Schema for xenoRefGene
  Database: cb3    Primary Table: xenoRefGene    Row Count: 131,831   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 588smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_059734varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrIvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 428970int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 432091int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 428971int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 432091int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 428970,429316,430197,430572...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 429106,429754,430362,430755...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 del-3varchar(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 incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,0,0,2,0,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
        cb3.all_est.qName (via xenoRefGene.name)
      cb3.all_mrna.qName (via xenoRefGene.name)
      cb3.xenoMrna.qName (via xenoRefGene.name)
      cb3.xenoRefFlat.name (via xenoRefGene.name)
      cb3.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
588NM_059734chrI+4289704320914289714320918428970,429316,430197,430572,431489,431776,431961,432010,429106,429754,430362,430755,431732,431919,432004,432091,0del-3cmplincmpl0,0,0,0,0,0,2,0,
631NM_001130632chrII-607403460741186074034607411816074034,6074118,0tor1l1incmplincmpl0,
634NM_001005065chrI+655015865510996550158655109956550158,6550401,6550666,6550849,6551049,6550227,6550572,6550831,6550955,6551099,0abhd17bincmplincmpl0,0,0,0,1,
674NM_001004953chrIII+11740411117410151174041111741015311740411,11740856,11740919,11740525,11740880,11741015,0sbdsincmplincmpl0,0,0,
618NM_001005047chrI-438842143887844388421438878414388421,4388784,0chmp1bincmplincmpl0,
596NM_001111973chrIV+155841615616551558416156165541558416,1560086,1560137,1561484,1558551,1560122,1560506,1561655,0LOC542400incmplincmpl0,0,0,0,
611NM_001111971chrV+352374135242073523741352420733523741,3523910,3524102,3523861,3524051,3524207,0LOC542396incmplincmpl0,0,0,
686NM_001111988chrX-13276375132779581327637513277958513276375,13276562,13276940,13277651,13277901,13276518,13276881,13277600,13277774,13277958,0LOC542418cmplincmpl1,0,0,0,0,
656NM_001111987chrIII-935240593538589352405935385259352405,9352585,9352823,9353690,9353768,9352542,9352769,9353621,9353708,9353858,0LOC542417cmplincmpl1,0,0,0,0,
600NM_001111987chrX-203404420363832034044203638082034044,2034219,2034579,2034733,2035366,2036162,2036262,2036323,2034178,2034533,2034686,2035076,2035590,2036207,2036273,2036383,0LOC542417cmplincmpl1,2,0,2,0,0,0,0,

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