Schema for refGene
  Database: mm10    Primary Table: refGene    Row Count: 47,382   Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 113smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_169016varchar(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 42070756int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 42121514int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 42121514int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 42121514int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 42070756,42071088,42071399,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 42071000,42071182,42071532,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Ccl19-ps2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-1,-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
        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)
      mm10.all_est.qName (via refGene.name)
      mm10.all_mrna.qName (via refGene.name)
      mm10.ccdsInfo.mrnaAcc (via refGene.name)
      mm10.kgXref.refseq (via refGene.name)
      mm10.knownToRefSeq.value (via refGene.name)
      mm10.mrnaOrientInfo.name (via refGene.name)
      mm10.refFlat.name (via refGene.name)
      mm10.refSeqAli.qName (via refGene.name)
      mm10.wgEncodeGencodeRefSeqVM14.rnaAcc (via refGene.name)
      mm10.wgEncodeGencodeRefSeqVM16.rnaAcc (via refGene.name)
      mm10.wgEncodeGencodeRefSeqVM18.rnaAcc (via refGene.name)
      mm10.wgEncodeGencodeRefSeqVM22.rnaAcc (via refGene.name)
      mm10.wgEncodeGencodeRefSeqVM24.rnaAcc (via refGene.name)
      mm10.wgEncodeGencodeRefSeqVM25.rnaAcc (via refGene.name)
      mm10.xenoMrna.qName (via refGene.name)
      mm10.xenoRefGene.name (via refGene.name)
      mm10.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
113NR_169016chr4-42070756421215144212151442121514642070756,42071088,42071399,42072505,42113537,42121442,42071000,42071182,42071532,42073233,42113617,42121514,0Ccl19-ps2unkunk-1,-1,-1,-1,-1,-1,
130NM_001040426chr9-599669306051103559972395604971261859966930,59976187,59979768,59982723,59987258,59987924,59988963,59997005,59999940,60002850,60056850,60252649,60375952,60394098,60 ...59972538,59976332,59979948,59982897,59987432,59988129,59989093,59997281,60000037,60003026,60057055,60252786,60376055,60394546,60 ...0Thsd4cmplcmpl1,0,0,0,0,2,1,1,0,1,0,1,0,2,0,2,0,-1,
800NM_001099347chrX-28270692282936322827081428292001928270692,28271202,28273750,28282029,28282405,28285655,28286229,28291904,28293495,28270883,28271301,28273832,28282093,28282531,28285690,28286296,28292024,28293632,0Gm10230cmplcmpl0,0,2,1,1,2,1,0,-1,
985NM_001170918chr14-52489934524956955249002052490962252489934,52495128,52490972,52495695,0Olfr1507cmplcmpl0,-1,
1723NM_001115153chr5+14918455914921543414918777414921526110149184559,149185484,149187707,149188344,149193839,149198644,149201759,149204268,149209642,149213351,149184806,149185661,149187876,149188473,149194440,149198758,149201889,149204394,149209800,149215434,0Uspl1cmplcmpl-1,-1,0,0,0,1,1,2,2,1,
1062NM_028197chr10-62558469625784576255900762578377762558469,62563235,62566036,62569458,62570398,62575049,62577963,62559883,62563351,62566121,62569642,62570478,62575148,62578457,0Kifbpcmplcmpl0,1,0,2,0,0,0,
1184NM_028195chr15+785970467862201978597200786205641378597046,78602692,78604635,78605846,78606956,78608125,78609761,78611448,78615716,78618375,78619261,78619788,78620494,78597219,78602775,78604700,78605913,78607075,78608206,78609874,78611597,78615828,78618452,78619333,78619943,78622019,0Cyth4cmplcmpl0,1,0,2,0,2,2,1,0,1,0,0,2,
78NM_001039692chr18-6024449613609860265556112362196024449,6027574,6027959,6028193,6031729,6033140,6034449,6037017,6039353,6049276,6052861,6057516,6061846,6064340,6065704,6069830, ...6026730,6027677,6028094,6028271,6031828,6033257,6034552,6037116,6039455,6049358,6052923,6057591,6061972,6064421,6065845,6070091, ...0Arhgap12cmplcmpl2,1,1,1,1,1,0,0,0,2,0,0,0,0,0,0,0,-1,-1,
11NM_001159557chr5-177816891784979217785721178288941617781689,17785721,17787685,17788251,17795578,17796995,17798228,17811180,17813012,17814112,17814672,17820439,17828774,17829455,17 ...17783349,17785886,17787740,17788325,17795697,17797183,17798298,17811227,17813104,17814292,17814820,17820600,17828981,17829549,17 ...0Cd36cmplcmpl-1,0,2,0,1,2,1,2,0,0,2,0,0,-1,-1,-1,
84NR_153433chr19-117751171181940311819403118194031011775117,11777087,11782799,11785389,11785684,11786524,11788168,11789556,11803493,11818691,11776588,11777170,11783136,11785524,11785758,11786633,11788236,11789631,11803577,11819403,0Stx3unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,

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