Schema for refGene
  Database: canFam1    Primary Table: refGene    Row Count: 2,060   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 905smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001003068varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr20varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 41982734int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 41987773int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 41984430int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 41987649int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 41982734,41984429,41984755,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 41984035,41984621,41984909,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 GNAT1varchar(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 -1,1,0,2,2,0,2,1,0,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
        canFam1.all_est.qName (via refGene.name)
      canFam1.all_mrna.qName (via refGene.name)
      canFam1.refFlat.name (via refGene.name)
      canFam1.refSeqAli.qName (via refGene.name)
      canFam1.xenoMrna.qName (via refGene.name)
      canFam1.xenoRefGene.name (via refGene.name)
      canFam1.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
905NM_001003068chr20-41982734419877734198443041987649941982734,41984429,41984755,41985184,41985584,41985807,41986062,41986312,41987543,41984035,41984621,41984909,41985314,41985713,41985965,41986204,41986355,41987773,0GNAT1cmplcmpl-1,1,0,2,2,0,2,1,0,
828NM_001002967chr5+319287773193706231928801319370621031928777,31929680,31930019,31930301,31932013,31932352,31933341,31933853,31935360,31936961,31928906,31929925,31930168,31930427,31932181,31932497,31933475,31934013,31935464,31937062,0MMP3cmplcmpl0,0,2,1,1,1,2,1,2,1,
1079NM_001003080chr18+64798797648014276479898064801336464798797,64800487,64800946,64801171,64799094,64800634,64801072,64801427,0FTH1cmplcmpl0,0,0,0,
114NM_001002980chr20+4337476543405289433747654340528911843374765,43375332,43376135,43376376,43376560,43376955,43377196,43377422,43377646,43377878,43378069,43378302,43378986,43379220,43 ...43374850,43375513,43376295,43376470,43376722,43377119,43377326,43377539,43377793,43377995,43378219,43378431,43379130,43379346,43 ...0COL7A1cmplincmpl0,1,2,0,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, ...
91NM_001128838chr38+19172784192859721917278419285972519172784,19283846,19284795,19285269,19285880,19172845,19284113,19285074,19285548,19285972,0CD1A8cmplincmpl0,1,1,1,1,
1029NM_001003201chrX-58270466582740645827054858274064858270466,58271099,58271426,58272040,58272823,58273176,58273574,58273949,58270749,58271169,58271520,58272203,58272963,58273361,58273728,58274064,0IL2RGcmplcmpl0,2,1,0,1,2,1,0,
611NM_001003191chr6-3464803347808634649703478033123464803,3466490,3468854,3470404,3473550,3473842,3474260,3474763,3475409,3475726,3476217,3477823,3465140,3466626,3469031,3470489,3473697,3474021,3474413,3474951,3475552,3475908,3476403,3478086,0GUSBcmplcmpl1,0,0,2,2,0,0,1,2,0,0,0,
1085NM_001003200chr13+65597821656011136559782765600017465597821,65599060,65599475,65599995,65597891,65599196,65599559,65601113,0CXCL8cmplcmpl0,1,2,2,
907NM_001003190chr9-42250417422529124225041742252912642250417,42250624,42251266,42251843,42252348,42252822,42250443,42250723,42251377,42251914,42252476,42252912,0OBP2Bcmplcmpl1,1,1,2,0,0,
906NM_001003189chr9-42160839421646374216102442164566742160839,42161007,42161163,42161728,42162174,42163545,42164470,42160871,42161050,42161265,42161839,42162248,42163679,42164637,0CANF2cmplcmpl-1,1,1,1,2,0,0,

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