Schema for refFlat
  Database: mm7    Primary Table: refFlat    Row Count: 47,406   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName Gm30476varchar(255) values Name of gene as it appears in genome browser.
name NR_169083varchar(255) values Name of gene
chrom chr17varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 71325527int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 71326248int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 71326248int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 71326248int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 71325527,71325941,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 71325698,71326248,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      hgFixed.gbCdnaInfo.acc (via refFlat.name)
      hgFixed.gbSeq.acc (via refFlat.name)
      hgFixed.imageClone.acc (via refFlat.name)
      hgFixed.refLink.mrnaAcc (via refFlat.name)
      hgFixed.refSeqStatus.mrnaAcc (via refFlat.name)
      hgFixed.refSeqSummary.mrnaAcc (via refFlat.name)
      knownGeneV39.kgXref.refseq (via refFlat.name)
      knownGeneV39.knownToRefSeq.value (via refFlat.name)
      mm7.dupSpMrna.dupMrnaID (via refFlat.name)
      mm7.dupSpMrna.mrnaID (via refFlat.name)
      mm7.kgXref.refseq (via refFlat.name)
      mm7.knownToRefSeq.value (via refFlat.name)
      mm7.mrnaOrientInfo.name (via refFlat.name)
      mm7.mrnaRefseq.mrna (via refFlat.name)
      mm7.mrnaRefseq.refseq (via refFlat.name)
      mm7.refGene.name (via refFlat.name)
      mm7.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Gm30476NR_169083chr17+71325527713262487132624871326248271325527,71325941,71325698,71326248,
Klc1NM_001361613chr12+10928155610931964310929691610931908615109281556,109283136,109296915,109298948,109300519,109301407,109302615,109303194,109306247,109306539,109309867,109310030,10931208 ...109281647,109283239,109297177,109299179,109300598,109301633,109302703,109303296,109306421,109306639,109309917,109310098,10931219 ...
Fam228bNM_001382827chr12-469651847046154697239470387864696518,4697704,4698377,4699456,4703770,4704286,4697365,4697785,4698569,4699525,4703902,4704615,
Tnks2NM_001163635chr19+365349163659416236535222365914882736534916,36546218,36549973,36552184,36553162,36553486,36555575,36558487,36559739,36562770,36562971,36566636,36568324,36572297,36 ...36535421,36546443,36550069,36552221,36553238,36553581,36555642,36558674,36559861,36562862,36563050,36566808,36568404,36572443,36 ...
Eif6NM_010579chr2-1555606941555677831555609591555672916155560694,155563694,155564049,155564722,155566982,155567184,155560969,155563876,155564226,155564898,155567068,155567783,
Itgb1NM_010578chr8+12729425512734218112731401412734069016127294255,127314014,127315675,127318854,127321809,127322528,127324723,127325808,127326186,127328593,127328876,127330985,12733141 ...127294561,127314081,127315761,127319077,127321980,127322767,127324879,127325904,127326276,127328734,127329076,127331224,12733163 ...
Zfp467NM_020589chr6-48396662484058754839798148403495548396662,48401996,48402674,48403461,48405402,48399504,48402110,48402788,48403537,48405875,
Rps14NM_020600chr18+61164034611679856116584161167937561164034,61165839,61166368,61167251,61167869,61164125,61165990,61166530,61167328,61167985,
Plce1NM_019588chr19+382248793848578438224941384814323238224879,38321126,38352478,38399133,38402503,38405923,38417247,38420239,38421657,38422495,38425384,38425593,38427451,38429366,38 ...38226135,38321415,38352795,38399279,38402762,38406129,38417923,38420422,38421775,38422604,38425507,38425730,38427690,38429428,38 ...
Slc7a9NM_021291chr7+323422043235906032342825323589211332342204,32342775,32345394,32346419,32347079,32347583,32348602,32349139,32350033,32352872,32353800,32356621,32358856,32342480,32342912,32345542,32346662,32347205,32347683,32348647,32349263,32350137,32352969,32353950,32356796,32359060,

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