Schema for refGene
  Database: galGal5    Primary Table: refGene    Row Count: 7,730   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 940smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001006447varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr4varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 46590244int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 46598689int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 46590648int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 46598654int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 10int(10) unsigned range Number of exons
exonStarts 46590244,46591808,46592268,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 46590782,46591893,46592384,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 COPS4varchar(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 1,0,1,1,0,2,0,1,2,0,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
        galGal5.all_est.qName (via refGene.name)
      galGal5.all_mrna.qName (via refGene.name)
      galGal5.mrnaOrientInfo.name (via refGene.name)
      galGal5.refFlat.name (via refGene.name)
      galGal5.refSeqAli.qName (via refGene.name)
      galGal5.xenoMrna.qName (via refGene.name)
      galGal5.xenoRefGene.name (via refGene.name)
      galGal5.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
940NM_001006447chr4-465902444659868946590648465986541046590244,46591808,46592268,46592665,46593195,46594210,46594844,46596155,46597087,46598565,46590782,46591893,46592384,46592836,46593346,46594364,46594948,46596307,46597167,46598689,0COPS4cmplcmpl1,0,1,1,0,2,0,1,2,0,
592NM_205422chr17-9921959951969929119951787992195,992911,993175,993629,994272,994714,995091,992348,992937,993277,993740,994343,994854,995196,0EXFABPcmplcmpl-1,1,1,1,2,0,0,
647NM_205421chr20-821112382214608211742822146068211123,8212511,8213282,8213989,8218805,8220940,8211892,8212636,8213370,8214115,8218972,8221460,0GATA5cmplcmpl0,1,0,0,1,0,
9NM_205419chr18+208416821317492084350213164162084168,2118343,2124492,2125229,2127942,2131312,2085374,2118532,2124642,2125283,2128017,2131749,0NTN1cmplcmpl0,1,1,1,1,1,
1370NM_205420chr2+1029356831029516021029356831029516026102935683,102938535,102941579,102943168,102943348,102951434,102936191,102938702,102941705,102943256,102943455,102951602,0GATA6cmplcmpl0,1,0,0,1,0,
692NM_205417chr5-14094421140971531409462714097131714094421,14095062,14095358,14095852,14096294,14096380,14097123,14094726,14095239,14095448,14095981,14096338,14096385,14097153,0TNNI2cmplcmpl0,0,0,0,1,2,0,
11NM_205416chr11-17821800178273321782211417827283817821800,17823093,17823521,17824030,17824423,17824985,17825955,17827109,17822282,17823209,17823908,17824078,17824535,17825074,17826139,17827332,0IRF8cmplcmpl0,1,1,1,0,1,0,0,
714NM_205415chr13-169773721698333116978243169822901016977372,16978759,16979510,16980010,16980327,16980589,16980880,16981232,16982203,16983206,16978341,16978895,16979542,16980136,16980463,16980639,16981057,16981332,16982295,16983331,0IRF1cmplcmpl1,0,1,1,0,1,1,0,0,-1,
700NM_205414chrZ+15144262151555301514466515155199715144262,15144584,15145524,15148682,15150693,15152382,15155082,15144465,15144693,15145714,15148942,15150980,15152550,15155530,0ISL1cmplcmpl-1,0,1,2,1,0,0,
649NM_205413chr19+841026784134278410401841327158410267,8411381,8411711,8412343,8412891,8410571,8411608,8411989,8412509,8413427,0LHX1cmplcmpl0,2,1,0,1,

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