Schema for refFlat
  Database: panTro3    Primary Table: refFlat    Row Count: 2,832   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 DEFB119varchar(255) values Name of gene as it appears in genome browser.
name NM_001101673varchar(255) values Name of gene
chrom chr20varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 28109581int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 28122796int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 28109581int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 28122796int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 28109581,28122735,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 28109775,28122796,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)
      panTro3.mrnaOrientInfo.name (via refFlat.name)
      panTro3.refGene.name (via refFlat.name)
      panTro3.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
DEFB119NM_001101673chr20-28109581281227962810958128122796228109581,28122735,28109775,28122796,
CRYGANM_001100602chr2B-2130239532130267302130239532130267303213023953,213026377,213026721,213024226,213026620,213026730,
ICAM4NM_001194939chr19+10476606104774321047660610477432210476606,10477129,10477000,10477432,
GPR75NM_001205039chr2A-54700188547069855470040754702030254700188,54706779,54702139,54706985,
ASB3NM_001205040chr2A-545121225463314954512646546113031054512122,54536033,54542693,54556821,54558952,54571092,54571841,54596511,54611107,54632960,54512834,54536164,54542951,54557019,54559130,54571228,54571954,54596670,54611316,54633149,
NR0B1NM_001194935chrX-30512173305171743051233030517159230512173,30515991,30512575,30517174,
ITGAMNM_001194934chr16+314307323150409531430732315040333131430732,31432359,31436361,31436777,31436996,31441825,31442718,31444254,31446432,31447557,31447806,31448853,31469661,31469889,31 ...31430760,31432465,31436465,31436848,31437114,31441956,31442864,31444408,31446583,31447631,31447936,31448996,31469802,31470102,31 ...
CABYRNM_001246579chr18+19839696198621131984376419857464619839696,19843740,19844009,19856181,19859955,19862028,19839753,19843909,19844063,19857480,19860553,19862113,
SRP9NM_001246578chr1+2049437062049570392049437892049559293204943706,204949146,204955809,204943861,204949215,204957039,
LARP6NM_001246577chr15-68374627683972146837512968397171368374627,68379375,68396971,68376194,68379586,68397214,

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