Schema for refGene
  Database: bosTau2    Primary Table: refGene    Row Count: 17,810   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 989smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001034330varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr8varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 52974581int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 52995175int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 52975262int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 52995127int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 14int(10) unsigned range Number of exons
exonStarts 52974581,52976860,52977069,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 52975456,52976979,52977177,...longblob   Exon end positions (or start positions for minus strand item)
id 351176int(10) unsigned range  
name2 PRPF4varchar(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 1,2,2,2,2,1,2,0,2,0,2,1,0,0,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
        bosTau2.all_est.qName (via refGene.name)
      bosTau2.all_mrna.qName (via refGene.name)
      bosTau2.refFlat.name (via refGene.name)
      bosTau2.refSeqAli.qName (via refGene.name)
      bosTau2.xenoMrna.qName (via refGene.name)
      bosTau2.xenoRefGene.name (via refGene.name)
      bosTau2.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
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsidname2cdsStartStatcdsEndStatexonFrames
989NM_001034330chr8-529745815299517552975262529951271452974581,52976860,52977069,52977287,52979879,52982326,52982894,52984399,52985000,52985264,52985767,52992021,52994178,52995100,52975456,52976979,52977177,52977410,52979969,52982450,52982953,52984494,52985094,52985344,52985855,52992208,52994356,52995175,351176PRPF4cmplcmpl1,2,2,2,2,1,2,0,2,0,2,1,0,0,
595NM_001034393chr17-139239114011391393268140090031392391,1397770,1400519,1393573,1397853,1401139,351109SFRP2cmplcmpl1,2,0,
657NM_174218chr10+947845894785659478565947856519478458,9478565,349263WARS1unkunk-1,
928NM_174218chr21-449896674501212544990257450120691144989667,44992029,44994604,44994944,44996884,44997798,44997856,44998933,45004978,45006219,45011955,44990419,44992170,44994778,44995057,44996985,44997851,44997981,44999053,45005087,45006433,45012125,349264WARS1cmplcmpl0,0,0,1,2,0,2,2,1,0,0,
657NM_174348chr7-952211495326829523320953262879522114,9523587,9523966,9524301,9524950,9530296,9532561,9523505,9523836,9524221,9524583,9525259,9530557,9532682,349086ICAM1cmplcmpl1,1,1,1,1,1,0,
665NM_174348chr7+10606564106070671060706710607067110606564,10607067,349087ICAM1unkunk-1,
879NM_174347chr22-38571556385766953857188138574422438571556,38572706,38573492,38576580,38572283,38572796,38574472,38576695,349088HYAL2cmplcmpl0,0,0,-1,
804NM_174346chr19+28769948287719882876999228771863428769948,28770558,28771643,28771812,28769995,28770723,28771733,28771988,349089HSPE1cmplcmpl0,0,0,0,
766NM_174345chr15-23815033238194592381525923818666923815033,23815744,23816175,23816614,23817022,23817661,23817961,23818461,23819389,23815457,23815977,23816374,23816817,23817578,23817814,23818167,23818671,23819459,349090HSPA8cmplcmpl0,1,0,1,0,0,1,0,-1,
978NM_174344chr10-51570885515727945157088551572794251570885,51572020,51572003,51572794,349091HSPA2incmplcmpl2,0,

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