Schema for xenoRefGene
  Database: papHam1    Primary Table: xenoRefGene    Row Count: 635,835   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 585smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001256941varchar(255) Name of gene (usually transcript_id from GTF)
chrom scaffold449varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 90633int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 116257int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 90633int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 116257int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 20int(10) unsigned Number of exons
exonStarts 90633,92189,94289,98038,986...longblob Exon start positions (or end positions for minus strand item)
exonEnds 90735,92300,94307,98143,987...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 prpf40avarchar(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 cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,0,2,0,0,1,0,0,0,2,0...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)
      papHam1.all_mrna.qName (via xenoRefGene.name)
      papHam1.refGene.name (via xenoRefGene.name)
      papHam1.refSeqAli.qName (via xenoRefGene.name)
      papHam1.xenoRefFlat.name (via xenoRefGene.name)
      papHam1.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585NM_001256941scaffold449+90633116257906331162572090633,92189,94289,98038,98691,99103,100336,101331,102425,107986,108269,108360,108464,109095,109572,113211,113425,113575,114608,1 ...90735,92300,94307,98143,98756,99269,100444,101488,102559,108103,108359,108362,108582,109236,109651,113298,113492,113646,114698,1 ...0prpf40aincmplcmpl0,0,0,0,0,2,0,0,1,0,0,0,2,0,0,0,0,1,0,0,
585NM_138492Contig783049+814014014018,140,0PRELID2unkunk-1,
585NM_001082158Contig370243+3426773426772342,614,577,677,0IGLL1incmplcmpl1,0,
585NM_001144108scaffold19807+15021241215021241261502,1779,4271,4533,12120,12360,1559,1815,4325,4566,12145,12412,0PKNOX2incmplincmpl0,0,0,1,1,2,
73NM_001144098scaffold2254-11514014582611531214582612115140,117645,119988,121700,124536,126989,127786,130883,132219,141249,144068,145775,115323,117829,120170,122142,124752,127142,128010,131057,132337,141325,144107,145826,0MEP1Bincmplcmpl1,2,0,1,1,1,2,2,1,0,0,1,
585NM_001171307scaffold24042+193210766193210766111932,2471,3046,4882,7385,8445,9006,9186,9651,10144,10624,2153,2678,3304,5053,7547,8535,9090,9305,9760,10308,10766,0CGNincmplcmpl1,0,0,0,0,0,0,0,2,0,2,
585NM_001171297scaffold12157+19197241351919724135419197,22943,23205,23992,19377,23184,23304,24135,0LYSMD1cmplcmpl0,0,1,1,
585NM_001171296scaffold12157-25768263232576826323125768,26323,0TNFAIP8L2cmplcmpl0,
585NM_001171305scaffold11340+54966570295496657029654966,55363,55835,56156,56630,56937,55106,55571,55981,56238,56747,57029,0PSMB4cmplincmpl0,2,0,2,0,0,
585NM_001171295scaffold12157+427655315242765531522342765,45203,45612,45833,46577,46902,47203,47497,48220,48719,49213,49609,50066,50498,50696,50925,51300,51841,52442,52637,52784,52 ...42883,45318,45676,45890,46679,46993,47323,47586,48438,48852,49365,49783,50213,50565,50751,50970,51396,52101,52585,52763,52874,53 ...0SEMA6Ccmplincmpl0,1,2,0,0,0,1,1,0,2,0,2,2,2,0,1,1,1,0,0,0,0,2,

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