Schema for refGene
  Database: canFam4    Primary Table: refGene    Row Count: 2,380   Data last updated: 2020-05-05
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 623smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001193298varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 5045043int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 5080782int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 5045075int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 5080759int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 5045043,5072902,5074883,507...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 5045204,5073031,5074913,507...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 CYB5Avarchar(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 0,0,0,0,2,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
        canFam4.all_est.qName (via refGene.name)
      canFam4.all_mrna.qName (via refGene.name)
      canFam4.mrnaOrientInfo.name (via refGene.name)
      canFam4.refFlat.name (via refGene.name)
      canFam4.refSeqAli.qName (via refGene.name)
      canFam4.xenoMrna.qName (via refGene.name)
      canFam4.xenoRefGene.name (via refGene.name)
      canFam4.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
623NM_001193298chr1+504504350807825045075508075955045043,5072902,5074883,5078937,5080677,5045204,5073031,5074913,5078972,5080782,0CYB5Acmplcmpl0,0,0,0,2,
86NM_001002949chr1+13811586139784821381224113978279313811586,13811959,13978144,13811733,13812826,13978482,0BCL2cmplcmpl-1,0,0,
697NR_036669chr1-14743640147443691474436914744369114743640,14744369,0PPIAP1unkunk-1,
701NM_001286988chr1-152609411531250715262077153122321115260941,15266785,15271350,15276716,15279565,15285934,15295460,15299927,15302583,15303233,15311986,15262583,15267037,15271468,15276838,15279702,15286188,15295648,15300095,15302703,15303528,15312507,0CDH20cmplcmpl1,1,0,1,2,0,1,1,1,0,0,
708NM_001080724chr1+16214420162154191621442016215419116214420,16215419,0MC4Rcmplcmpl0,
711NM_001195771chr1-16558933165622681655893416562266216558933,16562208,16559041,16562268,0PMAIP1cmplcmpl1,0,
715NM_001003312chr1-17115191171307391711522417130669617115191,17115892,17117997,17120237,17124148,17130582,17115278,17115950,17118117,17120387,17124258,17130739,0SEC11Ccmplcmpl0,2,2,2,0,0,
720NR_049246chr1-17698571176986291769862917698629117698571,17698629,0MIR122unkunk-1,
92NM_001003268chr1+201661712052344220170938205230301920166171,20170938,20287827,20290938,20346833,20398090,20398697,20471810,20475497,20481496,20489442,20490634,20493507,20496329,20 ...20166697,20171011,20287889,20291035,20346898,20398217,20398747,20471916,20475631,20481629,20489510,20490713,20493584,20496533,20 ...0TCF4cmplcmpl-1,0,1,0,1,0,1,0,1,0,1,0,1,0,0,1,2,1,-1,
746NM_001371796chr1-21174395211874572117597221187433921174395,21176910,21178444,21179338,21181363,21182666,21185687,21186436,21187349,21176107,21177057,21178558,21179448,21181517,21182897,21185894,21186670,21187457,0CUPIN1cmplcmpl0,0,0,1,0,0,0,0,0,

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