Schema for kgTxInfo
  Database: mm10    Primary Table: kgTxInfo    Row Count: 63,814   Data last updated: 2018-04-13
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 uc007afh.1varchar(255) values Name of transcript
category codingvarchar(255) values coding/nearCoding/noncoding for now
sourceAcc NM_008866.2varchar(255) values Accession of genbank transcript patterned on (may be refSeq)
isRefSeq 1tinyint(3) unsigned range Is a refSeq
sourceSize 2447int(11) range Number of bases in source, excluding poly-A tail.
aliCoverage 0.994279double range Fraction of bases in source aligning.
aliIdRatio 1double range matching/total bases in alignment
genoMapCount 1int(11) range Number of times source aligns in genome.
exonCount 9int(11) range Number of exons (excludes gaps from frame shift/stops)
orfSize 693int(11) range Size of ORF
cdsScore 1494.5double range Score of best CDS according to txCdsPredict
startComplete 1tinyint(3) unsigned range Starts with ATG
endComplete 1tinyint(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
        mm10.bioCycPathway.kgID (via
      mm10.ccdsKgMap.geneId (via
      mm10.ceBlastTab.query (via
      mm10.dmBlastTab.query (via
      mm10.drBlastTab.query (via (via (via
      mm10.hgBlastTab.query (via
      mm10.keggPathway.kgID (via
      mm10.kgAlias.kgID (via
      mm10.kgColor.kgID (via
      mm10.kgProtAlias.kgID (via
      mm10.kgProtMap2.qName (via
      mm10.kgSpAlias.kgID (via
      mm10.kgTargetAli.qName (via
      mm10.kgXref.kgID (via
      mm10.knownAttrs.kgID (via
      mm10.knownBlastTab.query (via (via
      mm10.knownCanonical.transcript (via (via (via (via (via
      mm10.knownIsoforms.transcript (via (via (via (via (via (via (via (via (via
      mm10.knownToSuper.gene (via (via (via (via
      mm10.rnBlastTab.query (via
      mm10.scBlastTab.query (via
      mm10.ucscScop.ucscId (via

Sample Rows

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