Schema for xenoRefGene
  Database: calMil1    Primary Table: xenoRefGene    Row Count: 409,319   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 600smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001270730varchar(255) values Name of gene (usually transcript_id from GTF)
chrom KI635987varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1983269int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1990928int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1983296int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1990928int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 1983269,1990097,1990853,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1983410,1990439,1990928,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 BCL2L13varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 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
        calMil1.all_est.qName (via xenoRefGene.name)
      calMil1.all_mrna.qName (via xenoRefGene.name)
      calMil1.xenoRefFlat.name (via xenoRefGene.name)
      calMil1.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
600NM_001270730KI635987+198326919909281983296199092831983269,1990097,1990853,1983410,1990439,1990928,0BCL2L13cmplcmpl0,0,0,
600NM_001270729KI635987+198326919909281983296199092831983269,1990097,1990853,1983410,1990439,1990928,0BCL2L13cmplcmpl0,0,0,
600NM_001270728KI635987+198326919909281983269198341031983269,1990097,1990853,1983410,1990439,1990928,0BCL2L13incmplincmpl1,-1,-1,
600NM_001270727KI635987+197288919909281972889199092831972889,1990097,1990853,1973030,1990439,1990928,0BCL2L13incmplcmpl0,0,0,
600NM_001270726KI635987+197288919909281972889199092841972889,1983269,1990097,1990853,1973030,1983410,1990439,1990928,0BCL2L13incmplcmpl0,0,0,0,
586NM_001270725KI635864+14682117066814682117066816146821,147733,147844,147949,149985,150313,156604,160519,161976,162111,162601,163670,164027,165475,166044,170626,146863,147775,147886,148027,150000,150361,156721,160603,162078,162114,162721,163718,164114,165517,166182,170668,0ATAD5incmplincmpl0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,
10NM_001270724KI635856+12582373125930631258237312593063412582373,12591313,12591381,12592982,12582430,12591377,12591383,12593063,0RNF148incmplincmpl0,0,1,0,
592NM_175875KI635968-102749010346031027490103460331027490,1029491,1034081,1027535,1029533,1034603,0SIX5incmplincmpl0,0,0,
633NR_073590KI635869+6341282636466263646626364662216341282,6343550,6344624,6344848,6345433,6352169,6353046,6353873,6354296,6355510,6355647,6356330,6357048,6358268,6359183,6359879, ...6341354,6343655,6344705,6344908,6345490,6352229,6353121,6353960,6354398,6355621,6355650,6356458,6357138,6358407,6359273,6360014, ...0QARS1unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585NM_001108874KI635927+23032559842303255984523032,23092,51838,52843,55882,23059,23131,51970,52948,55984,0Tmem161aincmplincmpl0,0,0,0,0,

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