Schema for refFlat
  Database: bosTau9    Primary Table: refFlat    Row Count: 14,561   Data last updated: 2019-05-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName KCNE1varchar(255) values Name of gene as it appears in genome browser.
name NM_001077977varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1040522int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1047018int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1046439int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1046829int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 1040522,1041573,1046389,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1040594,1041668,1047018,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      bosTau9.mrnaOrientInfo.name (via refFlat.name)
      bosTau9.refGene.name (via refFlat.name)
      bosTau9.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
KCNE1NM_001077977chr1+104052210470181046439104682931040522,1041573,1046389,1040594,1041668,1047018,
FAM243ANM_001077124chr1-109912411001431099325110008111099124,1100143,
SMIM11ANM_001114516chr1-110287811183121105555111211441102878,1105542,1112102,1118250,1103061,1105720,1112201,1118312,
KCNE2NM_001077084chr1-112394011317481124229112460121123940,1131642,1124613,1131748,
PLAURNM_174423chr18-51865095518783765186539151878357751865095,51866545,51868122,51869019,51874855,51876386,51878308,51865645,51866692,51868257,51869170,51875001,51876497,51878376,
CRYZL1NM_001035037chr1+1909585194320719183141942914131909585,1918308,1919950,1920756,1922869,1924592,1933204,1934464,1936832,1938586,1939736,1942228,1942814,1909641,1918380,1920028,1920829,1922914,1924661,1933338,1934576,1936931,1938708,1939842,1942274,1943207,
DONSONNM_001083445chr1+1943960195400119439601953367101943960,1945008,1946022,1947128,1948520,1949322,1949512,1950463,1951841,1953229,1944257,1945089,1946226,1947307,1948699,1949404,1949617,1950662,1952054,1954001,
SONNM_001083694chr1-1954260198511719550111985068131954260,1955689,1955906,1957761,1961941,1963068,1970278,1970660,1972709,1974168,1978268,1981826,1984991,1955170,1955805,1955978,1957909,1962058,1963179,1970467,1970807,1972871,1977311,1980071,1981993,1985117,
DNPEPNM_001045952chr2-10730788110732012110730796810732012114107307881,107308383,107314722,107314947,107315394,107316266,107317279,107318401,107318617,107318999,107319350,107319649,10731985 ...107308019,107308551,107314824,107314987,107315555,107316350,107317357,107318509,107318693,107319130,107319476,107319763,10731994 ...
PRPF3NM_001046051chr3-203119942033062120312208203282761620311994,20314418,20315516,20315853,20317037,20317323,20318120,20320078,20320901,20321742,20322707,20323161,20324554,20326647,20 ...20312355,20314480,20315600,20315972,20317151,20317423,20318264,20320158,20321068,20322049,20322928,20323245,20324701,20326778,20 ...

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