Schema for refFlat
  Database: fr3    Primary Table: refFlat    Row Count: 655   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName smc2varchar(255) values Name of gene as it appears in genome browser.
name NM_001032624varchar(255) values Name of gene
chrom HE591990varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 45672int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 51792int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 45672int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 51792int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 26int(10) unsigned range Number of exons
exonStarts 45672,45934,46175,46373,464...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 45840,46084,46298,46412,466...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      fr3.mrnaOrientInfo.name (via refFlat.name)
      fr3.refGene.name (via refFlat.name)
      fr3.refSeqAli.qName (via refFlat.name)
      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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
smc2NM_001032624HE591990+456725179245672517922645672,45934,46175,46373,46497,46706,46833,47155,47389,47792,48019,48507,48727,48922,49212,49421,49634,49929,50150,50299,50645,50 ...45840,46084,46298,46412,46608,46751,47067,47305,47623,47952,48137,48646,48847,49127,49348,49546,49828,50073,50227,50415,50654,50 ...
gp91phoxNM_001032732chr8-6533349653854065342976538517146533349,6534123,6534520,6534735,6534955,6535498,6535827,6536005,6536208,6536841,6537269,6537451,6538077,6538472,6533664,6534415,6534645,6534882,6535118,6535752,6535920,6536138,6536390,6536990,6537354,6537562,6538170,6538540,
mbnl3NM_001038003chr14-184501718512531845017185125351845017,1845789,1846112,1846415,1851079,1845206,1846029,1846316,1846580,1851253,
mycaNM_001037875chr10+637930563809016379307638085626379305,6380245,6379953,6380901,
becn1NM_001037874chr1-101342041013671310134204101367131110134204,10134439,10134684,10134833,10135093,10135415,10135815,10136034,10136215,10136442,10136586,10134373,10134582,10134745,10134983,10135240,10135606,10135956,10136125,10136274,10136507,10136713,
il21NM_001037993chr14-11872889118749351187323411874917511872889,11873461,11873574,11874650,11874770,11873366,11873494,11873688,11874692,11874935,
b3gat1NM_001037992chr11+8232988314518232988314514823298,825164,829224,831364,823410,825676,829521,831451,
mir153aNR_105341chr10-580635558064265806426580642615806355,5806426,
il15NM_001033048chr17-823771782411098237843824095568237717,8238128,8239146,8239308,8239607,8240904,8237948,8238260,8239191,8239396,8239690,8241109,
prlrbNM_001078625chr21-10626415106316661062689510630614910626415,10627649,10627811,10627984,10628305,10629299,10629988,10630532,10631555,10627570,10627719,10627908,10628126,10628469,10629469,10630121,10630687,10631666,

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