Schema for refFlat
  Database: canFam2    Primary Table: refFlat    Row Count: 2,325   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName UCP1varchar(255) values Name of gene as it appears in genome browser.
name NM_001003046varchar(255) values Name of gene
chrom chr19varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 5283507int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 5290786int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 5283507int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 5290786int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 5283507,5287092,5287393,528...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 5283715,5287293,5287495,528...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      canFam2.refGene.name (via refFlat.name)
      canFam2.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
UCP1NM_001003046chr19+528350752907865283507529078655283507,5287092,5287393,5288700,5290671,5283715,5287293,5287495,5288881,5290786,
TMEM47NM_001003045chrX-29629155296597022963237029659510329629155,29642594,29659284,29632549,29642735,29659702,
DHRS4NM_001048234chr8+705223870641937052320706377287052238,7053556,7059172,7061291,7061458,7061816,7062142,7063657,7052451,7053734,7059274,7061362,7061510,7061951,7062198,7064193,
CCR4NM_001003020chr23-685516868562516855168685625116855168,6856251,
ASB17NM_001003018chr6+73787417738045467378752473804466373787417,73802295,73804259,73787925,73802575,73804546,
ALBNM_001003026chr13+650461846510741665090945651060481665046184,65090945,65091839,65092935,65094561,65095210,65095920,65097482,65098797,65100348,65101692,65102839,65103577,65105264,65 ...65046215,65091024,65091897,65093068,65094773,65095343,65096018,65097612,65099012,65100481,65101790,65102978,65103801,65105397,65 ...
QKINM_001003021chr1+548442715500086954844286550007661054844271,54846266,54846277,54884342,54907093,54960067,54991928,54993556,54996612,55000749,54844386,54846277,54846280,54884487,54907210,54960211,54992016,54993856,54996687,55000869,
GNAQNM_001003249chr1+83802421839969318380246083996709683802421,83903861,83920025,83922795,83983673,83996518,83802607,83904016,83920154,83922925,83983827,83996931,
PAX8NM_001003248chr17-404184954047421040418495404742101040418495,40426381,40433170,40433788,40438404,40438843,40439277,40440739,40442925,40474185,40418600,40426483,40433301,40433912,40438580,40438969,40439366,40440937,40443091,40474210,
KCNB2NM_001003247chr29+24248153246041482424815324604141824248153,24248691,24602299,24602976,24603599,24603769,24603780,24604018,24248687,24248732,24602971,24603599,24603768,24603780,24604017,24604148,

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