Schema for xenoRefGene
  Database: ornAna2    Primary Table: xenoRefGene    Row Count: 710,922   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 605smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_025216varchar(255) Name of gene (usually transcript_id from GTF)
chrom chrUn_DS181354v1varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 2737090int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 2737243int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 2737090int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 2737243int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned Number of exons
exonStarts 2737090,longblob Exon start positions (or end positions for minus strand item)
exonEnds 2737243,longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 WNT10Avarchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 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
        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)
      ornAna2.all_est.qName (via xenoRefGene.name)
      ornAna2.all_mrna.qName (via xenoRefGene.name)
      ornAna2.refGene.name (via xenoRefGene.name)
      ornAna2.refSeqAli.qName (via xenoRefGene.name)
      ornAna2.xenoRefFlat.name (via xenoRefGene.name)
      ornAna2.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
605NM_025216chrUn_DS181354v1+273709027372432737090273724312737090,2737243,0WNT10Aincmplincmpl0,
592NM_001164503chr20+9789971008297978997100829719978997,984336,985869,986019,986976,987273,987762,988149,988451,989478,989758,990150,990195,990825,990918,991093,995596,1001264,1 ...979114,984374,985899,986097,987183,987495,988122,988317,988496,989748,989858,990176,990342,990882,990996,991327,995724,1001354,1 ...0Akap11incmplincmpl0,0,0,0,0,0,0,0,2,0,1,0,0,0,0,1,0,2,1,
594NM_001159706chrUn_DS180905v1+1231560126030412315601260304131231560,1236037,1237126,1243384,1243902,1244874,1246209,1249507,1253923,1254028,1255719,1258049,1260112,1231743,1236162,1237310,1243469,1244006,1244958,1246264,1249575,1254011,1254033,1255983,1258127,1260304,0Folh1incmplcmpl0,0,2,0,1,0,0,1,0,1,0,0,0,
585NM_001205308chrUn_AAPN01390690v1-1052671052671105,267,0VWFincmplincmpl0,
585NM_053448chrUn_DS184009v1-37828379703782837970137828,37970,0Hdac3incmplincmpl0,
585NM_053448chrUn_DS189115v1+79681701579681701567968,12705,14110,15858,16045,16904,8070,12844,14229,15949,16140,17015,0Hdac3incmplincmpl0,0,1,0,1,0,
585NM_053447chrUn_DS189115v1+796520110796520110117965,9022,11798,12703,14108,15852,16041,16907,18143,18713,19954,8079,9148,11871,12842,14250,15945,16152,17046,18252,18837,20110,0Hdac2incmplincmpl0,0,0,1,2,0,0,0,1,2,0,
585NM_001003145chrUn_DS200594v1+10786110191078611019110786,11019,0KCNH2incmplincmpl1,
585NM_166970chrUn_AAPN01109399v1-5319753197153,197,0dncincmplincmpl0,
585NM_022301chrUn_AAPN01415384v1-3324134134131332,413,0Pi4kaunkunk-1,

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