Schema for xenoRefGene
  Database: cavPor3    Primary Table: xenoRefGene    Row Count: 337,367   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 77smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001025697varchar(255) values Name of gene (usually transcript_id from GTF)
chrom scaffold_93varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 4442975int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 4503737int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 4442975int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 4503564int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 4442975,4444745,4450076,445...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 4443135,4444844,4450191,445...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Hsdl2varchar(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 0,1,1,2,1,1,0,1,1,1,-1,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
        cavPor3.all_est.qName (via xenoRefGene.name)
      cavPor3.all_mrna.qName (via xenoRefGene.name)
      cavPor3.refGene.name (via xenoRefGene.name)
      cavPor3.refSeqAli.qName (via xenoRefGene.name)
      cavPor3.xenoMrna.qName (via xenoRefGene.name)
      cavPor3.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
77NM_001025697scaffold_93+4442975450373744429754503564114442975,4444745,4450076,4451799,4453137,4474905,4477480,4490206,4493534,4503457,4503680,4443135,4444844,4450191,4451903,4453236,4475102,4477546,4490314,4493669,4503567,4503737,0Hsdl2incmplcmpl0,1,1,2,1,1,0,1,1,1,-1,
77NM_001083918scaffold_70-4334517523407643345175234076104334517,4335000,4738950,4739106,4739446,4739730,4739887,5153834,5233610,5233914,4334553,4335116,4739022,4739194,4739562,4739803,4739976,5153966,5233746,5234076,0Zfp991incmplincmpl0,1,1,0,1,0,1,1,0,0,
850NM_001287360scaffold_8+34748066347482943474806634748294134748066,34748294,0LOC100209449incmplincmpl0,
87NM_019835scaffold_45-151886301521015415191338152101541915188630,15189765,15189854,15189967,15190407,15190716,15190818,15190944,15191150,15191231,15191338,15192154,15196421,15197226,15 ...15188813,15189789,15189917,15190015,15190441,15190755,15190917,15191027,15191177,15191257,15191489,15192252,15196545,15197414,15 ...0B4galt5incmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,0,2,0,0,0,1,1,0,
718NM_001199839scaffold_13-175339511753872317536679175378431617533951,17534087,17534141,17534343,17534496,17534993,17535214,17535671,17535755,17536159,17536305,17536644,17536682,17537411,17 ...17534037,17534126,17534288,17534468,17534611,17535204,17535661,17535743,17536032,17536288,17536344,17536680,17536831,17537851,17 ...0BCL2L2cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,0,0,-1,-1,
77NM_001197042scaffold_73+4538474468035945384744680359264538474,4552894,4558103,4560603,4563116,4563250,4577393,4585408,4588359,4588523,4588615,4593279,4599862,4600187,4601537,4602754, ...4538545,4552967,4558175,4560672,4563214,4563251,4577462,4585480,4588500,4588526,4588778,4593422,4599998,4600195,4601666,4602889, ...0SLIT3incmplincmpl0,2,0,0,0,2,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,2,0,2,0,
74NM_007253scaffold_168-1559179176066317492231760660151559179,1567790,1749223,1749703,1749918,1750059,1751526,1751841,1753147,1754125,1755178,1755395,1758871,1760460,1760555,1559203,1567806,1749383,1749786,1749951,1750195,1751656,1751908,1753417,1754247,1755306,1755436,1758885,1760513,1760663,0CYP4F8cmplincmpl-1,-1,2,0,0,2,1,0,0,0,1,2,1,0,0,
777NM_001199453scaffold_10+252147752522965525214775252267523225214775,25214814,25216154,25216526,25216841,25217882,25217984,25219318,25220011,25220207,25220480,25220723,25220876,25221256,25 ...25214814,25215330,25216231,25216688,25216916,25217976,25217986,25219488,25220188,25220209,25220647,25220727,25221005,25221409,25 ...0THBS1incmplincmpl0,0,0,0,0,0,1,0,1,1,0,2,0,0,0,0,0,1,0,1,2,0,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,
619NM_012558scaffold_42+451572745443544515733454435474515727,4531234,4533238,4537909,4540718,4542015,4544156,4515903,4531397,4533332,4538048,4540855,4542136,4544354,0Fbp1cmplincmpl0,2,0,2,0,2,0,
785NM_001369275scaffold_25+26263995263149342626399526314764926263995,26272465,26276225,26281739,26287449,26299200,26304440,26314665,26314858,26264112,26272625,26276314,26281854,26287536,26299317,26304625,26314764,26314934,0Acot7incmplcmpl0,0,1,0,1,1,1,0,-1,

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