Schema for refGene
  Database: canFam5    Primary Table: refGene    Row Count: 2,322   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 619smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_128902varchar(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 4518940int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 4519069int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 4519069int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 4519069int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 4518940,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 4519069,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MIR8907varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,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
        canFam5.all_est.qName (via refGene.name)
      canFam5.all_mrna.qName (via refGene.name)
      canFam5.mrnaOrientInfo.name (via refGene.name)
      canFam5.refFlat.name (via refGene.name)
      canFam5.refSeqAli.qName (via refGene.name)
      canFam5.xenoMrna.qName (via refGene.name)
      canFam5.xenoRefGene.name (via refGene.name)
      canFam5.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
619NR_128902chr1-451894045190694519069451906914518940,4519069,0MIR8907unkunk-1,
622NM_001193298chr1+492023549559414920267495591854920235,4948066,4950045,4954097,4955836,4920396,4948195,4950075,4954132,4955941,0CYB5Acmplcmpl0,0,0,0,2,
86NM_001002949chr1+13633482137999721363413813799769413633482,13633856,13634349,13799634,13633630,13634349,13634714,13799972,0BCL2cmplcmpl-1,0,1,0,
696NR_036669chr1-14563520145642481456424814564248114563520,14564248,0PPIAP1unkunk-1,
700NM_001286988chr1-150796841513116415080820151308891315079684,15085526,15085566,15085736,15090112,15095454,15098298,15104655,15114148,15118612,15121267,15121917,15130643,15081326,15085566,15085736,15085776,15090230,15095576,15098435,15104909,15114336,15118780,15121387,15122212,15131164,0CDH20cmplcmpl1,0,0,1,0,1,2,0,1,1,1,0,0,
707NM_001080724chr1+16032382160333811603238216033381116032382,16033381,0MC4Rcmplcmpl0,
709NM_001195771chr1-16376896163802461637689716380244216376896,16380186,16377004,16380246,0PMAIP1cmplcmpl1,0,
714NM_001003312chr1-16932844169483871693287716948317616932844,16933543,16935648,16937892,16941802,16948230,16932931,16933601,16935768,16938042,16941912,16948387,0SEC11Ccmplcmpl0,2,2,2,0,0,
718NR_049246chr1-17532432175324901753249017532490117532432,17532490,0MIR122unkunk-1,
92NM_001003268chr1+200000572035687820004799203564661920000057,20004799,20121535,20124646,20180497,20231728,20232335,20305214,20308900,20314897,20322841,20324033,20326912,20329736,20 ...20000583,20004872,20121597,20124743,20180562,20231855,20232385,20305320,20309034,20315030,20322909,20324112,20326989,20329940,20 ...0TCF4cmplcmpl-1,0,1,0,1,0,1,0,1,0,1,0,1,0,0,1,2,1,-1,

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