Schema for xenoRefGene
  Database: anoCar2    Primary Table: xenoRefGene    Row Count: 322,947   Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001001936varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrUn_GL344115varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1126int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 62995int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1126int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 62995int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 16int(10) unsigned range Number of exons
exonStarts 1126,4351,21476,21638,30411...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1252,4396,21567,21640,30615...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 AFAP1L2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('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 0,0,0,1,0,0,0,0,0,0,0,0,0,0...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
        anoCar2.all_est.qName (via xenoRefGene.name)
      anoCar2.all_mrna.qName (via xenoRefGene.name)
      anoCar2.xenoMrna.qName (via xenoRefGene.name)
      anoCar2.xenoRefFlat.name (via xenoRefGene.name)
      anoCar2.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
585NM_001001936chrUn_GL344115+112662995112662995161126,4351,21476,21638,30411,33242,46579,47799,54232,56023,56089,57279,58735,60222,62325,62968,1252,4396,21567,21640,30615,33425,46684,48009,54379,56074,56131,57324,58792,60414,62409,62995,0AFAP1L2incmplcmpl0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,
591NM_018448chrUn_GL343256+87768990994187769490978116877689,886192,891127,893278,893977,894323,894792,895652,896341,896683,899407,902047,905503,906472,909571,909879,877759,886339,891281,893402,894234,894429,894871,895946,896480,898173,899510,902217,905668,906584,909829,909941,0CAND1cmplcmpl0,2,0,1,2,1,2,0,0,1,0,1,0,0,0,-1,
1709NM_018447chr2+1474193461474296571474193461474296579147419346,147420720,147420785,147423228,147423924,147425984,147426179,147427939,147429528,147419492,147420778,147420792,147423313,147424035,147426062,147426259,147428022,147429657,0EMC3incmplcmpl0,2,0,1,2,2,2,1,0,
1766NM_018446chr2-1548783891548901771548783891548901779154878389,154878874,154884560,154885714,154886744,154886842,154888601,154888772,154890093,154878553,154878977,154884725,154885825,154886747,154886926,154888739,154888820,154890177,0GLT8D1incmplincmpl1,0,0,0,0,0,0,0,0,
585NM_018445chrUn_GL343941+33641352633364135263333641,34276,35176,33719,34351,35263,0SELENOSincmplcmpl2,0,0,
263NM_001114473chr2+1992597001994722341992597001994722343199259700,199330205,199472185,199259743,199330236,199472234,0zgc:172128incmplincmpl0,1,2,
140NM_001008807chr6-70630605707430937063060570743093570630605,70710793,70711004,70743017,70743080,70630653,70710817,70711023,70743032,70743093,0Krt77incmplincmpl0,0,1,1,0,
588NM_001099507chrUn_GL343220+5083175085915083175085913508317,508387,508552,508350,508411,508591,0Vom2r50incmplincmpl0,1,1,
146NM_001013020chr4-76856740772528727685674077252872576856740,76967353,77040176,77040239,77252581,76856767,76967866,77040221,77040611,77252872,0PCDHB7incmplincmpl1,0,0,0,0,
787NM_001111365chr2+26577073265779312657707326577931226577073,26577868,26577127,26577931,0Apn3incmplincmpl0,0,

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