Schema for xenoRefGene
  Database: danRer5    Primary Table: xenoRefGene    Row Count: 266,487   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 703smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_129182varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr4varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 15521274int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 15521343int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 15521343int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 15521343int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 15521274,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 15521343,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MIR182varchar(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,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
        danRer5.all_est.qName (via xenoRefGene.name)
      danRer5.all_mrna.qName (via xenoRefGene.name)
      danRer5.refGene.name (via xenoRefGene.name)
      danRer5.refSeqAli.qName (via xenoRefGene.name)
      danRer5.xenoMrna.qName (via xenoRefGene.name)
      danRer5.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
703NR_129182chr4+15521274155213431552134315521343115521274,15521343,0MIR182unkunk-1,
100NM_001376624chr7+290927812915903629092781291563793529092781,29094728,29095340,29115991,29117357,29117596,29122733,29122847,29123313,29123939,29124492,29124705,29124833,29125364,29 ...29092834,29094975,29095454,29116303,29117489,29117713,29122817,29122906,29123551,29124050,29124598,29124758,29124899,29125493,29 ...0MADDincmplcmpl0,2,0,0,0,0,0,0,2,0,0,1,0,0,0,2,1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,-1,
810NM_001366349chr20-29529979296000962952997929600096529529979,29533755,29581477,29591142,29599955,29530129,29533863,29581579,29591298,29600096,0AIG1cmplincmpl0,0,0,0,0,
103NM_001086522chr9-316590733179081731659073317908171831659073,31659169,31670254,31682279,31685674,31691764,31694614,31697180,31699952,31724699,31726897,31727380,31740919,31747913,31 ...31659157,31659211,31670461,31682452,31685726,31691977,31694754,31697328,31700072,31724732,31727080,31727515,31741206,31748124,31 ...0sema5b.Sincmplincmpl0,0,0,1,0,0,1,0,0,2,0,0,1,0,0,0,0,2,
770NM_001017442chr9-24369743243718642436974324371864324369743,24371150,24371534,24369785,24371357,24371864,0GJA5cmplincmpl0,0,0,
833NM_001108977chr6-325075883253349032507588325334901132507588,32507818,32511278,32513870,32514168,32514319,32516598,32519623,32520099,32533076,32533469,32507669,32507935,32511431,32514080,32514219,32514451,32516727,32519636,32520168,32533226,32533490,0Epha2incmplincmpl0,0,0,1,0,0,0,0,0,0,0,
853NM_001304722chr16+35148076351924693518986935192469635148076,35168669,35168863,35181553,35189776,35192412,35148223,35168810,35168866,35181655,35189878,35192469,0PLEKHO1cmplincmpl-1,-1,-1,-1,0,0,
586NM_001128220Zv7_NA695-13925714718314366414718310139257,139325,139360,142692,142805,143186,143664,144304,147024,147078,139314,139348,139461,142769,142850,143202,143829,144421,147066,147183,0VGLL4incmplincmpl-1,-1,-1,-1,-1,-1,0,0,0,0,
726NM_001044659chr4-18483058185074321848305818507432818483058,18485875,18488639,18488670,18491134,18501342,18502385,18507387,18483193,18486013,18488642,18488862,18491215,18501482,18502482,18507432,0MYBPC2incmplincmpl0,0,0,0,0,1,0,0,
100NM_001083606chr8+285540542866111628576945286565903428554054,28556668,28576886,28577162,28577341,28577512,28583363,28583722,28584118,28588419,28591079,28594775,28597298,28601764,28 ...28554094,28556861,28577076,28577228,28577436,28577514,28583558,28583842,28584120,28588573,28591208,28594931,28597397,28601890,28 ...0PTCH1cmplincmpl-1,-1,0,2,2,1,0,0,0,2,0,0,0,0,0,0,0,0,1,0,0,1,0,2,0,0,0,-1,-1,-1,-1,-1,-1,-1,

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