Schema for refGene
  Database: xenTro2    Primary Table: refGene    Row Count: 9,500   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001016546varchar(255) values Name of gene (usually transcript_id from GTF)
chrom scaffold_686varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 54023int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 58472int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 56207int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 57953int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 54023,56185,56529,57824,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 54046,56520,56546,58472,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 gs17varchar(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,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)
      xenTro2.all_est.qName (via refGene.name)
      xenTro2.all_mrna.qName (via refGene.name)
      xenTro2.mrnaOrientInfo.name (via refGene.name)
      xenTro2.refFlat.name (via refGene.name)
      xenTro2.refSeqAli.qName (via refGene.name)
      xenTro2.xenoRefGene.name (via refGene.name)
      xenTro2.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585NM_001016546scaffold_686+54023584725620757953454023,56185,56529,57824,54046,56520,56546,58472,0gs17cmplcmpl-1,0,1,0,
597NM_001100257scaffold_105-169216216985171694360169831131692162,1696252,1698010,1694615,1696452,1698517,0dlx1cmplcmpl0,1,0,
597NM_001100257scaffold_105-169295616935841693584169358411692956,1693584,0dlx1unkunk-1,
597NM_001100257scaffold_105-169295616935841693584169358411692956,1693584,0dlx1unkunk-1,
597NM_001100257scaffold_105-169295616935841693584169358411692956,1693584,0dlx1unkunk-1,
590NM_001016474scaffold_163+72715774647672720574580412727157,728048,728461,729979,730173,735175,735466,736302,740860,742767,743993,745601,727232,728090,728649,730038,730214,735259,735518,736527,740966,742838,744167,746476,0lnpkcmplcmpl0,0,0,2,1,0,0,1,1,2,1,1,
594NM_001016537scaffold_72-1185175119660311856831196568101185175,1188794,1189762,1190597,1192223,1192500,1193367,1194308,1195477,1196406,1185692,1189030,1189862,1190764,1192365,1192618,1193576,1194394,1195709,1196603,0aldh3a2cmplcmpl0,1,0,1,0,2,0,1,0,0,
585NM_001113038scaffold_399+81371191981731120938137,9963,10980,8248,10091,11919,0arl14epcmplcmpl0,0,2,
597NM_001112938scaffold_13-162846416732661629496167311461628464,1632930,1634629,1636619,1638387,1672621,1629572,1633216,1634779,1636964,1638539,1673266,0slain1cmplcmpl2,1,1,1,2,0,
73NM_001112937scaffold_550-21085128884421128728838320210851,215077,215379,216542,217166,217761,219080,219398,220697,222949,225005,226192,227499,228681,229188,229928,231306,244465,25 ...211409,215193,215486,216630,217241,217920,219169,219531,220805,223046,225129,226341,227609,228726,229254,230018,231409,244604,25 ...0hectd2cmplcmpl1,0,1,0,0,0,1,0,0,2,1,2,0,0,0,0,2,1,0,0,

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