Schema for xenoRefGene
  Database: caeRem2    Primary Table: xenoRefGene    Row Count: 271,110   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 1601smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_165001varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrUnvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 133187181int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 133187947int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 133187947int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 133187947int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 133187181,133187360,1331875...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 133187328,133187520,1331877...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2  varchar(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,-1,-1,-1,-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
        caeRem2.all_est.qName (via xenoRefGene.name)
      caeRem2.all_mrna.qName (via xenoRefGene.name)
      caeRem2.xenoMrna.qName (via xenoRefGene.name)
      caeRem2.xenoRefFlat.name (via xenoRefGene.name)
      caeRem2.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
1601NR_165001chrUn-1331871811331879471331879471331879475133187181,133187360,133187530,133187851,133187908,133187328,133187520,133187754,133187880,133187947,0unkunk-1,-1,-1,-1,-1,
882NM_001077989chrUn-38950645389507923895064538950792138950645,38950792,0MED31incmplincmpl0,
1601NR_042706chrUn-1331871631331879691331879691331879692133187163,133187909,133187744,133187969,0unkunk-1,-1,
911NM_062111chrUn-42775166427757754277516642775775242775166,42775667,42775466,42775775,0bath-30incmplincmpl0,0,
1127NM_177236chrUn+711186237112574771118623711257471071118623,71119348,71119500,71119872,71120046,71121728,71122208,71122502,71123852,71125708,71118824,71119423,71119863,71119875,71120109,71121962,71122352,71123546,71123909,71125747,0Atp2b3incmplincmpl0,0,0,0,0,0,0,0,0,0,
1116NR_101584chrUn-69661275696614076966140769661407169661275,69661407,0T23G11.12unkunk-1,
1541NR_101577chrUn-1254109431254110331254110331254110331125410943,125411033,0K07G5.7unkunk-1,
850NM_001269541chrUn-34828599348287133482859934828713134828599,34828713,0T16G1.13incmplincmpl0,
850NM_001269540chrUn-34840965348425233484096534842523634840965,34841162,34841375,34841519,34842280,34842487,34841022,34841300,34841471,34841629,34842419,34842523,0T16G1.2cmplincmpl2,2,0,1,0,0,
748NM_001256480chrUn+21411549214116692141154921411669121411549,21411669,0Gm4724incmplincmpl0,

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