Schema for xenoRefGene
  Database: felCat9    Primary Table: xenoRefGene    Row Count: 220,244   Data last updated: 2019-04-01
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 253smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001357296varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrC1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 189640436int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 189701901int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 189640907int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 189701893int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 189640436,189640592,1896409...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 189640473,189640607,1896410...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Ica1lvarchar(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,-1,0,1,2,0,0,2,1,0,0,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
        felCat9.all_est.qName (via xenoRefGene.name)
      felCat9.all_mrna.qName (via xenoRefGene.name)
      felCat9.refGene.name (via xenoRefGene.name)
      felCat9.refSeqAli.qName (via xenoRefGene.name)
      felCat9.xenoMrna.qName (via xenoRefGene.name)
      felCat9.xenoRefFlat.name (via xenoRefGene.name)
      felCat9.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
253NM_001357296chrC1-18964043618970190118964090718970189311189640436,189640592,189640903,189667650,189667877,189692581,189694052,189696570,189697320,189698724,189701731,189640473,189640607,189641021,189667652,189668101,189692680,189694178,189696769,189697444,189698797,189701901,0Ica1lcmplcmpl-1,-1,0,1,2,0,0,2,1,0,0,
1373NM_000943chrA1-1033273511033401431033275711033400536103327351,103327552,103330437,103333153,103333712,103339936,103327453,103327700,103330622,103333247,103333826,103340143,0PPICcmplcmpl-1,0,1,0,0,0,
585NM_213737chrA1+90188922119020792201390188,91109,91997,90230,91203,92211,0PPGRP-Scmplcmpl0,0,0,
585NM_001244284chrA1+90188101902902071014001290188,91109,91997,93602,94964,96654,100055,101218,101641,101687,101805,101876,90230,91209,92197,93721,95117,96853,100171,101528,101670,101711,101856,101902,0PGLYRP4cmplcmpl0,0,0,2,1,1,2,1,-1,-1,-1,-1,
11NM_009924chrC1-17801823178299961780556517806609417801823,17805454,17805514,17829915,17801881,17805493,17806616,17829996,0Cnr2cmplcmpl-1,-1,0,-1,
267NM_024264chrC1+2038155182038464572038155182038464259203815518,203840549,203843805,203844119,203844480,203845455,203845780,203845942,203846368,203815635,203840739,203843992,203844314,203844656,203845622,203845862,203846155,203846457,0Cyp27a1incmplincmpl1,0,0,1,1,0,2,0,1,
636NR_135904chrD2-6741802675708167570816757081136741802,6742955,6742981,6743035,6743093,6743165,6743220,6743256,6743971,6744049,6746263,6749707,6756982,6741910,6742971,6743010,6743077,6743109,6743209,6743229,6743423,6744022,6744281,6746352,6749767,6757081,0ASAH2Bunkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
1413NM_001244666chrD1-10853315910855344510853392810855258917108533159,108533363,108533392,108533660,108533853,108533968,108544572,108544865,108545682,108545938,108546081,108550913,10855109 ...108533328,108533381,108533621,108533809,108533968,108533983,108544694,108544972,108545764,108545995,108546198,108550984,10855115 ...0STX5cmplcmpl-1,-1,-1,-1,2,2,0,1,0,0,0,1,2,0,0,-1,-1,
79NM_001244692chrF2-6968602726424869709517040335386968602,6968756,6968892,6969122,6969170,6969352,6969504,6969895,6969990,6970046,6970175,6970455,6970685,6970823,6970944,6974047, ...6968730,6968866,6969090,6969161,6969326,6969475,6969671,6969959,6970026,6970088,6970334,6970667,6970809,6970854,6971092,6974191, ...0St18incmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,0,2,2,2,2,2,2,2,0,0,1,2,2,1,1,0,1,0,0,0,-1,-1,-1,
76NM_001284448chrE2-366871537145353668715371453553668715,3669965,3670276,3672328,3714499,3668833,3670015,3670554,3672614,3714535,0NCR1cmplincmpl2,1,2,1,0,

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