Schema for refFlat
  Database: xenTro2    Primary Table: refFlat    Row Count: 9,500   Data last updated: 2020-09-02
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName thul16varchar(255) values Name of gene as it appears in genome browser.
name NM_001011392varchar(255) values Name of gene
chrom scaffold_185varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1490483int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1503003int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1490937int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1501342int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 13int(10) unsigned range Number of exons
exonStarts 1490483,1491783,1492040,149...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1490984,1491824,1492144,149...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)
      xenTro2.mrnaOrientInfo.name (via refFlat.name)
      xenTro2.refGene.name (via refFlat.name)
      xenTro2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
thul16NM_001011392scaffold_185+1490483150300314909371501342131490483,1491783,1492040,1493291,1494822,1495935,1496916,1497552,1498947,1499266,1500960,1501264,1502372,1490984,1491824,1492144,1493381,1494921,1496086,1497111,1497644,1499063,1499349,1501040,1501363,1503003,
thbs3NM_001011401scaffold_3512-6821140011861140014682,1370,3487,4082,4424,4967,5385,9426,9462,10331,10532,11313,11340,11356,1245,1510,3660,4279,4473,5146,5579,9449,9481,10450,10692,11340,11356,11400,
thbs3NM_001011401scaffold_3931+236594192403941992365,5742,6798,7249,8251,8620,8824,9047,9276,2491,5949,7055,7352,8278,8703,8876,9196,9419,
adh1NM_001011391scaffold_111+233802323546642338023235422882338023,2344221,2344719,2348488,2349084,2350996,2352424,2354203,2338125,2344363,2344807,2348708,2349345,2351132,2352563,2354664,
gpkowNM_001011390scaffold_154+156684215763341566899157581061566842,1573359,1573600,1574263,1575169,1575633,1567045,1573517,1573731,1574370,1575371,1576334,
zdhhc5NM_001044485scaffold_714+28221733493728259133422811282217,306348,306556,309684,313385,315535,330539,331733,332334,333579,334089,282740,306470,306714,309857,313490,315547,330668,331857,332435,334007,334937,
puraNM_001113869scaffold_65-3651033663803654763663251365103,366380,
fip1l1NM_001044425scaffold_107+50519254711550521154683517505192,509877,510135,512497,513192,513841,514625,517711,518305,519701,524697,527288,534650,535999,541718,546102,546690,505368,509926,510193,512592,513257,513949,514756,517821,518402,519861,524736,527315,534705,536055,541944,546258,547115,
zc3h3NM_001044484scaffold_789+30502339471030522039357312305023,306338,308960,332930,354722,359574,360260,361014,367884,379468,379767,393541,305266,307467,309157,333072,354901,359653,360416,361084,368016,379632,379925,394710,
birc5lNM_001044483scaffold_176+196082519653491960891196469241960825,1963088,1963879,1964596,1960987,1963198,1963997,1965349,

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