Schema for xenoRefGene
  Database: sacCer3    Primary Table: xenoRefGene    Row Count: 31,843   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_052819varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrVIIvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 158898int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 158985int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 158985int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 158985int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 158898,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 158985,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 F54F12.3varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,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
        hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      sacCer3.all_est.qName (via xenoRefGene.name)
      sacCer3.all_mrna.qName (via xenoRefGene.name)
      sacCer3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
586NR_052819chrVII-1588981589851589851589851158898,158985,0F54F12.3unkunk-1,
73NM_001086217chrXIV-5063536195535063536195532506353,619361,506569,619553,0dnaja2.Lincmplincmpl0,0,
589NM_001086214chrXV+5451035463065451035463062545103,545334,545280,546306,0psmc3.Sincmplincmpl0,0,
587NM_001086211chrII-2908122916312908122916314290812,291028,291340,291523,290998,291202,291493,291631,0ola1.Lincmplincmpl0,0,0,0,
591NM_001155440chrXVI+9115669117919115669117911911566,911791,0LOC100282532incmplincmpl0,
587NM_001155439chrVII-2817112835952817112835954281711,282365,282968,283544,281930,282863,283511,283595,0LOC100282531incmplincmpl0,0,0,0,
585NM_001185145chrVI-53259543785325954378153259,54378,0Arp1incmplcmpl0,
585NM_001185146chrVI-53259543785325954378153259,54378,0Arp1incmplcmpl0,
590NM_001324843chrXIII+7022997030407022997030405702299,702422,702638,702761,702842,702344,702575,702725,702824,703040,0LOC107764380incmplincmpl0,0,0,0,0,
591NM_001183691chrXV+8328128341958328128341951832812,834195,0YTM1cmplcmpl0,

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