Schema for refGene
  Database: danRer10    Primary Table: refGene    Row Count: 16,812   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 105smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001190304varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr20varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 34255153int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 34389728int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 34255752int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 34389406int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 107int(10) unsigned range Number of exons
exonStarts 34255153,34256201,34256453,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 34256119,34256328,34256573,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 hmcn1varchar(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 2,1,1,1,1,1,1,1,1,1,0,1,1,1...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
        danRer10.all_est.qName (via refGene.name)
      danRer10.all_mrna.qName (via refGene.name)
      danRer10.mrnaOrientInfo.name (via refGene.name)
      danRer10.refFlat.name (via refGene.name)
      danRer10.refSeqAli.qName (via refGene.name)
      danRer10.xenoMrna.qName (via refGene.name)
      danRer10.xenoRefGene.name (via refGene.name)
      danRer10.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
105NM_001190304chr20-3425515334389728342557523438940610734255153,34256201,34256453,34258274,34260543,34261290,34261501,34263251,34263557,34263791,34265480,34265807,34266008,34266460,34 ...34256119,34256328,34256573,34258637,34260672,34261416,34261615,34263386,34263677,34263854,34265718,34265929,34266146,34266607,34 ...0hmcn1cmplcmpl2,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,0,1,1,0,1,1,1,1,1,1,2,1,2,1,0,1,0,1,1,2,1,2,1,1,1,0,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1, ...
94NM_001327975chr6-224660662255214722466496225520581222466066,22468338,22470060,22470421,22475803,22481493,22481827,22482022,22487564,22521129,22523190,22552036,22466653,22468390,22470157,22470517,22475921,22481631,22481909,22482151,22487738,22521479,22523455,22552147,0sept9bcmplcmpl2,1,0,0,2,2,1,1,1,2,1,0,
748NM_200720chr9-21455814214577322145613721457617421455814,21456370,21456574,21457545,21456294,21456493,21456684,21457732,0sap18cmplcmpl2,2,0,0,
785NM_131702chr7-26223391262267542622481026226496226223391,26225861,26225057,26226754,0sox19bcmplcmpl2,0,
776NM_213039chr5+25080698250942062508367325092976625080698,25083671,25086901,25087102,25088099,25092827,25080824,25083830,25087001,25087206,25088231,25094206,0zfand5acmplcmpl-1,0,1,2,1,1,
586NM_001302253chr14+16025716806816025716806810160257,161397,163266,165253,165566,165966,167030,167247,167518,167790,160408,161556,163402,165337,165732,166097,167174,167384,167691,168068,0gpc2cmplcmpl0,1,1,0,0,1,0,0,2,1,
585NM_001199968chr20+1096171167401096691166976109617,111593,112427,113778,114075,115591,109866,111885,113183,113982,114193,116740,0olfcb1cmplcmpl0,2,0,0,0,1,
670NM_153673chr8-111663641119182611167268111917172011166364,11169372,11169603,11171551,11171790,11171997,11172477,11174611,11174851,11176595,11178376,11180456,11183328,11183580,11 ...11167532,11169528,11169721,11171667,11171904,11172064,11172605,11174752,11174993,11176690,11178677,11180628,11183499,11183746,11 ...0unc45bcmplcmpl0,0,2,0,0,2,0,0,2,0,2,1,1,0,0,0,1,0,0,0,
106NM_200425chr25+353842103540084035384311354002471035384210,35386290,35388405,35388677,35391348,35395022,35396284,35398302,35398418,35400223,35384432,35386454,35388550,35388767,35391531,35395202,35396447,35398341,35398641,35400840,0lsm14aacmplcmpl0,1,0,1,1,1,1,2,2,0,
612NM_205679chr11+356666335737313566681357291743566663,3571211,3571448,3572779,3566853,3571323,3571506,3573731,0cdabcmplcmpl0,1,2,0,

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