Schema for refGene
  Database: rheMac2    Primary Table: refGene    Row Count: 6,342   Data last updated: 2016-02-16
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 599smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_032452varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr16varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1845793int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1845903int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1845903int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1845903int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 1845793,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1845903,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MIR212varchar(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,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)
      rheMac2.all_est.qName (via refGene.name)
      rheMac2.all_mrna.qName (via refGene.name)
      rheMac2.refFlat.name (via refGene.name)
      rheMac2.refSeqAli.qName (via refGene.name)
      rheMac2.xenoMrna.qName (via refGene.name)
      rheMac2.xenoRefGene.name (via refGene.name)
      rheMac2.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
599NR_032452chr16-184579318459031845903184590311845793,1845903,0MIR212unkunk-1,
1161NR_032510chrX-75596276755963647559636475596364175596276,75596364,0MIR384unkunk-1,
811NM_001114945chr4+29649897296533862964989729653386429649897,29650288,29650596,29653361,29650042,29650389,29650706,29653386,0ZNRD1cmplcmpl0,1,0,2,
111NM_001110539chr11-403012254051013740301225405101373940301225,40303534,40316509,40321940,40322615,40322794,40323086,40323923,40336338,40336584,40353950,40380322,40382099,40383018,40 ...40301315,40303639,40316601,40322074,40322707,40322889,40323216,40324121,40336509,40336758,40354118,40380499,40382261,40383309,40 ...0ADAMTS20cmplcmpl0,0,1,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,1,1,0,1,2,0,0,2,2,1,2,0,0,1,0,1,0,
1838NR_032538chr7+1643363771643364571643364571643364571164336377,164336457,0MIR487Aunkunk-1,
997NM_001042737chr19+54104232541107275410428754106773354104232,54106690,54110333,54104316,54106791,54110727,0SEPW1cmplcmpl0,1,-1,
1961NM_001047121chr3+1803836491803874111803836491803874115180383649,180384718,180386167,180386821,180387258,180383689,180384878,180386421,180386958,180387411,0PRSS1cmplcmpl0,1,2,1,0,
165NM_001194425chr7-96859278968865299686092796886198596859278,96862078,96864478,96866552,96885841,96860959,96862152,96864615,96866672,96886529,0EGLN3cmplcmpl1,2,0,0,0,
1173NM_001194513chr16+77108636771141827710863677114182377108636,77110873,77113788,77108672,77111511,77114182,0TSPAN10cmplcmpl0,0,2,
1219NR_031977chr12-83148686831487768314877683148776183148686,83148776,0MIR153-1unkunk-1,

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