Schema for xenoRefGene
  Database: allMis1    Primary Table: xenoRefGene    Row Count: 425,570   Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001172097varchar(255) values Name of gene (usually transcript_id from GTF)
chrom JH738332varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 261627int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 341258int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 261627int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 341258int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 261627,270521,276620,294263...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 261708,270648,276723,294359...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Cacul1varchar(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 2,1,2,0,0,2,2,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
        allMis1.all_est.qName (via xenoRefGene.name)
      allMis1.all_mrna.qName (via xenoRefGene.name)
      allMis1.refGene.name (via xenoRefGene.name)
      allMis1.refSeqAli.qName (via xenoRefGene.name)
      allMis1.xenoMrna.qName (via xenoRefGene.name)
      allMis1.xenoRefFlat.name (via xenoRefGene.name)
      allMis1.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
73NM_001172097JH738332+2616273412582616273412587261627,270521,276620,294263,304847,338787,341222,261708,270648,276723,294359,304951,338829,341258,0Cacul1incmplincmpl2,1,2,0,0,2,2,
73NM_001172096JH738332+2616273412582616273412558261627,270521,276620,294263,304847,330432,338786,341222,261708,270648,276723,294359,304951,330569,338829,341258,0Cacul1incmplcmpl2,1,2,0,0,0,2,0,
587NM_001171245JH736073+2678032679652678032679651267803,267965,0LOC100329102incmplincmpl0,
585NM_001004737JH734681-1040601116861040601116863104060,104165,111623,104117,104348,111686,0OR5K2incmplincmpl0,0,0,
73NM_001099744JH739753-10862616591910877016591913108626,108770,109088,109244,109434,109446,109583,112715,113644,117823,145501,165804,165860,108674,108959,109160,109313,109445,109450,109905,112863,113849,117916,145617,165857,165919,0SYBUincmplcmpl-1,0,0,0,0,2,2,1,0,0,1,2,0,
585NM_001110744JH731618+1164031171351164031171352116403,117042,116607,117135,0apoa5.Lincmplincmpl0,0,
585NM_001200970JH731901+61361664746136166474361361,64694,66399,61481,64826,66474,0si:ch211-236d3.4incmplcmpl0,0,0,
585NM_001200969JH732180+1157201161611157201161612115720,116083,115831,116161,0odf3bincmplincmpl0,0,
585NM_001290436JH736857-22472226432247222643122472,22643,0Zscan22incmplincmpl0,
585NM_001276278JH736923+623763306237633016237,6330,01110025L11Rikincmplincmpl0,

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