Schema for refGene
  Database: equCab1    Primary Table: refGene    Row Count: 1,960   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 657smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001081804varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr7varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 9452605int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 9464376int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 9453881int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 9464364int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 10int(10) unsigned range Number of exons
exonStarts 9452605,9454668,9456554,945...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 9453982,9454772,9456714,945...longblob   Exon end positions (or start positions for minus strand item)
id 20873int(10) unsigned range  
name2 MMP13varchar(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 1,2,1,2,1,1,1,2,0,0,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
        equCab1.all_est.qName (via refGene.name)
      equCab1.all_mrna.qName (via refGene.name)
      equCab1.mrnaOrientInfo.name (via refGene.name)
      equCab1.refFlat.name (via refGene.name)
      equCab1.refSeqAli.qName (via refGene.name)
      equCab1.xenoMrna.qName (via refGene.name)
      equCab1.xenoRefGene.name (via refGene.name)
      equCab1.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
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsidname2cdsStartStatcdsEndStatexonFrames
657NM_001081804chr7-9452605946437694538819464364109452605,9454668,9456554,9457678,9458820,9460347,9462781,9463090,9463913,9464241,9453982,9454772,9456714,9457812,9458938,9460509,9462907,9463239,9464155,9464376,20873MMP13cmplcmpl1,2,1,2,1,1,1,2,0,0,
90NM_001081793chr11+179548081796798917954808179679892417954808,17956569,17956778,17956982,17957430,17958863,17959121,17961501,17962431,17962580,17962623,17962850,17963380,17963608,17 ...17954996,17956691,17956876,17957152,17957467,17958920,17959333,17961684,17962488,17962623,17962731,17962976,17963448,17963756,17 ...20874ITGA2Bcmplcmpl0,2,1,0,2,2,2,1,1,1,0,0,0,2,0,0,2,2,0,0,0,0,0,0,
631NM_001081792chr5-6053729610008760550296100000176053729,6055028,6056135,6058523,6059481,6060687,6061749,6067566,6071251,6073729,6075451,6076220,6076929,6077578,6081098,6083432, ...6054442,6055084,6056166,6058643,6059667,6060897,6061935,6067752,6071434,6073915,6075637,6076406,6077115,6077686,6081485,6083523, ...20875SELPcmplcmpl-1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,
737NM_001346193chr11+19944182199500411994424719949890819944182,19945759,19946251,19947014,19947779,19947997,19948308,19949795,19944679,19945842,19946408,19947176,19947905,19948218,19948334,19950041,19843KRT17cmplcmpl0,0,2,0,0,0,2,1,
738NM_001346185chr11+20067206200710932006725420070868720067206,20068424,20068765,20069475,20069741,20070039,20070690,20067713,20068507,20068922,20069637,20069867,20070260,20071093,19844KRT36cmplcmpl0,0,2,0,0,0,2,
738NM_001346182chr11+20140916201448412014105520144449720140916,20141508,20142120,20143131,20143387,20143685,20144364,20141403,20141591,20142277,20143293,20143513,20143906,20144841,19845KRT34cmplcmpl0,0,2,0,0,0,2,
819NR_033077chrUn+30757624307577203075772030757720130757624,30757720,19547MIR19B-2unkunk-1,
1013NR_032977chr20-56143606561436665614366656143666156143606,56143666,19548MIR30C-2unkunk-1,
747NR_033076chrUn-21294424212945042129450421294504121294424,21294504,19549MIR1912unkunk-1,
819NR_033075chrUn+30757283307573423075734230757342130757283,30757342,19550MIR18Bunkunk-1,

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