Schema for xenoRefGene
  Database: droYak1    Primary Table: xenoRefGene    Row Count: 339,469   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 723smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001128289varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr2Rvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 18120049int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 18121033int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 18120049int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 18121033int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 18120049,18120847,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 18120193,18121033,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 kaznavarchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        droYak1.all_est.qName (via xenoRefGene.name)
      droYak1.all_mrna.qName (via xenoRefGene.name)
      droYak1.xenoMrna.qName (via xenoRefGene.name)
      droYak1.xenoRefFlat.name (via xenoRefGene.name)
      droYak1.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
723NM_001128289chr2R-18120049181210331812004918121033218120049,18120847,18120193,18121033,0kaznaincmplincmpl0,0,
629NM_001128285chr2L-588099558810825880995588108215880995,5881082,0ugt5e1incmplincmpl0,
597NM_001128285chr2R+158573815859481585738158594821585738,1585816,1585759,1585948,0ugt5e1incmplincmpl0,0,
597NM_001128285chr2R+158914315893471589143158934711589143,1589347,0ugt5e1incmplincmpl0,
806NM_001128285chr3R-29027611290276922902761129027692129027611,29027692,0ugt5e1incmplincmpl0,
801NM_001128256chr3R-28412208284136362841220828413636628412208,28412394,28412792,28412961,28413143,28413327,28412321,28412575,28412901,28413082,28413315,28413636,0lats2incmplincmpl1,0,2,1,0,0,
908NR_045523chrU-42368194423684114236841142368411242368194,42368324,42368238,42368411,0Marchf2unkunk-1,-1,
679NM_001094406chr3L+12366300123667951236630012366795212366300,12366735,12366711,12366795,0miox.Sincmplincmpl0,0,
739NM_001104406chr3R+201863572019171320188697201895691220186357,20188327,20188670,20188817,20189071,20189282,20189408,20190339,20190646,20191153,20191369,20191490,20186491,20188588,20188748,20189001,20189224,20189345,20190320,20190597,20191126,20191298,20191476,20191713,0CG45049cmplcmpl-1,-1,0,0,1,1,1,-1,-1,-1,-1,-1,
793NM_001110028chr3R+27315766273328202731576627332820627315766,27315973,27331731,27332124,27332433,27332586,27315814,27316147,27332022,27332220,27332529,27332820,0cnot6bincmplincmpl0,0,0,0,0,0,

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