Schema for xenoRefGene
  Database: sorAra1    Primary Table: xenoRefGene    Row Count: 799,185   Data last updated: 2020-09-01
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001097214varchar(255) Name of gene (usually transcript_id from GTF)
chrom scaffold_231054varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 88563int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 88681int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 88681int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 88681int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned Number of exons
exonStarts 88563,longblob Exon start positions (or end positions for minus strand item)
exonEnds 88681,longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 bckdhavarchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') 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.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)
      sorAra1.all_mrna.qName (via xenoRefGene.name)
      sorAra1.xenoRefFlat.name (via xenoRefGene.name)
      sorAra1.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585NM_001097214scaffold_231054+88563886818868188681188563,88681,0bckdhaunkunk-1,
585NM_001044703scaffold_231272-42020432524202043252242020,43081,42059,43252,0Zscan21incmplincmpl0,0,
585NM_001046354scaffold_151301+13118915131189157131,1603,5657,11804,14005,14760,18792,504,1752,5789,11892,14223,14763,18915,0UGT2B10incmplincmpl0,1,0,0,1,0,0,
585NM_001085507scaffold_175005+78121398278129172317812,9577,9702,9816,9834,10005,10037,10086,10248,10335,10472,10531,10612,10918,11022,11103,11141,11286,11436,11661,11876,12347,1 ...9172,9587,9719,9824,9962,10018,10062,10130,10322,10422,10483,10566,10639,10936,11050,11112,11168,11306,11449,11779,11921,12362,1 ...0Zbtb34incmplincmpl0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585NM_001159667scaffold_48485-357136835713685357,677,769,1107,1305,452,682,1098,1254,1368,0frylincmplincmpl1,2,0,0,0,
585NM_001124291scaffold_210924-781072781072378,207,946,183,234,1072,0myl1incmplincmpl0,0,0,
585NR_024515scaffold_246850-241664166416622,4037,47,4166,0APLP2unkunk-1,-1,
585NM_001178332scaffold_203782+7829537829531782,953,0RPL32incmplincmpl0,
585NM_001178332scaffold_237225+44485446924448544692144485,44692,0RPL32incmplincmpl0,
585NM_001178331scaffold_131730-477462434774624324774,6162,5014,6243,0MAP2incmplcmpl0,0,

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