Schema for refGene
  Database: calJac3    Primary Table: refGene    Row Count: 235   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 1215smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001290346varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 82659914int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 82661490int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 82660016int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 82661428int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 82659914,82660428,82660685,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 82660214,82660593,82660805,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 GH1varchar(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 0,0,0,1,0,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
        calJac3.all_est.qName (via refGene.name)
      calJac3.all_mrna.qName (via refGene.name)
      calJac3.mrnaOrientInfo.name (via refGene.name)
      calJac3.refFlat.name (via refGene.name)
      calJac3.refSeqAli.qName (via refGene.name)
      calJac3.xenoMrna.qName (via refGene.name)
      calJac3.xenoRefGene.name (via refGene.name)
      calJac3.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
1215NM_001290346chr5-82659914826614908266001682661428582659914,82660428,82660685,82661013,82661418,82660214,82660593,82660805,82661174,82661490,0GH1cmplcmpl0,0,0,1,0,
1215NM_001290347chr5-82644347826459678264445082645907582644347,82644901,82645157,82645485,82645897,82644648,82645066,82645277,82645646,82645967,0GH1P6cmplcmpl0,0,0,1,0,
1215NM_001290352chr5-82630963826333448263096382633282582630963,82632281,82632539,82632868,82633272,82631161,82632446,82632659,82633029,82633344,0GH1P5cmplcmpl0,0,0,1,0,
760NM_001243071chr19-23018175230311322301941723027378823018175,23019415,23020414,23022821,23024110,23024797,23027363,23031025,23018344,23019525,23020591,23022911,23024242,23024839,23027397,23031132,0TNNI1cmplcmpl-1,0,0,0,0,0,0,-1,
1513NM_001267751chr12+1216854851216946071216855211216945788121685485,121686548,121689398,121689920,121690437,121692866,121693425,121694387,121685698,121686708,121689548,121690081,121690615,121692938,121693567,121694607,0CYP2E1cmplcmpl0,0,1,1,0,0,0,1,
1710NM_001302791chr7-1474635891474679301474641021474671823147463589,147464342,147466832,147464341,147464710,147467930,0ADORA3cmplcmpl1,2,0,
213NM_001302790chr7-1474444131475354071474447371474504535147444413,147447049,147447881,147450110,147535331,147444808,147447150,147447948,147450458,147535407,0TMIGD3cmplcmpl1,2,1,0,-1,
213NM_001302789chr7-1474444131475354071474446301475353756147444413,147447049,147447881,147450110,147451799,147535268,147444716,147447150,147447948,147450458,147451906,147535407,0TMIGD3cmplcmpl1,2,1,1,2,0,
213NM_001302788chr7-1474444131475354071474447371475353756147444413,147447049,147447881,147450110,147451799,147535331,147444808,147447150,147447948,147450458,147451906,147535407,0TMIGD3cmplcmpl1,2,1,1,2,0,
213NM_001302787chr7-1474444131475354071474447371475353756147444413,147447049,147447881,147450110,147451799,147535268,147444808,147447150,147447948,147450458,147451906,147535407,0TMIGD3cmplcmpl1,2,1,1,2,0,

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