Schema for refGene
  Database: hg19    Primary Table: refGene    Row Count: 81,407   Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 2085smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_046630varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr3varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 196666747int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 196669405int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 196669405int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 196669405int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 196666747,196667841,196669263,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 196666995,196668013,196669405,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 NCBP2-AS1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -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
        hg19.all_est.qName (via refGene.name)
      hg19.all_mrna.qName (via refGene.name)
      hg19.ccdsInfo.mrnaAcc (via refGene.name)
      hg19.kgXref.refseq (via refGene.name)
      hg19.knownToRefSeq.value (via refGene.name)
      hg19.mrnaOrientInfo.name (via refGene.name)
      hg19.refFlat.name (via refGene.name)
      hg19.refSeqAli.qName (via refGene.name)
      hg19.ucscRetroInfo5.refSeq (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV24lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV27lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV28lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV31lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV33lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV34lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV35lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV36lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV37lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV38lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV39lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV40lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV41lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV42lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV43lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV44lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV45lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV46lift37.rnaAcc (via refGene.name)
      hg19.wgEncodeGencodeRefSeqV47lift37.rnaAcc (via refGene.name)
      hg19.xenoEst.qName (via refGene.name)
      hg19.xenoMrna.qName (via refGene.name)
      hg19.xenoRefGene.name (via refGene.name)
      hg19.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
2085NR_046630chr3+1966667471966694051966694051966694053196666747,196667841,196669263,196666995,196668013,196669405,0NCBP2-AS1unkunk-1,-1,-1,
2051NR_046598chr3+1922328101922343621922343621922343622192232810,192234269,192233297,192234362,0FGF12-AS2unkunk-1,-1,
1312NR_046514chr13+95364969953681999536819995368199295364969,95365891,95365647,95368199,0SOX21-AS1unkunk-1,-1,
585NR_106918chr1-17368174361743617436117368,17436,0MIR6859-1unkunk-1,
585NR_107062chr1-17368174361743617436117368,17436,0MIR6859-2unkunk-1,
585NR_107063chr1-17368174361743617436117368,17436,0MIR6859-3unkunk-1,
585NR_128720chr1-17368174361743617436117368,17436,0MIR6859-4unkunk-1,
585NR_036051chr1+30365305033050330503130365,30503,0MIR1302-2unkunk-1,
585NR_036266chr1+30365305033050330503130365,30503,0MIR1302-9unkunk-1,
585NR_036267chr1+30365305033050330503130365,30503,0MIR1302-10unkunk-1,

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