Schema for refGene
  Database: panTro2    Primary Table: refGene    Row Count: 2,852   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1548smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001110241varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr4varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 126227658int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 126294712int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 126227658int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 126294712int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 126227658,126278951,126294526,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 126227865,126279055,126294712,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 FGF2varchar(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 0,1,0,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)
      panTro2.all_est.qName (via refGene.name)
      panTro2.all_mrna.qName (via refGene.name)
      panTro2.mrnaOrientInfo.name (via refGene.name)
      panTro2.refFlat.name (via refGene.name)
      panTro2.refSeqAli.qName (via refGene.name)
      panTro2.xenoMrna.qName (via refGene.name)
      panTro2.xenoRefGene.name (via refGene.name)
      panTro2.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1548NM_001110241chr4+1262276581262947121262276581262947123126227658,126278951,126294526,126227865,126279055,126294712,0FGF2cmplcmpl0,1,0,
820NM_001044376chr6-30831170308449133083117030844913730831170,30834157,30834408,30835004,30842325,30844238,30844475,30831853,30834190,30834524,30835027,30842556,30844334,30844913,0TRIM26cmplcmpl1,1,2,0,0,0,0,
1677NM_001042629chrX-1431839011431841711431839011431841711143183901,143184171,0SPANXN2cmplincmpl0,
1689NM_001042629chrX+1447234561447235151447234561447235151144723456,144723515,0SPANXN2cmplincmpl0,
990NM_001042628chr6+53106355531067055310635553106705153106355,53106705,0SPANXN3incmplcmpl1,
199NM_001246529chr3-13248856213253242913248885513253234111132488562,132490088,132495309,132504880,132506462,132508176,132509139,132512352,132521182,132527624,132532200,132489015,132490180,132495412,132505079,132506526,132508326,132509229,132512504,132521315,132527711,132532429,0RUVBL1cmplcmpl2,0,2,1,0,0,0,1,0,0,0,
175NM_001246528chrX+10759969910766463010759988710766415313107599699,107636666,107639582,107642060,107646400,107646682,107649434,107650147,107650456,107660397,107662262,107663419,10766408 ...107599897,107636777,107639654,107642159,107646502,107646755,107649514,107650335,107650535,107660543,107662319,107663528,10766463 ...0ATG4Acmplcmpl0,1,1,1,1,1,2,1,0,1,0,0,1,
766NM_001008987chrY-23729338237544182372936423754347723729338,23731013,23741430,23750233,23751711,23753729,23754344,23729466,23731171,23741602,23750331,23751892,23753807,23754418,0RPS4Y1cmplcmpl0,1,0,1,0,0,0,
620NM_001009093chr20+460333946192204616850461761224603339,4616845,4603553,4619220,0PRNPcmplcmpl-1,0,
107NM_001009103chr7+362280003633239736228017363313831336228000,36259465,36290555,36298473,36300578,36306897,36309546,36310952,36312914,36317750,36325334,36330165,36331343,36228081,36259568,36290664,36298533,36300714,36307015,36309639,36311049,36312966,36317876,36325470,36330305,36332397,0SEPTIN7cmplcmpl0,0,1,0,1,2,0,0,1,2,2,0,2,

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