Schema for refGene
  Database: dm6    Primary Table: refGene    Row Count: 36,533   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 663smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001382103varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr3Rvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 10264305int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 10302898int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 10291246int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 10302299int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 15int(10) unsigned range Number of exons
exonStarts 10264305,10291099,10291572,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 10264878,10291452,10291772,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Nuak1varchar(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 -1,0,2,1,0,1,1,1,2,2,2,0,2,...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
        dm6.all_est.qName (via refGene.name)
      dm6.all_mrna.qName (via refGene.name)
      dm6.mrnaOrientInfo.name (via refGene.name)
      dm6.refFlat.name (via refGene.name)
      dm6.refSeqAli.qName (via refGene.name)
      dm6.xenoMrna.qName (via refGene.name)
      dm6.xenoRefGene.name (via refGene.name)
      dm6.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
663NM_001382103chr3R+102643051030289810291246103022991510264305,10291099,10291572,10291836,10292115,10293193,10295320,10296733,10297439,10297768,10298245,10298448,10299001,10299633,10 ...10264878,10291452,10291772,10292054,10292713,10294318,10296061,10297109,10297697,10297897,10298375,10298591,10299058,10299752,10 ...0Nuak1cmplcmpl-1,0,2,1,0,1,1,1,2,2,2,0,2,2,1,
663NM_001382098chr3R+102643051030846710291246103077201410264305,10291099,10291572,10291836,10292115,10293193,10296733,10297439,10297768,10298245,10298448,10299633,10303309,10307422,10264878,10291452,10291772,10292054,10292713,10294318,10297109,10297697,10297897,10298375,10298591,10299752,10307366,10308467,0Nuak1cmplcmpl-1,0,2,1,0,1,1,2,2,2,0,2,1,2,
663NM_001382101chr3R+102643051030846710291246103074771610264305,10291099,10291572,10291836,10292115,10293193,10295320,10296733,10297439,10297768,10298245,10298448,10299001,10299633,10 ...10264878,10291452,10291772,10292054,10292713,10294318,10296061,10297109,10297697,10297897,10298375,10298591,10299058,10299752,10 ...0Nuak1cmplcmpl-1,0,2,1,0,1,1,1,2,2,2,0,2,2,1,2,
663NM_001382102chr3R+102643051030846710291246103074771410264305,10291099,10291572,10291836,10292115,10293193,10296733,10297439,10297768,10298245,10298448,10299633,10303309,10307422,10264878,10291452,10291772,10292054,10292713,10294318,10297109,10297697,10297897,10298375,10298591,10299752,10307366,10308467,0Nuak1cmplcmpl-1,0,2,1,0,1,1,2,2,2,0,2,1,2,
663NM_001382104chr3R+102845891030289810291246103022991410284589,10291099,10291572,10291836,10292115,10293193,10295320,10296733,10297439,10297768,10298245,10298448,10299633,10301943,10284712,10291452,10291772,10292054,10292713,10294318,10296061,10297109,10297697,10297897,10298375,10298591,10299752,10302898,0Nuak1cmplcmpl-1,0,2,1,0,1,1,1,2,2,2,0,2,1,
663NM_001382105chr3R+102845891030289810291246103022991310284589,10291099,10291572,10291836,10292115,10293193,10296733,10297439,10297768,10298245,10298448,10299633,10301943,10284712,10291452,10291772,10292054,10292713,10294318,10297109,10297697,10297897,10298375,10298591,10299752,10302898,0Nuak1cmplcmpl-1,0,2,1,0,1,1,2,2,2,0,2,1,
663NM_001382100chr3R+102845891030846710291246103074771410284589,10291099,10291572,10291836,10292115,10293193,10296733,10297439,10297768,10298245,10298448,10299633,10303309,10307422,10284712,10291452,10291772,10292054,10292713,10294318,10297109,10297697,10297897,10298375,10298591,10299752,10307366,10308467,0Nuak1cmplcmpl-1,0,2,1,0,1,1,2,2,2,0,2,1,2,
659NM_001382202chr3R-979776898010269798438980073029797768,9800668,9800590,9801026,0CG9467cmplcmpl2,0,
659NM_001382203chr3R-979776898010269798288980073029797768,9800668,9800590,9801026,0CG9467cmplcmpl2,0,
82NM_001382173chr3R+987468099888769875140987535079874680,9930363,9943480,9943676,9982278,9986647,9986896,9876223,9930545,9943587,9943894,9982370,9986833,9988876,0CG46467cmplcmpl0,-1,-1,-1,-1,-1,-1,

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