Schema for refGene
  Database: danRer4    Primary Table: refGene    Row Count: 19,100   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 639smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001045429varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr14varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 7118502int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 7152468int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 7118571int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 7152343int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 20int(10) unsigned range Number of exons
exonStarts 7118502,7122128,7126217,712...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 7118638,7122185,7126413,712...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 zgc:153681varchar(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 0,1,1,2,0,0,0,0,1,0,0,2,0,0...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
        danRer4.all_est.qName (via refGene.name)
      danRer4.all_mrna.qName (via refGene.name)
      danRer4.mrnaOrientInfo.name (via refGene.name)
      danRer4.refFlat.name (via refGene.name)
      danRer4.refSeqAli.qName (via refGene.name)
      danRer4.xenoMrna.qName (via refGene.name)
      danRer4.xenoRefGene.name (via refGene.name)
      danRer4.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
639NM_001045429chr14+7118502715246871185717152343207118502,7122128,7126217,7126597,7131885,7137026,7137274,7137429,7137618,7141527,7141817,7145465,7148189,7149089,7149243,7151356, ...7118638,7122185,7126413,7126721,7131969,7137131,7137355,7137499,7137707,7141635,7141927,7145502,7148258,7149145,7149348,7151412, ...0zgc:153681cmplcmpl0,1,1,2,0,0,0,0,1,0,0,2,0,0,2,2,1,0,1,2,
1112NM_001111155chr14+69113807691211996911463169120680369113807,69114566,69119727,69113842,69114716,69121199,0znf973cmplcmpl-1,0,1,
591NM_001114890chr17+84155189846984215289833112841551,842141,846772,847020,847208,852665,853001,857984,872675,886763,887062,898251,841601,842267,846840,847132,847405,852923,853164,858135,872711,886965,887207,898469,0hhatcmplcmpl-1,0,1,0,1,0,0,1,2,2,0,1,
911NM_001110463chr19-42781974428060724278243342805966542781974,42788908,42790983,42804444,42805939,42783474,42789013,42791124,42804591,42806072,0plekho1acmplcmpl0,0,0,0,0,
950NM_001109724chr6-47881289478816544788153747881654147881289,47881654,0tead3bcmplincmpl0,
77NM_001123292chr8+4292754438434242927544384342104292754,4335653,4339925,4350716,4353543,4359543,4364063,4366135,4378536,4384099,4293312,4335870,4340061,4350871,4353684,4359744,4364207,4366752,4378848,4384342,0grm6acmplcmpl0,0,1,2,1,1,1,1,0,0,
825NM_001128799chr22-31487407314909583148742831490921231487407,31490886,31488533,31490958,0zgc:194330cmplcmpl2,0,
712NM_001024405chr9-16687208166923821668735616692274916687208,16687534,16687687,16689569,16689772,16689985,16691576,16692051,16692232,16687440,16687593,16687763,16689617,16689858,16690142,16691705,16692063,16692382,0uchl3cmplcmpl0,1,0,0,1,0,0,0,0,
793NM_001044317chr22-273739132738173827373914273816821227373913,27374340,27374531,27374928,27376885,27377099,27377272,27379329,27379568,27379739,27379909,27381679,27374213,27374437,27374706,27375042,27377029,27377160,27377424,27379486,27379666,27379823,27380013,27381738,0tmem161acmplcmpl1,0,2,2,2,1,2,1,2,2,0,0,
659NM_001044816chr12+974714897618559747148976185569747148,9748157,9751723,9753913,9759835,9761651,9747287,9748264,9751849,9754025,9759990,9761855,0nudt13cmplcmpl0,1,0,0,1,0,

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