Schema for refGene
  Database: taeGut1    Primary Table: refGene    Row Count: 1,267   Data last updated: 2020-09-01
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 75smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001245268varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 2322980int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 2381582int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 2323027int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 2380903int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 2322980,2340930,2380775,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 2323036,2340982,2381582,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LOC100190510varchar(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 0,0,1,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
        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)
      taeGut1.all_est.qName (via refGene.name)
      taeGut1.all_mrna.qName (via refGene.name)
      taeGut1.mrnaOrientInfo.name (via refGene.name)
      taeGut1.refFlat.name (via refGene.name)
      taeGut1.refSeqAli.qName (via refGene.name)
      taeGut1.xenoMrna.qName (via refGene.name)
      taeGut1.xenoRefGene.name (via refGene.name)
      taeGut1.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
75NM_001245268chr1+232298023815822323027238090332322980,2340930,2380775,2323036,2340982,2381582,0LOC100190510cmplcmpl0,0,1,
98NM_001177414chr8+263203312636311026320448263610082026320331,26340497,26341394,26341539,26345068,26348786,26349670,26350630,26351292,26351543,26351830,26352516,26352857,26354621,26 ...26320470,26340648,26341444,26341688,26345191,26348920,26349865,26350748,26351372,26351737,26351911,26352857,26352975,26354774,26 ...0DNAJC6cmplcmpl0,1,2,1,0,0,2,2,0,2,1,1,0,1,1,1,1,1,0,0,
709NM_001198579chr10+16269223162790181626933016276090316269223,16271878,16275815,16269760,16272406,16279018,0NR2F2cmplcmpl0,1,1,
13NM_001198538chr4+376726273798834037672627379868112737672627,37687127,37851968,37871395,37892183,37896130,37902791,37903523,37903770,37905271,37908385,37924733,37932262,37933527,37 ...37672859,37687406,37852206,37871634,37892306,37896345,37903002,37903625,37903965,37905472,37908571,37924880,37932479,37933647,37 ...0TENM3cmplcmpl0,1,1,2,1,1,0,1,1,1,1,1,1,2,2,0,1,1,2,1,0,2,1,0,0,1,0,
1421NR_049043chr1+1096619661096620371096620371096620371109661966,109662037,0MIR99-1unkunk-1,
587NR_049051chrZ_random+3281603282323282323282321328160,328232,0MIR122unkunk-1,
1345NR_048950chr3+99620779996208669962086699620866199620779,99620866,0MIR1329unkunk-1,
710NM_001245184chr6+16430816164345751643082316434443516430816,16431083,16431822,16433483,16434350,16430923,16431210,16431922,16433639,16434575,0NDUFB8cmplcmpl0,1,2,0,0,
585NM_001245322chr10_random+1242631261111242941259258124263,124337,124425,124816,125068,125555,125851,125921,124337,124424,124445,124935,125162,125740,125921,126111,0PPIBcmplcmpl0,2,2,1,0,1,0,2,
653NM_001245195chr20+8989609900511289897119001963118989609,8992165,8992849,8994048,8999129,9000676,9001449,9001572,9001949,9004177,9004814,8989714,8992229,8992955,8994139,8999263,9000733,9001572,9001604,9002096,9004249,9005112,0TCEA2cmplcmpl0,2,0,1,2,1,1,2,1,-1,-1,

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