Schema for xenoRefGene
  Database: droYak2    Primary Table: xenoRefGene    Row Count: 173,200   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 688smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001298057varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 13582891int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 13600731int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 13585358int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 13600093int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 29int(10) unsigned range Number of exons
exonStarts 13582891,13583107,13583269,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 13583011,13583251,13583339,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 CARPAvarchar(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 cmplenum('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,...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
        droYak2.all_est.qName (via xenoRefGene.name)
      droYak2.all_mrna.qName (via xenoRefGene.name)
      droYak2.xenoMrna.qName (via xenoRefGene.name)
      droYak2.xenoRefFlat.name (via xenoRefGene.name)
      droYak2.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
688NM_001298057chrX-135828911360073113585358136000932913582891,13583107,13583269,13583393,13583592,13583646,13583687,13583762,13583874,13584114,13584219,13584421,13584672,13584887,13 ...13583011,13583251,13583339,13583559,13583628,13583676,13583746,13583832,13584070,13584165,13584410,13584609,13584878,13585030,13 ...0CARPAcmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,0,1,0,0,1,1,0,-1,-1,-1,-1,-1,
609NM_001297956chrX+324262532450943242700324467763242625,3242776,3243423,3243888,3244016,3245055,3242752,3243411,3243825,3243987,3244859,3245094,0CG3309cmplcmpl0,1,0,0,2,-1,
692NM_001298055chrX+14024824140251511402484114025144214024824,14025009,14024889,14025151,0CG32726cmplcmpl0,0,
609NM_001297955chrX-324518132480423245301324788463245181,3245301,3245546,3246231,3246525,3247951,3245203,3245540,3246176,3246460,3247900,3248042,0Mcm3cmplcmpl-1,1,1,0,0,-1,
692NM_001298054chrX-140289331403235814029287140322341014028933,14029029,14029053,14029095,14029277,14029591,14030757,14030894,14031995,14032259,14029009,14029044,14029085,14029226,14029537,14030682,14030823,14031054,14032250,14032358,0CG9657cmplcmpl-1,-1,-1,-1,2,0,0,2,0,-1,
609NM_001297954chrX-325678332586023256966325860163256783,3256966,3257118,3257918,3258264,3258388,3256804,3257109,3257161,3258241,3258300,3258602,0CG4198cmplincmpl-1,1,0,0,1,0,
731NM_001308053chr3L-19202663192063851920266319206385419202663,19202905,19203524,19206286,19202780,19203000,19203633,19206385,0RAB26incmplincmpl0,1,0,0,
743NM_001308053chr3L+20713555207198652071357620719865320713555,20719291,20719778,20713642,20719483,20719865,0RAB26cmplincmpl0,0,0,
616NM_001308053chr3L_random+412064741243984120647412439844120647,4123404,4124061,4124281,4120746,4123513,4124163,4124398,0RAB26incmplincmpl0,0,1,0,
692NM_001298053chrX-14036497140372961403699814037284914036497,14036606,14036774,14036833,14036857,14036880,14036998,14037089,14037212,14036593,14036747,14036810,14036846,14036865,14036902,14037055,14037133,14037296,0CG42705cmplincmpl-1,-1,-1,-1,-1,-1,0,0,0,

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