Schema for refGene
  Database: xenTro3    Primary Table: refGene    Row Count: 9,395   Data last updated: 2020-09-02
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001006923varchar(255) values Name of gene (usually transcript_id from GTF)
chrom GL173326varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 326000int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 365435int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 327029int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 354979int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 18int(10) unsigned range Number of exons
exonStarts 326000,328074,328450,328604...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 327275,328208,328518,328762...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 sema3flvarchar(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 0,1,2,0,0,1,0,2,1,0,1,1,0,0...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
        hgFixed.gbCdnaInfo.acc (via refGene.name)
      hgFixed.gbMiscDiff.acc (via refGene.name)
      hgFixed.gbSeq.acc (via refGene.name)
      hgFixed.gbWarn.acc (via refGene.name)
      hgFixed.imageClone.acc (via refGene.name)
      hgFixed.refLink.mrnaAcc (via refGene.name)
      hgFixed.refSeqStatus.mrnaAcc (via refGene.name)
      hgFixed.refSeqSummary.mrnaAcc (via refGene.name)
      knownGeneV39.kgXref.refseq (via refGene.name)
      knownGeneV39.knownToRefSeq.value (via refGene.name)
      xenTro3.all_est.qName (via refGene.name)
      xenTro3.all_mrna.qName (via refGene.name)
      xenTro3.mrnaOrientInfo.name (via refGene.name)
      xenTro3.refFlat.name (via refGene.name)
      xenTro3.refSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
587NM_001006923GL173326-32600036543532702935497918326000,328074,328450,328604,329291,329841,330341,331046,332087,333043,334579,336469,337822,338434,339823,340108,354879,365183,327275,328208,328518,328762,329333,329930,330564,331191,332157,333158,334719,336589,337916,338554,339886,340269,354991,365435,0sema3flcmplcmpl0,1,2,0,0,1,0,2,1,0,1,1,0,0,0,1,0,-1,
588NM_001016746GL172676-4415874584254436584583597441587,445172,445535,449852,450826,452335,458305,443717,445224,445633,450051,450949,452485,458425,0anp32acmplcmpl1,0,1,0,0,0,0,
594NM_001016745GL172780-119620412013651197548120132941196204,1198597,1199859,1201183,1197563,1198659,1199900,1201365,0pde6hcmplcmpl0,1,2,0,
585NM_001016745GL172795-79050872908052782442479050,79184,82294,87252,79173,80605,82478,87290,0pde6hcmplcmpl-1,0,0,-1,
590NM_001016744GL173047-7041477097337078847092064704147,707872,709074,709705,705602,707980,709215,709733,0znf706lcmplcmpl-1,0,0,-1,
615NM_001016743GL172660-398480139937223986487399350023984801,3993020,3986592,3993722,0hand1cmplcmpl0,0,
73NM_001016742GL173435-3901784014983930784014985390178,392053,396531,398171,401328,392027,393220,396582,398281,401498,0cdk4cmplincmpl-1,2,2,0,1,
603NM_001016801GL172670-2373168238714323743972387113102373168,2375187,2376034,2376674,2376894,2378404,2378844,2380933,2381248,2387066,2374424,2375247,2376121,2376791,2377014,2378608,2378985,2381077,2381636,2387143,0letm2cmplcmpl0,0,0,0,0,0,0,0,2,0,
603NM_001016738GL172739+2362431238451223624372384312122362431,2362748,2365019,2370247,2370462,2372586,2373689,2374959,2376069,2378765,2379908,2384273,2362473,2362898,2365101,2370330,2370562,2372697,2373791,2375028,2376152,2378831,2379989,2384512,0etfacmplcmpl0,0,0,1,0,1,1,1,1,0,0,0,
587NM_001016736GL172865-3030413109993030743087856303041,303981,306077,307647,308637,310920,303223,304102,306183,307758,308795,310999,0xpacmplcmpl1,0,1,1,0,-1,

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