Schema for kgTxInfo
  Database: hg18    Primary Table: kgTxInfo    Row Count: 66,803   Data last updated: 2009-03-03
Format description: Various bits of information about a transcript from the txGraph/txCds system (aka KG3)
On download server: MariaDB table dump directory
fieldexampleSQL type info description
name uc001aaa.2varchar(255) values Name of transcript
category noncodingvarchar(255) values coding/nearCoding/noncoding for now
sourceAcc BC032353.1varchar(255) values Accession of genbank transcript patterned on (may be refSeq)
isRefSeq 0tinyint(3) unsigned range Is a refSeq
sourceSize 1673int(11) range Number of bases in source, excluding poly-A tail.
aliCoverage 0.896593double range Fraction of bases in source aligning.
aliIdRatio 0.995119double range matching/total bases in alignment
genoMapCount 3int(11) range Number of times source aligns in genome.
exonCount 3int(11) range Number of exons (excludes gaps from frame shift/stops)
orfSize 0int(11) range Size of ORF
cdsScore 19.5double range Score of best CDS according to txCdsPredict
startComplete 0tinyint(3) unsigned range Starts with ATG
endComplete 0tinyint(3) unsigned range Ends with stop codon
nonsenseMediatedDecay 0tinyint(3) unsigned range If true, is a nonsense mediated decay candidate.
retainedIntron 0tinyint(3) unsigned range True if has a retained intron compared to overlapping transcripts
bleedIntoIntron 0int(11) range If nonzero number of bases start or end of tx bleeds into intron
strangeSplice 0int(11) range Count of splice sites not gt/ag, gc/ag, or at/ac
atacIntrons 0int(11) range Count of number of at/ac introns
cdsSingleInIntron 0tinyint(3) unsigned range True if CDS is single exon and in intron of other transcript.
cdsSingleInUtr3 0tinyint(3) unsigned range True if CDS is single exon and in 3' UTR of other transcript.
selenocysteine 0tinyint(3) unsigned range If true TGA codes for selenocysteine
genomicFrameShift 0tinyint(3) unsigned range True if genomic version has frame shift we cut out
genomicStop 0tinyint(3) unsigned range True if genomic version has stop codon we cut out

Connected Tables and Joining Fields
        hg18.bioCycPathway.kgID (via kgTxInfo.name)
      hg18.ccdsKgMap.geneId (via kgTxInfo.name)
      hg18.ceBlastTab.query (via kgTxInfo.name)
      hg18.dmBlastTab.query (via kgTxInfo.name)
      hg18.drBlastTab.query (via kgTxInfo.name)
      hg18.foldUtr3.name (via kgTxInfo.name)
      hg18.foldUtr5.name (via kgTxInfo.name)
      hg18.gnfAtlas2Distance.query (via kgTxInfo.name)
      hg18.gnfAtlas2Distance.target (via kgTxInfo.name)
      hg18.gnfU95Distance.query (via kgTxInfo.name)
      hg18.gnfU95Distance.target (via kgTxInfo.name)
      hg18.humanHprdP2P.query (via kgTxInfo.name)
      hg18.humanHprdP2P.target (via kgTxInfo.name)
      hg18.humanVidalP2P.query (via kgTxInfo.name)
      hg18.humanVidalP2P.target (via kgTxInfo.name)
      hg18.humanWankerP2P.query (via kgTxInfo.name)
      hg18.humanWankerP2P.target (via kgTxInfo.name)
      hg18.keggPathway.kgID (via kgTxInfo.name)
      hg18.kgAlias.kgID (via kgTxInfo.name)
      hg18.kgColor.kgID (via kgTxInfo.name)
      hg18.kgProtAlias.kgID (via kgTxInfo.name)
      hg18.kgProtMap2.qName (via kgTxInfo.name)
      hg18.kgSpAlias.kgID (via kgTxInfo.name)
      hg18.kgTargetAli.qName (via kgTxInfo.name)
      hg18.kgXref.kgID (via kgTxInfo.name)
      hg18.knownBlastTab.query (via kgTxInfo.name)
      hg18.knownBlastTab.target (via kgTxInfo.name)
      hg18.knownCanonToDecipher.name (via kgTxInfo.name)
      hg18.knownCanonical.protein (via kgTxInfo.name)
      hg18.knownCanonical.transcript (via kgTxInfo.name)
      hg18.knownGene.name (via kgTxInfo.name)
      hg18.knownGeneMrna.name (via kgTxInfo.name)
      hg18.knownGenePep.name (via kgTxInfo.name)
      hg18.knownIsoforms.transcript (via kgTxInfo.name)
      hg18.knownToAllenBrain.name (via kgTxInfo.name)
      hg18.knownToDecipher.name (via kgTxInfo.name)
      hg18.knownToEnsembl.name (via kgTxInfo.name)
      hg18.knownToGnf1h.name (via kgTxInfo.name)
      hg18.knownToGnfAtlas2.name (via kgTxInfo.name)
      hg18.knownToHInv.name (via kgTxInfo.name)
      hg18.knownToHprd.name (via kgTxInfo.name)
      hg18.knownToKeggEntrez.name (via kgTxInfo.name)
      hg18.knownToLocusLink.name (via kgTxInfo.name)
      hg18.knownToMupit.name (via kgTxInfo.name)
      hg18.knownToPfam.name (via kgTxInfo.name)
      hg18.knownToRefSeq.name (via kgTxInfo.name)
      hg18.knownToSuper.gene (via kgTxInfo.name)
      hg18.knownToTreefam.name (via kgTxInfo.name)
      hg18.knownToU133.name (via kgTxInfo.name)
      hg18.knownToU133Plus2.name (via kgTxInfo.name)
      hg18.knownToU95.name (via kgTxInfo.name)
      hg18.knownToVisiGene.name (via kgTxInfo.name)
      hg18.mmBlastTab.query (via kgTxInfo.name)
      hg18.rnBlastTab.query (via kgTxInfo.name)
      hg18.scBlastTab.query (via kgTxInfo.name)
      hg18.ucscScop.ucscId (via kgTxInfo.name)
      knownGeneV39.bioCycPathway.kgID (via kgTxInfo.name)
      knownGeneV39.ceBlastTab.query (via kgTxInfo.name)
      knownGeneV39.dmBlastTab.query (via kgTxInfo.name)
      knownGeneV39.drBlastTab.query (via kgTxInfo.name)
      knownGeneV39.foldUtr3.name (via kgTxInfo.name)
      knownGeneV39.foldUtr5.name (via kgTxInfo.name)
      knownGeneV39.gnfAtlas2Distance.query (via kgTxInfo.name)
      knownGeneV39.gnfAtlas2Distance.target (via kgTxInfo.name)
      knownGeneV39.kgAlias.kgID (via kgTxInfo.name)
      knownGeneV39.kgColor.kgID (via kgTxInfo.name)
      knownGeneV39.kgProtAlias.kgID (via kgTxInfo.name)
      knownGeneV39.kgSpAlias.kgID (via kgTxInfo.name)
      knownGeneV39.kgTargetAli.qName (via kgTxInfo.name)
      knownGeneV39.kgXref.kgID (via kgTxInfo.name)
      knownGeneV39.knownAttrs.kgID (via kgTxInfo.name)
      knownGeneV39.knownBlastTab.query (via kgTxInfo.name)
      knownGeneV39.knownBlastTab.target (via kgTxInfo.name)
      knownGeneV39.knownCanonical.protein (via kgTxInfo.name)
      knownGeneV39.knownCanonical.transcript (via kgTxInfo.name)
      knownGeneV39.knownCds.name (via kgTxInfo.name)
      knownGeneV39.knownGene.name (via kgTxInfo.name)
      knownGeneV39.knownGeneMrna.name (via kgTxInfo.name)
      knownGeneV39.knownGenePep.name (via kgTxInfo.name)
      knownGeneV39.knownIsoforms.transcript (via kgTxInfo.name)
      knownGeneV39.knownToEnsembl.name (via kgTxInfo.name)
      knownGeneV39.knownToGnfAtlas2.name (via kgTxInfo.name)
      knownGeneV39.knownToHprd.name (via kgTxInfo.name)
      knownGeneV39.knownToLocusLink.name (via kgTxInfo.name)
      knownGeneV39.knownToMrna.name (via kgTxInfo.name)
      knownGeneV39.knownToMrnaSingle.name (via kgTxInfo.name)
      knownGeneV39.knownToMupit.name (via kgTxInfo.name)
      knownGeneV39.knownToPfam.name (via kgTxInfo.name)
      knownGeneV39.knownToRefSeq.name (via kgTxInfo.name)
      knownGeneV39.knownToSuper.gene (via kgTxInfo.name)
      knownGeneV39.knownToTag.name (via kgTxInfo.name)
      knownGeneV39.knownToU133.name (via kgTxInfo.name)
      knownGeneV39.knownToU95.name (via kgTxInfo.name)
      knownGeneV39.knownToVisiGene.name (via kgTxInfo.name)
      knownGeneV39.knownToWikipedia.name (via kgTxInfo.name)
      knownGeneV39.mmBlastTab.query (via kgTxInfo.name)
      knownGeneV39.rnBlastTab.query (via kgTxInfo.name)
      knownGeneV39.scBlastTab.query (via kgTxInfo.name)
      knownGeneV39.ucscScop.ucscId (via kgTxInfo.name)

Sample Rows
 
namecategorysourceAccisRefSeqsourceSizealiCoveragealiIdRatiogenoMapCountexonCountorfSizecdsScorestartCompleteendCompletenonsenseMediatedDecayretainedIntronbleedIntoIntronstrangeSpliceatacIntronscdsSingleInIntroncdsSingleInUtr3selenocysteinegenomicFrameShiftgenomicStop
uc001aaa.2noncodingBC032353.1016730.8965930.99511933019.5000000000000
uc009vip.1noncodingAX748260.1031010.8916480.983502220-23.5000116880000000
uc009vjg.1noncodingBC048429.1019170.3693270.977401530234000000000000
uc001aal.1codingNM_001005484.1191811119181805.5110000000000
uc009vjh.1codingAY972817.1088810.994369237381331100000000000
uc001aaq.1noncodingDQ599874.10320.9687512810151000000000000
uc001aar.1noncodingDQ599768.10320.7513610142.5000000000000
uc001aas.1noncodingDQ574670.10320.96875127100000000000000
uc001aat.1noncodingDQ596298.1028111610151000000000000
uc001aau.1noncodingDQ599768.1032113610177000000000000

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