Schema for xenoRefGene
  Database: dp3    Primary Table: xenoRefGene    Row Count: 122,793   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 630smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_123892varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrXL_group1avarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 5951755int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 5954078int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 5954078int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 5954078int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 10int(10) unsigned range Number of exons
exonStarts 5951755,5951902,5952381,595...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 5951817,5951915,5952412,595...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 lncRNA:CR45018varchar(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,-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
        dp3.all_est.qName (via xenoRefGene.name)
      dp3.all_mrna.qName (via xenoRefGene.name)
      dp3.xenoMrna.qName (via xenoRefGene.name)
      dp3.xenoRefFlat.name (via xenoRefGene.name)
      dp3.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
630NR_123892chrXL_group1a-5951755595407859540785954078105951755,5951902,5952381,5952662,5952836,5953045,5953253,5953348,5953478,5954035,5951817,5951915,5952412,5952827,5953033,5953229,5953322,5953422,5953538,5954078,0lncRNA:CR45018unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
613NM_001040405chr2+371628937181013716289371810163716289,3716640,3716760,3717033,3717601,3718032,3716607,3716700,3716997,3717339,3717616,3718101,0agsincmplincmpl0,0,0,0,2,0,
617NM_001200538chr3-430316243034234303162430342324303162,4303309,4303279,4303423,0ntmt1incmplincmpl0,0,
675NM_001123602chr3-11820915118220991182091511822099611820915,11821062,11821281,11821428,11821725,11822000,11820996,11821272,11821410,11821644,11821893,11822099,0LOC100136478incmplincmpl0,0,0,0,0,0,
681NM_001300504chr2-12705348127058321270534812705832212705348,12705754,12705669,12705832,0RpS30cmplcmpl0,0,
614NM_001289494chr4_group3+390193739026723901937390267233901937,3902279,3902597,3902246,3902534,3902672,0Txkincmplincmpl0,0,0,
759NM_001078205chr2+22837284228588102283728422858810722837284,22846316,22850713,22850826,22850889,22858373,22858711,22837348,22846466,22850748,22850883,22851261,22858517,22858810,0coupincmplincmpl0,1,1,0,0,0,0,
624NM_206115chr3-511887651192995118876511929915118876,5119299,0CG33468incmplincmpl0,
624NM_206115chr3-512140151217315121401512173115121401,5121731,0CG33468incmplincmpl0,
624NM_206114chr3-511786551179855117865511798515117865,5117985,0CG33469incmplincmpl0,

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