Schema for refGene
  Database: danRer7    Primary Table: refGene    Row Count: 17,283   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 830smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_200398varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr10varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 32234966int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 32242325int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 32235432int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 32242043int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 32234966,32235408,32235618,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 32235091,32235542,32235721,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 tmem218varchar(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 -1,0,2,0,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
        danRer7.all_est.qName (via refGene.name)
      danRer7.all_mrna.qName (via refGene.name)
      danRer7.mrnaOrientInfo.name (via refGene.name)
      danRer7.refFlat.name (via refGene.name)
      danRer7.refSeqAli.qName (via refGene.name)
      danRer7.xenoMrna.qName (via refGene.name)
      danRer7.xenoRefGene.name (via refGene.name)
      danRer7.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
830NM_200398chr10+32234966322423253223543232242043432234966,32235408,32235618,32241908,32235091,32235542,32235721,32242325,0tmem218cmplcmpl-1,0,2,0,
115NM_200819chr8+448046644494801944804744449477991044804664,44874496,44935783,44935784,44939191,44939346,44940850,44941035,44941236,44947751,44804750,44874671,44935784,44935910,44939261,44939417,44940958,44941140,44941299,44948019,0kcnip3acmplcmpl0,0,1,0,0,1,0,0,0,0,
854NM_201218chr25+35326186353426353532622835342094935326186,35326609,35328503,35331795,35334070,35334483,35335036,35335213,35341792,35326278,35326674,35328689,35331978,35334173,35334615,35335123,35335314,35342635,0bnip2cmplcmpl0,2,1,1,1,2,2,2,1,
752NM_200816chr16-219302862197801221930616219779261121930286,21938306,21940804,21942518,21949104,21952261,21962237,21963943,21966281,21966533,21977904,21930919,21938518,21940997,21942641,21949220,21952393,21962359,21964076,21966432,21966775,21978012,0hdac9bcmplcmpl0,1,0,0,1,1,2,1,0,1,0,
97NM_200800chr23+254232602543762725426755254371121025423260,25426694,25426861,25433300,25433413,25433893,25434034,25434165,25434404,25437013,25423453,25426768,25426969,25433324,25433537,25433952,25434085,25434250,25434531,25437627,0fam3acmplcmpl-1,0,1,1,1,2,1,1,2,0,
881NM_200006chr6+38827149388333623882736438832537438827149,38827346,38829841,38832400,38827259,38827494,38830009,38833362,0slc48a1bcmplcmpl-1,0,1,1,
772NM_200915chr4-245843652460272424584630246022871324584365,24589139,24589326,24590192,24593052,24593419,24594005,24594291,24597643,24598536,24599921,24602164,24602640,24584734,24589212,24589425,24590266,24593100,24593571,24594132,24594342,24597765,24598703,24600038,24602311,24602724,0rbm17cmplcmpl1,0,0,1,1,2,1,1,2,0,0,0,-1,
1006NM_200845chr7+55225595552316385522560155231596555225595,55226086,55229150,55231240,55231518,55225604,55226238,55229256,55231306,55231638,0rps17cmplcmpl0,0,2,0,0,
797NM_200492chr2+27800334278046862780337027804686427800334,27800736,27803300,27804517,27800383,27800791,27803698,27804686,0tmem68cmplincmpl-1,-1,0,1,
770NM_001128536chr9+24288754243466872429897724346475824288754,24298960,24330681,24330953,24333121,24343479,24346127,24346414,24289109,24299080,24330725,24331045,24333218,24343591,24346269,24346687,0tmem163acmplcmpl-1,0,1,0,2,0,1,2,

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