Schema for xenoRefGene
  Database: bosTau4    Primary Table: xenoRefGene    Row Count: 321,099   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 1006smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001190varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr18varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 55233495int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 55243226int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 55233870int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 55243226int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 13int(10) unsigned range Number of exons
exonStarts 55233495,55233593,55233757,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 55233563,55233617,55233800,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 BCAT2varchar(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 -1,-1,-1,0,0,0,1,2,0,0,0,0,0,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
        bosTau4.all_est.qName (via xenoRefGene.name)
      bosTau4.all_mrna.qName (via xenoRefGene.name)
      bosTau4.refGene.name (via xenoRefGene.name)
      bosTau4.refSeqAli.qName (via xenoRefGene.name)
      bosTau4.xenoMrna.qName (via xenoRefGene.name)
      bosTau4.xenoRefFlat.name (via xenoRefGene.name)
      bosTau4.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
1006NM_001190chr18-552334955524322655233870552432261355233495,55233593,55233757,55233854,55234700,55234883,55235195,55235445,55237966,55238277,55238493,55242624,55243148,55233563,55233617,55233800,55233909,55234769,55235015,55235281,55235588,55238130,55238397,55238604,55242828,55243226,0BCAT2incmplcmpl-1,-1,-1,0,0,0,1,2,0,0,0,0,0,
1347NM_012757chr9+99951960999527979995196099952797199951960,99952797,0Mas1incmplincmpl0,
111NM_012755chr9+403739244058519040532816405851901340373924,40473291,40532809,40534861,40542170,40544960,40546065,40548717,40552118,40554471,40554632,40572978,40584981,40373981,40473342,40533063,40534958,40542269,40545064,40546215,40548882,40552298,40554548,40554789,40573107,40585190,0Fyncmplcmpl-1,-1,0,1,2,2,1,1,1,1,0,1,1,
18NM_012754chr10-785935047864347678593992786432811078593504,78593978,78596718,78614224,78620658,78623855,78633893,78641308,78643063,78643240,78593554,78594182,78596894,78614358,78620802,78624150,78634010,78641481,78643240,78643476,0Esr2cmplcmpl-1,2,1,2,2,1,1,2,2,0,
604NM_001173587chr16-254896925658092548969256580982548969,2552763,2553341,2554189,2554934,2555224,2557129,2565734,2549161,2552855,2553421,2554254,2555072,2555362,2557246,2565809,0s41a2incmplcmpl0,1,2,0,0,0,0,0,
997NM_031556chr4-540063175404197954008128540417941354006317,54006413,54006522,54006797,54006887,54007063,54007499,54007609,54008007,54008107,54040152,54041764,54041930,54006356,54006495,54006598,54006860,54007021,54007207,54007513,54007645,54008017,54008470,54040317,54041881,54041979,0Cav1cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,0,0,0,-1,
873NM_031555chr13-378192233785737137819223378573651137819223,37819880,37820298,37822413,37829102,37837414,37839745,37840757,37851640,37856990,37857311,37819412,37820204,37820443,37822479,37829325,37837522,37839838,37840853,37851700,37857259,37857371,0Bfsp1cmplincmpl0,0,1,1,0,0,0,0,0,1,0,
676NM_031554chr22+119437971197356911944025119735221211943797,11944022,11967065,11967520,11967784,11968014,11968667,11969134,11970855,11971619,11971863,11973327,11943845,11944077,11967273,11967630,11967936,11968152,11968817,11969283,11970970,11971758,11971994,11973569,0Acvr2bcmplcmpl-1,0,1,2,1,0,0,0,2,0,1,0,
1140NM_031553chr5-72795214728135067279572272802854872795214,72795704,72796354,72797125,72798430,72800596,72802760,72813395,72795626,72795755,72796434,72797207,72798628,72800727,72802854,72813506,0Nfybincmplcmpl-1,0,1,0,0,1,0,-1,
720NM_001108440chr18-177727301779961817773272177847361517772730,17773272,17773769,17774205,17776252,17777646,17779356,17779864,17782741,17783452,17784587,17791421,17795304,17799119,17 ...17772796,17773412,17773913,17774320,17776306,17777754,17779481,17779972,17782817,17783576,17784775,17791462,17795452,17799174,17 ...0Brd7cmplincmpl-1,1,1,0,0,2,1,1,0,2,0,-1,-1,-1,-1,

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