Schema for refGene
  Database: panTro5    Primary Table: refGene    Row Count: 2,968   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 201smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001110817varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 134330779int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 134371302int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 134330926int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 134370711int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 134330779,134344015,1343458...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 134330953,134344122,1343460...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 HPRT1varchar(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 0,0,2,0,0,0,2,1,0,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)
      panTro5.all_est.qName (via refGene.name)
      panTro5.all_mrna.qName (via refGene.name)
      panTro5.mrnaOrientInfo.name (via refGene.name)
      panTro5.refFlat.name (via refGene.name)
      panTro5.refSeqAli.qName (via refGene.name)
      panTro5.xenoMrna.qName (via refGene.name)
      panTro5.xenoRefGene.name (via refGene.name)
      panTro5.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
201NM_001110817chrX+1343307791343713021343309261343707119134330779,134344015,134345847,134357110,134360833,134364144,134369019,134369237,134370663,134330953,134344122,134346031,134357176,134360851,134364227,134369066,134369314,134371302,0HPRT1cmplcmpl0,0,2,0,0,0,2,1,0,
955NM_001246417chr3-48593018486086264859338248608375448593018,48599927,48603464,48607596,48593544,48600003,48603653,48608626,0CSPG5cmplcmpl0,2,2,0,
77NM_001246416chr2B-4369850446390943701944463774244369850,4380888,4385332,4386500,4388855,4391015,4393840,4395342,4396623,4397927,4399141,4402208,4408163,4423691,4424618,4424956, ...4370248,4381002,4385417,4386538,4388938,4391124,4393903,4395396,4396695,4398009,4399215,4402271,4408280,4423778,4424669,4425049, ...0CCDC93cmplcmpl0,0,2,0,1,0,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,
96NM_001038649chr1+245057312457187924505840245716131124505731,24521502,24523552,24528999,24531394,24533130,24557260,24558756,24562327,24564561,24571410,24505920,24521644,24523679,24529123,24531573,24533632,24557419,24558939,24562448,24564736,24571879,0MACO1cmplcmpl0,2,0,1,2,1,2,2,2,0,1,
1004NM_001038012chr18-549401915497639654940191549763961154940191,54940794,54943746,54944329,54948639,54952368,54955940,54960856,54962708,54969847,54976329,54940326,54940854,54943911,54944437,54948738,54952475,54956075,54961005,54962828,54969974,54976396,0FECHcmplcmpl0,0,0,0,0,1,1,2,2,1,0,
1004NM_001042435chr15+54992016550425405499201655042540954992016,54995204,55020324,55022359,55030078,55030662,55031984,55040520,55041752,54992145,54995677,55020911,55022430,55030222,55030921,55032037,55040671,55042540,0PMLcmplcmpl0,0,2,1,0,0,1,0,1,
586NM_001042627chr16-1899441906741899491906373189944,190220,190542,190078,190425,190674,0HBA2cmplcmpl0,2,0,
737NM_001246588chr19+200177462002664320017773200263371320017746,20018610,20019698,20019878,20020361,20020639,20022262,20022651,20022910,20024329,20025786,20025985,20026148,20017888,20018734,20019784,20020000,20020549,20020780,20022338,20022728,20023008,20024404,20025875,20026057,20026643,0DDX49cmplcmpl0,1,2,1,0,2,2,0,2,1,1,0,0,
1486NM_001246587chr1-1181692781181879401181698731181710492118169278,118187740,118171076,118187940,0TENT5Ccmplcmpl0,-1,
1201NM_001246586chr9+80812983808277288081692980827193680812983,80816842,80823112,80824670,80826224,80826498,80813009,80816946,80823153,80824792,80826381,80827728,0CYLC2cmplcmpl-1,0,2,1,0,1,

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