Schema for refGene
  Database: felCat3    Primary Table: refGene    Row Count: 743   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001009343varchar(255) values Name of gene (usually transcript_id from GTF)
chrom scaffold_140121varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 45391int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 132652int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 45429int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 132588int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 45391,46043,47063,80175,896...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 45469,46111,47173,80238,897...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 KITLGvarchar(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 2,0,1,0,0,0,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
        felCat3.all_est.qName (via refGene.name)
      felCat3.all_mrna.qName (via refGene.name)
      felCat3.mrnaOrientInfo.name (via refGene.name)
      felCat3.refFlat.name (via refGene.name)
      felCat3.refSeqAli.qName (via refGene.name)
      felCat3.xenoMrna.qName (via refGene.name)
      felCat3.xenoRefGene.name (via refGene.name)
      felCat3.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
73NM_001009343scaffold_140121-4539113265245429132588645391,46043,47063,80175,89613,132573,45469,46111,47173,80238,89727,132652,0KITLGcmplcmpl2,0,1,0,0,0,
586NM_001009341scaffold_146444+1580081601511580081593552158008,158712,158265,160151,0FOSincmplcmpl1,2,
586NM_001009340scaffold_213849-1578071581451580091581451157807,158145,0BCL2cmplincmpl2,
585NM_001009338scaffold_179425-10549109961076510996110549,10996,0CASP3cmplincmpl0,
585NM_001009338scaffold_179428-58156643425815664329458156,58652,61799,64276,58333,58781,61924,64342,0CASP3incmplcmpl1,1,2,0,
587NM_001009337scaffold_213672-2983292999532983652999125298329,298841,299162,299493,299902,298566,299003,299279,299654,299953,0GH1cmplcmpl0,0,0,1,0,
585NM_001009336scaffold_8891-45520474214552047421545520,46244,47095,47107,47129,45543,47094,47106,47128,47421,0ADRB3cmplcmpl1,0,1,1,0,
587NM_001009200scaffold_124042-3472613499273472613499187347261,347378,347652,348228,348680,349228,349770,347293,347483,347849,348295,348782,349351,349927,0TNFRSF4incmplcmpl1,1,2,1,1,1,0,
585NM_001009834scaffold_83731+920109092010902920,1082,1082,1090,0KLRAP1incmplincmpl1,2,
585NM_001009837scaffold_176470-48940494564945649456248940,49351,49037,49456,0KITunkunk-1,-1,

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