Schema for xenoRefGene
  Database: ce11    Primary Table: xenoRefGene    Row Count: 33,497   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 651smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_017072varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrIIvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 8651790int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 8655569int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 8651790int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 8655569int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 8651790,8652580,8652736,865...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 8651874,8652724,8652874,865...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Cps1varchar(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 0,0,0,0,0,0,0,0,0,0,0,0,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
        ce11.all_est.qName (via xenoRefGene.name)
      ce11.all_mrna.qName (via xenoRefGene.name)
      ce11.refGene.name (via xenoRefGene.name)
      ce11.refSeqAli.qName (via xenoRefGene.name)
      ce11.xenoMrna.qName (via xenoRefGene.name)
      ce11.xenoRefFlat.name (via xenoRefGene.name)
      ce11.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
651NM_017072chrII+8651790865556986517908655569128651790,8652580,8652736,8652949,8653189,8653536,8654246,8654393,8654828,8655035,8655221,8655395,8651874,8652724,8652874,8653171,8653474,8653884,8654366,8654786,8654888,8655104,8655305,8655569,0Cps1incmplincmpl0,0,0,0,0,0,0,0,0,0,0,0,
640NM_001006929chrIII-723320172339447233201723394437233201,7233769,7233928,7233549,7233855,7233944,0ndufs8incmplcmpl0,1,0,
641NM_001099794chrIII+738512173856597385121738565927385121,7385488,7385421,7385659,0tbpincmplincmpl0,0,
697NM_001109785chrV+14686163146884251468616314688425614686163,14686363,14686933,14687113,14688158,14688395,14686310,14686885,14687065,14688094,14688320,14688425,0HSP90AA1incmplcmpl0,0,0,0,0,0,
630NM_001110783chrIV+5975680598367259756805983672125975680,5976251,5977645,5977759,5978829,5978928,5979234,5979593,5982979,5983270,5983369,5983471,5975830,5976722,5977729,5978337,5978904,5979102,5979285,5979692,5983213,5983345,5983411,5983672,0Ank1incmplincmpl0,0,0,0,0,0,0,0,0,0,0,0,
665NM_001006695chrI+10563628105643561056362810564353410563628,10563949,10564052,10564269,10563808,10563988,10564193,10564356,0ube2q2incmplcmpl0,0,0,0,
689NM_001255037chrIII+13693083136936221369308313693622213693083,13693493,13693335,13693622,0CYP40incmplincmpl0,0,
690NM_001093164chrIII-13764288137657261376428813765726613764288,13764443,13764848,13765055,13765446,13765588,13764396,13764815,13765034,13765220,13765536,13765726,0ugp2.Lincmplcmpl0,0,0,0,0,0,
654NM_001288694chrI-910847091100819108470911008139108470,9109406,9109910,9108515,9109607,9110081,0LOC102579157incmplincmpl0,0,0,
629NM_001288680chrIV-584461058463205844610584632055844610,5845046,5845108,5845978,5846267,5844946,5845072,5845282,5846042,5846320,0METK1incmplincmpl0,0,0,2,0,

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