Schema for xenoRefGene
  Database: saiBol1    Primary Table: xenoRefGene    Row Count: 593,440   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 589smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001014872varchar(255) Name of gene (usually transcript_id from GTF)
chrom JH378315varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 590714int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 596037int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 591160int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 593620int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 16int(10) unsigned Number of exons
exonStarts 590714,590791,591135,591681...longblob Exon start positions (or end positions for minus strand item)
exonEnds 590756,590830,591516,591917...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 DXOvarchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,0,2,1,2,0,0,1,2,1,1,2...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)
      saiBol1.all_mrna.qName (via xenoRefGene.name)
      saiBol1.xenoMrna.qName (via xenoRefGene.name)
      saiBol1.xenoRefFlat.name (via xenoRefGene.name)
      saiBol1.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
589NM_001014872JH378315+59071459603759116059362016590714,590791,591135,591681,592004,592351,592626,592806,592811,593149,593502,593575,593612,593720,594023,595927,590756,590830,591516,591917,592224,592487,592722,592810,592893,593154,593555,593593,593620,593959,594138,596037,0DXOcmplincmpl-1,-1,0,2,1,2,0,0,1,2,1,1,2,-1,-1,-1,
643NM_001005368JH378141+763500676398267637555763963637635006,7637486,7638884,7635119,7637625,7639826,0ZNF32cmplcmpl-1,0,1,
80NM_001164530JH378122-746605775736627573662757366227466057,7573648,7466148,7573662,0ZNF135unkunk-1,-1,
73NM_001164530JH378317+4656468010624656464742818465646,468292,472560,474227,474691,475620,475972,801019,465774,468385,473387,474381,475289,475902,476084,801062,0ZNF135incmplcmpl2,1,1,0,-1,-1,-1,-1,
74NM_001384953JH378288+1110342120380311387541202815521110342,1135304,1138739,1140198,1141769,1143673,1144214,1146403,1146633,1148116,1148339,1150114,1152241,1152794,1154686,1155754, ...1110403,1135413,1139049,1140258,1141838,1144194,1145348,1146487,1146714,1148203,1148429,1150174,1152307,1152876,1154770,1155844, ...0NLRC5cmplcmpl-1,-1,0,1,1,1,2,2,2,2,2,2,2,2,2,2,0,0,2,2,2,2,1,2,2,2,2,2,0,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,-1,-1,
80NM_006599JH378182+782000481574078157407815740737820004,7986215,8157376,7820025,7986257,8157407,0NFAT5unkunk-1,-1,-1,
79NM_006599JH378197+710590573373047337304733730437105905,7127213,7337265,7105926,7127243,7337304,0NFAT5unkunk-1,-1,-1,
9NM_006599JH378178+496886960146134968869496889154968869,5149891,5407724,5801627,6014578,4968891,5149913,5407756,5801652,6014613,0NFAT5incmplincmpl1,-1,-1,-1,-1,
78NM_006599JH378225-5768635590271257787805902376355768635,5769296,5770250,5770760,5771418,5771461,5771957,5772317,5772621,5773123,5773437,5773496,5774168,5774520,5774876,5775225, ...5769194,5770176,5770538,5771377,5771451,5771898,5772002,5772551,5772976,5773310,5773473,5774146,5774478,5774839,5775215,5775781, ...0NFAT5cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,0,1,2,2,2,1,1,0,1,1,2,0,2,1,1,0,
81NM_001300976JH378197+842384787094538709453870945328423847,8709426,8423948,8709453,0ANKRD42unkunk-1,-1,

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