Schema for xenoRefGene
  Database: bosTau7    Primary Table: xenoRefGene    Row Count: 324,139   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 170smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001245965varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr11varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 102200659int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 102239766int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 102200659int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 102239766int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 21int(10) unsigned range Number of exons
exonStarts 102200659,102214805,1022151...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 102200819,102214869,1022152...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 dnm1avarchar(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 incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,2,0,2,0,1,1,0,2,0,2,0,0,0...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
        bosTau7.all_est.qName (via xenoRefGene.name)
      bosTau7.all_mrna.qName (via xenoRefGene.name)
      bosTau7.refGene.name (via xenoRefGene.name)
      bosTau7.refSeqAli.qName (via xenoRefGene.name)
      bosTau7.xenoMrna.qName (via xenoRefGene.name)
      bosTau7.xenoRefFlat.name (via xenoRefGene.name)
      bosTau7.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
170NM_001245965chr11+10220065910223976610220065910223976621102200659,102214805,102215109,102215324,102215596,102216092,102216296,102217419,102217696,102218028,102220946,102226476,10222852 ...102200819,102214869,102215255,102215328,102215801,102216191,102216457,102217562,102217832,102218093,102221088,102226566,10222859 ...0dnm1acmplincmpl0,2,0,2,0,1,1,0,2,0,2,0,0,0,0,2,0,0,0,0,2,
785NM_011792chr15-262894842631287726291685263123763026289484,26289695,26289800,26289859,26289890,26289908,26290101,26290137,26290303,26290510,26290610,26290859,26290975,26291251,26 ...26289564,26289751,26289835,26289873,26289899,26289963,26290123,26290203,26290324,26290522,26290619,26290917,26291014,26291271,26 ...0Bace1cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,0,0,0,0,0,2,0,0,-1,-1,-1,-1,
16NM_001114464chr18-597207506050336359720750605033632259720750,59720987,60113929,60114149,60114206,60114284,60114726,60130803,60131309,60242123,60242168,60242258,60265880,60265970,60 ...59720819,59721080,60114065,60114182,60114266,60114306,60114792,60130949,60131594,60242141,60242234,60242510,60265940,60266099,60 ...0znf1004incmplincmpl1,1,0,0,0,2,2,0,0,0,0,0,0,0,0,0,0,2,0,0,1,0,
1160NM_001092952chrX+754063467545958275406346754595822075406346,75413097,75429794,75430596,75431275,75434098,75434367,75434686,75441883,75442157,75442302,75444857,75446956,75449056,75 ...75406448,75413179,75429875,75430676,75431382,75434136,75434510,75434757,75441972,75442222,75442405,75444923,75447062,75449145,75 ...0rps6ka1.Lincmplincmpl0,0,1,1,0,2,1,0,2,1,0,1,0,1,0,0,0,1,0,0,
162NM_001362113chr5+935292479361986093529508936187203293529247,93529490,93541688,93543675,93545901,93548570,93550200,93554307,93560087,93560750,93566061,93569152,93578145,93581627,93 ...93529314,93529598,93541775,93543845,93545997,93548726,93550399,93554432,93560173,93560783,93566170,93569218,93578260,93581723,93 ...0C2cd5cmplincmpl-1,0,0,0,2,1,1,2,1,0,0,1,1,2,2,1,2,0,0,0,0,0,0,0,1,1,1,0,0,0,-1,-1,
954NM_001384576chr18+484399974846173748440206484603481848439997,48440373,48449339,48453890,48454679,48454945,48455783,48456848,48457429,48458173,48458565,48460025,48460319,48460633,48 ...48440373,48440401,48449810,48454130,48454789,48455032,48456126,48456934,48457548,48458372,48458689,48460109,48460613,48460692,48 ...0SAMD4Bcmplcmpl0,0,1,1,1,0,0,1,0,2,0,1,1,-1,-1,-1,-1,-1,
770NM_001130230chr8+24273256242738262427325624273826124273256,24273826,0LOC100153661cmplcmpl0,
1250NM_001193894chr9+87214538872442088721478587244189587214538,87214785,87237317,87244042,87244151,87214601,87214977,87237595,87244130,87244208,0RAB32incmplcmpl-1,1,1,0,1,
1451NM_001096658chr1+1135186701135192201135186701135192203113518670,113518770,113519064,113518727,113518902,113519220,0tbcb.Sincmplincmpl0,0,0,
1232NM_001312236chr1+84838076848385328483807684838532184838076,84838532,0LOC106116716cmplcmpl0,

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