Schema for refGene
  Database: felCat8    Primary Table: refGene    Row Count: 447   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 1013smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001009199varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrC1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 56183848int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 56186599int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 56183848int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 56186507int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 56183848,56186470,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 56183889,56186599,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 GADD45Avarchar(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 0,2,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
        felCat8.all_est.qName (via refGene.name)
      felCat8.all_mrna.qName (via refGene.name)
      felCat8.mrnaOrientInfo.name (via refGene.name)
      felCat8.refFlat.name (via refGene.name)
      felCat8.refSeqAli.qName (via refGene.name)
      felCat8.xenoMrna.qName (via refGene.name)
      felCat8.xenoRefGene.name (via refGene.name)
      felCat8.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
1013NM_001009199chrC1+56183848561865995618384856186507256183848,56186470,56183889,56186599,0GADD45Acmplcmpl0,2,
1234NM_001009207chrB1-85066443850793868506644385079386585066443,85069494,85071588,85076896,85079287,85066554,85069632,85071633,85076981,85079386,0IL15cmplincmpl0,0,0,2,2,
934NM_001009197chrD4+45752322457530694575233045752915145752322,45753069,0IFNA7cmplcmpl0,
112NM_001009250chrB4+417897054183497341796188418334561041789705,41796133,41796353,41828511,41829075,41830721,41831784,41832549,41833007,41833425,41789780,41796237,41796524,41828670,41829360,41831057,41831985,41832674,41833075,41834973,0CD4cmplcmpl-1,0,1,1,1,1,1,1,0,2,
809NM_001290251chrE1+29447174294675242944726429467502829447174,29451912,29454780,29458121,29460073,29463601,29464134,29466972,29447867,29452008,29455014,29458293,29460139,29463628,29464233,29467524,0TRIM25cmplcmpl0,0,0,0,1,1,1,1,
995NM_001290249chrD2-53775305537842235377556253784223553775305,53777604,53783638,53783889,53784127,53775600,53777817,53783745,53784026,53784223,0RBP4cmplincmpl1,1,2,0,0,
1051NM_001290250chrD2+61105495611184656110557961118465661105495,61115723,61116171,61117224,61117389,61117857,61106149,61115819,61116405,61117256,61117505,61118465,0TRIM8cmplcmpl0,0,0,0,2,1,
936NM_001290248chrD4-46127379461336724612753946133662346127379,46129719,46133536,46127553,46130026,46133672,0CDKN2Acmplcmpl1,0,0,
776NM_001290247chrC1-25129787251584082512978725158408525129787,25140097,25141038,25146153,25158000,25130338,25140213,25141295,25146249,25158408,0TRIM62cmplcmpl1,2,0,0,0,
808NM_001290246chrD2+292376332926454029237696292627631029237633,29237717,29239193,29242675,29244709,29252045,29253430,29254856,29256525,29262434,29237707,29237791,29239310,29242917,29244862,29252193,29253510,29255043,29257089,29264540,0SIRT1cmplcmpl0,2,1,1,0,0,1,0,1,1,

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