Schema for refGene
  Database: bosTau7    Primary Table: refGene    Row Count: 15,132   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 665smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001013589varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 10563656int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 10567014int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 10564126int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 10566978int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 10563656,10564376,10564847,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 10564245,10564464,10564933,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 TPI1varchar(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 1,0,1,0,2,1,0,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
        bosTau7.all_est.qName (via refGene.name)
      bosTau7.all_mrna.qName (via refGene.name)
      bosTau7.mrnaOrientInfo.name (via refGene.name)
      bosTau7.refFlat.name (via refGene.name)
      bosTau7.refSeqAli.qName (via refGene.name)
      bosTau7.xenoMrna.qName (via refGene.name)
      bosTau7.xenoRefGene.name (via refGene.name)
      bosTau7.xenoRefSeqAli.qName (via refGene.name)
      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)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
665NM_001013589chr5-10563656105670141056412610566978710563656,10564376,10564847,10565207,10565418,10565618,10566863,10564245,10564464,10564933,10565340,10565503,10565742,10567014,0TPI1cmplcmpl1,0,1,0,2,1,0,
943NM_001013590chr10-470130234703633147013220470362521047013023,47014782,47016306,47016663,47017197,47018054,47019291,47021357,47034936,47036138,47013224,47014861,47016376,47016726,47017273,47018125,47019409,47021491,47035062,47036331,0TPM1cmplcmpl2,1,0,0,2,0,2,0,0,0,
1176NM_001014861chr15+774710447747819477471986774780451077471044,77471949,77472556,77473255,77473890,77474206,77474568,77477279,77477612,77477898,77471190,77472029,77472745,77473522,77474099,77474386,77474668,77477393,77477707,77478194,0NR1H3cmplcmpl-1,0,1,1,1,0,0,1,1,0,
1000NM_001014859chr22-54477454544827965447827954479302254477454,54482710,54479323,54482796,0CXCR6cmplcmpl0,-1,
680NM_001014860chr28-12456709124753041245732812458573412456709,12461510,12473184,12475245,12458623,12461570,12473241,12475304,0HNRNPFcmplcmpl0,-1,-1,-1,
837NM_001014891chr22-33115829331372913311659133137282333115829,33119240,33137106,33116764,33119458,33137291,0ARL6IP5cmplcmpl1,2,0,
746NM_001014889chr10+211734142117667521173485211766321121173414,21173846,21174315,21174622,21174799,21174916,21175564,21175785,21176022,21176374,21176551,21173533,21173879,21174378,21174709,21174830,21175014,21175633,21175853,21176077,21176461,21176675,0PSME2cmplcmpl0,0,0,0,0,1,0,0,2,0,0,
670NM_001014888chr11-11196643112308981119685411230867711196643,11197313,11198000,11203472,11207411,11220111,11230725,11196881,11197413,11198116,11203620,11207599,11220224,11230898,0DGUOKcmplcmpl0,2,0,2,0,1,0,
665NM_001076280chr5+10561140105635551056154710562354310561140,10561184,10561463,10561174,10561297,10563555,0SPSB2cmplcmpl-1,-1,0,
979NM_001076278chr26-51755058517580585175531251758044751755058,51755613,51755674,51756200,51756469,51757488,51757959,51755379,51755671,51755687,51756299,51756540,51757557,51758058,0FUOMcmplcmpl2,1,0,0,1,1,0,

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