UCSC Genes tables: Difference between revisions
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These are the lists of tables that were pushed with the latest UCSC Genes tracks. Please keep this page up to date when a new UCSC Genes track is released! [[QAing_UCSC_Genes]] has descriptions of tables, lists of related tables and lists of tables that we no longer release. | These are the lists of tables that were pushed with the latest UCSC Genes tracks. Please keep this page up to date when a new UCSC Genes track is released! [[QAing_UCSC_Genes]] has descriptions of tables, lists of related tables and lists of tables that we no longer release. | ||
==wiki pages about known genes== | |||
[[QAing UCSC Genes]]<br> | |||
[[UCSC Genes tables]]<br> | |||
[[UCSC Genes Staging Process]]<br> | |||
[[Post-Release-Checklist]] | |||
== Assembly databases == | == Assembly databases == | ||
;hg38 (released May 2014) | |||
:bioCycMapDesc | |||
:bioCycPathway | |||
:ceBlastTab | |||
:cgapAlias | |||
:cgapBiocDesc | |||
:cgapBiocPathway | |||
:dmBlastTab | |||
:drBlastTab | |||
:foldUtr3 | |||
:foldUtr5 | |||
:humanHprdP2P | |||
:humanVidalP2P | |||
:humanWankerP2P | |||
:keggMapDesc | |||
:keggPathway | |||
:kg7ToKg8 | |||
:kgAlias | |||
:kgColor | |||
:kgProtAlias | |||
:kgProtMap2 | |||
:kgSpAlias | |||
:kgTargetAli | |||
:kgTxInfo | |||
:kgXref | |||
:knownAlt | |||
:knownBlastTab | |||
:knownCanonical | |||
:knownGene | |||
:knownGeneMrna | |||
:knownGenePep | |||
:knownGeneTxMrna | |||
:knownGeneTxPep | |||
:knownIsoforms | |||
:knownToHprd | |||
:knownToKeggEntrez | |||
:knownToLocusLink | |||
:knownToLynx | |||
:knownToNextProt | |||
:knownToPfam | |||
:knownToRefSeq | |||
:knownToSuper | |||
:knownToVisiGene | |||
:knownToWikipedia | |||
:mmBlastTab | |||
:pfamDesc | |||
:rnBlastTab | |||
:scBlastTab | |||
:scopDesc | |||
:spMrna | |||
:ucscGenePfam | |||
:ucscScop | |||
;mm10 (released March 2014) | |||
:bioCycMapDesc | |||
:bioCycPathway | |||
:ccdsKgMap | |||
:ceBlastTab | |||
:cgapAlias | |||
:cgapBiocDesc | |||
:cgapBiocPathway | |||
:dmBlastTab | |||
:drBlastTab | |||
:foldUtr3 | |||
:foldUtr5 | |||
:hgBlastTab | |||
:keggMapDesc | |||
:keggPathway | |||
:kg6ToKg7 | |||
:kgAlias | |||
:kgColor | |||
:kgProtAlias | |||
:kgProtMap2 | |||
:kgSpAlias | |||
:kgTargetAli | |||
:kgTxInfo | |||
:kgXref | |||
:knownAlt | |||
:knownBlastTab | |||
:knownCanonical | |||
:knownGene | |||
:knownGeneMrna | |||
:knownGeneOld6 | |||
:knownGenePep | |||
:knownGeneTxMrna | |||
:knownGeneTxPep | |||
:knownIsoforms | |||
:knownToEnsembl | |||
:knownToKeggEntrez | |||
:knownToLocusLink | |||
:knownToPfam | |||
:knownToRefSeq | |||
:knownToSuper | |||
:knownToVisiGene | |||
:pfamDesc | |||
:rnBlastTab | |||
:scBlastTab | |||
:scopDesc | |||
:spMrna | |||
:ucscScop | |||
;hg19 (released June 2013) | |||
:bioCycMapDesc | |||
:bioCycPathway | |||
:ccdsKgMap | |||
:ceBlastTab | |||
:cgapAlias | |||
:cgapBiocDesc | |||
:cgapBiocPathway | |||
:dmBlastTab | |||
:drBlastTab | |||
:foldUtr3 | |||
:foldUtr5 | |||
:gnfAtlas2Distance | |||
:gnfU95Distance | |||
:humanHprdP2P | |||
:humanVidalP2P | |||
:humanWankerP2P | |||
:keggMapDesc | |||
:keggPathway | |||
:kg6ToKg7 | |||
:kgAlias | |||
:kgColor | |||
:kgProtAlias | |||
:kgProtMap2 | |||
:kgSpAlias | |||
:kgTargetAli | |||
:kgTxInfo | |||
:kgXref | |||
:knownAlt | |||
:knownBlastTab | |||
:knownCanonical | |||
:knownGene | |||
:knownGeneMrna | |||
:knownGenePep | |||
:knownGeneTxMrna | |||
:knownGeneTxPep | |||
:knownIsoforms | |||
:knownToAllenBrain | |||
:knownToEnsembl | |||
:knownToGnfAtlas2 | |||
:knownToHInv | |||
:knownToHprd | |||
:knownToKeggEntrez | |||
:knownToLocusLink | |||
:knownToPfam | |||
:knownToRefSeq | |||
:knownToSuper | |||
:knownToU133 | |||
:knownToU133Plus2 | |||
:knownToU95 | |||
:knownToVisiGene | |||
:mmBlastTab | |||
:pfamDesc | |||
:rnBlastTab | |||
:scBlastTab | |||
:scopDesc | |||
:spMrna | |||
:ucscScop | |||
;mm10 (released November 2012) | |||
:bioCycPathway | |||
:ceBlastTab | |||
:cgapAlias | |||
:cgapBiocDesc | |||
:cgapBiocPathway | |||
:dmBlastTab | |||
:drBlastTab | |||
:foldUtr3 | |||
:foldUtr5 | |||
:hgBlastTab | |||
:keggMapDesc | |||
:keggPathway | |||
:kgAlias | |||
:kgColor | |||
:kgProtAlias | |||
:kgProtMap2 | |||
:kgSpAlias | |||
:kgTargetAli | |||
:kgTxInfo | |||
:kgXref | |||
:knownAlt | |||
:knownBlastTab | |||
:knownCanonical | |||
:knownGene | |||
:knownGeneMrna | |||
:knownGenePep | |||
:knownGeneTxMrna | |||
:knownGeneTxPep | |||
:knownIsoforms | |||
:knownToEnsembl | |||
:knownToKeggEntrez | |||
:knownToLocusLink | |||
:knownToPfam | |||
:knownToRefSeq | |||
:knownToSuper | |||
:knownToVisiGene | |||
:pfamDesc | |||
:rnBlastTab | |||
:scBlastTab | |||
:scopDesc | |||
:spMrna | |||
:ucscScop | |||
;hg19 (released January 2012) | ;hg19 (released January 2012) | ||
| Line 109: | Line 325: | ||
== proteome database == | == proteome database == | ||
;proteins120806 (released November 2012) | |||
:hgnc | |||
:hgncXref | |||
:history | |||
:interProXref | |||
:pdbSP | |||
:pfamDesc | |||
:pfamXref | |||
:spDisease | |||
:spOldNew | |||
:spReactomeEvent | |||
:spReactomeId | |||
:spSecondaryID | |||
:spVariant | |||
:spXref3 | |||
:swInterPro | |||
:tableDescriptions | |||
:uniProtAlias | |||
;proteins111004 (released January 2012) | ;proteins111004 (released January 2012) | ||
| Line 145: | Line 381: | ||
:uniProtAlias | :uniProtAlias | ||
;note | ;note RGD Genes used a proteome database already on the public site so no proteome database was pushed. | ||
== uniProt database == | == uniProt database == | ||
| Line 188: | Line 424: | ||
:varAcc | :varAcc | ||
:varProtein | :varProtein | ||
;note RGD Genes used a uniProt database already on the public site so no uniProt database was pushed. | |||
== blastTab tables going to the new gene set== | == blastTab tables going to the new gene set== | ||
| Line 201: | Line 439: | ||
:ce6 | :ce6 | ||
:sacCer3 | :sacCer3 | ||
For the February 2012 rat RGD Genes release, the table: | |||
:rnBlastTab | |||
was pushed in each of these databases: | |||
:hg19 | |||
:mm9 | |||
:dm3 | |||
:ce6 | |||
:sacCer3 | |||
There is much more information on [[BlastTabs]] available. | There is much more information on [[BlastTabs]] available. | ||
Latest revision as of 18:40, 14 May 2014
These are the lists of tables that were pushed with the latest UCSC Genes tracks. Please keep this page up to date when a new UCSC Genes track is released! QAing_UCSC_Genes has descriptions of tables, lists of related tables and lists of tables that we no longer release.
wiki pages about known genes
QAing UCSC Genes
UCSC Genes tables
UCSC Genes Staging Process
Post-Release-Checklist
Assembly databases
- hg38 (released May 2014)
- bioCycMapDesc
- bioCycPathway
- ceBlastTab
- cgapAlias
- cgapBiocDesc
- cgapBiocPathway
- dmBlastTab
- drBlastTab
- foldUtr3
- foldUtr5
- humanHprdP2P
- humanVidalP2P
- humanWankerP2P
- keggMapDesc
- keggPathway
- kg7ToKg8
- kgAlias
- kgColor
- kgProtAlias
- kgProtMap2
- kgSpAlias
- kgTargetAli
- kgTxInfo
- kgXref
- knownAlt
- knownBlastTab
- knownCanonical
- knownGene
- knownGeneMrna
- knownGenePep
- knownGeneTxMrna
- knownGeneTxPep
- knownIsoforms
- knownToHprd
- knownToKeggEntrez
- knownToLocusLink
- knownToLynx
- knownToNextProt
- knownToPfam
- knownToRefSeq
- knownToSuper
- knownToVisiGene
- knownToWikipedia
- mmBlastTab
- pfamDesc
- rnBlastTab
- scBlastTab
- scopDesc
- spMrna
- ucscGenePfam
- ucscScop
- mm10 (released March 2014)
- bioCycMapDesc
- bioCycPathway
- ccdsKgMap
- ceBlastTab
- cgapAlias
- cgapBiocDesc
- cgapBiocPathway
- dmBlastTab
- drBlastTab
- foldUtr3
- foldUtr5
- hgBlastTab
- keggMapDesc
- keggPathway
- kg6ToKg7
- kgAlias
- kgColor
- kgProtAlias
- kgProtMap2
- kgSpAlias
- kgTargetAli
- kgTxInfo
- kgXref
- knownAlt
- knownBlastTab
- knownCanonical
- knownGene
- knownGeneMrna
- knownGeneOld6
- knownGenePep
- knownGeneTxMrna
- knownGeneTxPep
- knownIsoforms
- knownToEnsembl
- knownToKeggEntrez
- knownToLocusLink
- knownToPfam
- knownToRefSeq
- knownToSuper
- knownToVisiGene
- pfamDesc
- rnBlastTab
- scBlastTab
- scopDesc
- spMrna
- ucscScop
- hg19 (released June 2013)
- bioCycMapDesc
- bioCycPathway
- ccdsKgMap
- ceBlastTab
- cgapAlias
- cgapBiocDesc
- cgapBiocPathway
- dmBlastTab
- drBlastTab
- foldUtr3
- foldUtr5
- gnfAtlas2Distance
- gnfU95Distance
- humanHprdP2P
- humanVidalP2P
- humanWankerP2P
- keggMapDesc
- keggPathway
- kg6ToKg7
- kgAlias
- kgColor
- kgProtAlias
- kgProtMap2
- kgSpAlias
- kgTargetAli
- kgTxInfo
- kgXref
- knownAlt
- knownBlastTab
- knownCanonical
- knownGene
- knownGeneMrna
- knownGenePep
- knownGeneTxMrna
- knownGeneTxPep
- knownIsoforms
- knownToAllenBrain
- knownToEnsembl
- knownToGnfAtlas2
- knownToHInv
- knownToHprd
- knownToKeggEntrez
- knownToLocusLink
- knownToPfam
- knownToRefSeq
- knownToSuper
- knownToU133
- knownToU133Plus2
- knownToU95
- knownToVisiGene
- mmBlastTab
- pfamDesc
- rnBlastTab
- scBlastTab
- scopDesc
- spMrna
- ucscScop
- mm10 (released November 2012)
- bioCycPathway
- ceBlastTab
- cgapAlias
- cgapBiocDesc
- cgapBiocPathway
- dmBlastTab
- drBlastTab
- foldUtr3
- foldUtr5
- hgBlastTab
- keggMapDesc
- keggPathway
- kgAlias
- kgColor
- kgProtAlias
- kgProtMap2
- kgSpAlias
- kgTargetAli
- kgTxInfo
- kgXref
- knownAlt
- knownBlastTab
- knownCanonical
- knownGene
- knownGeneMrna
- knownGenePep
- knownGeneTxMrna
- knownGeneTxPep
- knownIsoforms
- knownToEnsembl
- knownToKeggEntrez
- knownToLocusLink
- knownToPfam
- knownToRefSeq
- knownToSuper
- knownToVisiGene
- pfamDesc
- rnBlastTab
- scBlastTab
- scopDesc
- spMrna
- ucscScop
- hg19 (released January 2012)
- bioCycMapDesc
- bioCycPathway
- ccdsKgMap
- ceBlastTab
- cgapAlias
- cgapBiocDesc
- cgapBiocPathway
- dmBlastTab
- drBlastTab
- foldUtr3
- foldUtr5
- gnfAtlas2Distance
- gnfU95Distance
- humanHprdP2P
- humanVidalP2P
- humanWankerP2P
- keggMapDesc
- keggPathway
- kg5ToKg6
- kgAlias
- kgColor
- kgProtAlias
- kgProtMap2
- kgSpAlias
- kgTargetAli
- kgTxInfo
- kgXref
- kgXrefOld5
- knownAlt
- knownBlastTab
- knownCanonical
- knownGene
- knownGeneMrna
- knownGeneOld5
- knownGenePep
- knownGeneTxMrna
- knownGeneTxPep
- knownIsoforms
- knownToAllenBrain
- knownToEnsembl
- knownToGnfAtlas2
- knownToHInv
- knownToHprd
- knownToKeggEntrez
- knownToLocusLink
- knownToPfam
- knownToRefSeq
- knownToSuper
- knownToTreefam
- knownToU133
- knownToU133Plus2
- knownToU95
- knownToVisiGene
- mmBlastTab
- pfamDesc
- rnBlastTab
- scBlastTab
- scopDesc
- spMrna
- ucscScop
- rn4 (released February 2012) RGD Genes
- affyExonTissuesGsMedianDistRgdGene2
- affyExonTissuesGsMedianRgdGene2
- affyExonTissuesGsRgdGene2
- ceBlastTab
- dmBlastTab
- drBlastTab
- rgdGene2Raw
- gnfAtlas2RgdGene2Distance
- hgBlastTab
- keggMapDesc
- keggPathway
- mmBlastTab
- rgdGene2
- rgdGene2BlastTab
- rgdGene2Canonical
- rgdGene2Isoforms
- rgdGene2KeggPathway
- rgdGene2Pep
- rgdGene2ToDescription
- rgdGene2ToDisplayId
- rgdGene2ToEnsembl
- rgdGene2ToGenbank
- rgdGene2ToGenbankAll
- rgdGene2ToGnfAtlas2
- rgdGene2ToKeggEntrez
- rgdGene2ToLocusLink
- rgdGene2ToPDB
- rgdGene2ToPfam
- rgdGene2ToRAE230
- rgdGene2ToRefSeq
- rgdGene2ToSymbol
- rgdGene2ToU34A
- rgdGene2ToUniProt
- rgdGene2Xref
- rgdGenePathway
- rgdPathway
- scBlastTab
proteome database
- proteins120806 (released November 2012)
- hgnc
- hgncXref
- history
- interProXref
- pdbSP
- pfamDesc
- pfamXref
- spDisease
- spOldNew
- spReactomeEvent
- spReactomeId
- spSecondaryID
- spVariant
- spXref3
- swInterPro
- tableDescriptions
- uniProtAlias
- proteins111004 (released January 2012)
- hgnc
- hgncXref
- history
- interProXref
- pbAnomLimit
- pbResAvgStd
- pbStamp
- pdbSP
- pepCCntDist
- pepHydroDist
- pepIPCntDist
- pepMolWtDist
- pepMwAa
- pepPi
- pepPiDist
- pepResDist
- pfamDesc
- pfamXref
- spDeleted
- spDisease
- spOldNew
- spOrganism
- spReactomeEvent
- spReactomeId
- spSecondaryID
- spVariant
- spXref2
- spXref3
- swInterPro
- tableDescriptions
- taxonNames
- uniProtAlias
- note RGD Genes used a proteome database already on the public site so no proteome database was pushed.
uniProt database
- sp111004 (released January 2012)
- accToKeyword
- accToTaxon
- author
- citation
- citationRc
- citationRp
- comment
- commentType
- commentVal
- commonName
- description
- displayId
- extDb
- extDbRef
- feature
- featureClass
- featureId
- featureType
- gene
- geneLogic
- history
- info
- keyword
- organelle
- otherAcc
- pathogenHost
- protein
- proteinEvidence
- proteinEvidenceType
- rcType
- rcVal
- reference
- referenceAuthors
- tableDescriptions
- taxon
- varAcc
- varProtein
- note RGD Genes used a uniProt database already on the public site so no uniProt database was pushed.
blastTab tables going to the new gene set
For the January 2012 human UCSC Genes release, the table:
- hgBlastTab
was pushed in each of these databases:
- mm9
- rn4
- dm3
- ce6
- sacCer3
For the February 2012 rat RGD Genes release, the table:
- rnBlastTab
was pushed in each of these databases:
- hg19
- mm9
- dm3
- ce6
- sacCer3
There is much more information on BlastTabs available.
