref.kgID)
      hg38.scBlastTab.query (via kgXref.kgID)
      hg38.ucscScop.ucscId (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)
      hg38.kgProtAlias.alias (via kgXref.protAcc)
      hg38.kgSpAlias.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)
      hg38.ccdsInfo.mrnaAcc (via kgXref.refseq)
      hg38.knownToRefSeq.value (via kgXref.refseq)
      hg38.mrnaOrientInfo.name (via kgXref.refseq)
      hg38.refFlat.name (via kgXref.refseq)
      hg38.refGene.name (via kgXref.refseq)
      hg38.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)
      hg38.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)
      hg38.kgSpAlias.spID (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
 
kgIDmRNAspIDspDisplayIDgeneSymbolrefseqprotAccdescriptionrfamAcctRnaName
ENST00000000233.10NM_001662P84085ARF5_HUMANARF5NM_001662NM_001662ADP ribosylation factor 5 (from RefSeq NM_001662.4)
ENST00000000412.8NM_002355P20645MPRD_HUMANM6PRNM_002355NM_002355mannose-6-phosphate receptor, cation dependent, transcript variant 1 (from RefSeq NM_002355.4)
ENST00000000442.11NM_004451Q569H8Q569H8_HUMANESRRANM_004451NM_004451estrogen related receptor alpha, transcript variant 1 (from RefSeq NM_004451.5)
ENST00000001008.6NM_002014Q02790FKBP4_HUMANFKBP4NM_002014NM_002014FKBP prolyl isomerase 4 (from RefSeq NM_002014.4)
ENST00000001146.7NM_019885Q9NR63CP26B_HUMANCYP26B1NM_019885NM_019885cytochrome P450 family 26 subfamily B member 1, transcript variant 1 (from RefSeq NM_019885.4)
ENST00000002125.9NR_146409Q7L592NDUF7_HUMANNDUFAF7NR_146409NR_146409NADH:ubiquinone oxidoreductase complex assembly factor 7, transcript variant 14 (from RefSeq NR_146409.3)
ENST00000002165.11NM_032020Q9BTY2FUCO2_HUMANFUCA2NM_032020NM_032020alpha-L-fucosidase 2 (from RefSeq NM_032020.5)
ENST00000002501.11NM_001042610Q9H9R9DBND1_HUMANDBNDD1NM_001042610NM_001042610dysbindin domain containing 1, transcript variant 1 (from RefSeq NM_001042610.3)
ENST00000002596.6NM_005114O14792HS3S1_HUMANHS3ST1NM_005114NM_005114heparan sulfate-glucosamine 3-sulfotransferase 1 (from RefSeq NM_005114.4)
ENST00000002829.8NM_004186Q13275SEM3F_HUMANSEMA3FNM_004186NM_004186semaphorin 3F, transcript variant 1 (from RefSeq NM_004186.5)

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