Schema for refFlat
  Database: xenTro3    Primary Table: refFlat    Row Count: 9,395   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 atg7varchar(255) values Name of gene as it appears in genome browser.
name NM_001129922varchar(255) values Name of gene
chrom GL174003varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 36235int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 71139int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 37217int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 70198int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 36235,37199,38488,40336,413...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 36269,37395,38543,40454,414...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)
      xenTro3.mrnaOrientInfo.name (via refFlat.name)
      xenTro3.refGene.name (via refFlat.name)
      xenTro3.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
atg7NM_001129922GL174003+362357113937217701981236235,37199,38488,40336,41361,41997,42274,42735,43395,48397,56463,70165,36269,37395,38543,40454,41450,42119,42365,42880,43554,48592,56588,71139,
trioNM_001129921GL172641+3792720407573837928954075455553792720,3871523,3886064,3903829,3907857,3911209,3912462,3916794,3917822,3919079,3919725,3923182,3924996,3927928,3929298,3930465, ...3792938,3871598,3886179,3904022,3908370,3911332,3912654,3916926,3918053,3919202,3919917,3923352,3925171,3928124,3929465,3930585, ...
klk15NM_001011435GL173018-14373203531459020320514373,15668,17387,18873,20277,14743,15805,17647,19036,20353,
slc25a26NM_001004820GL173000+255988528326553848791025598,26553,27182,34190,35427,70891,77723,82773,83929,84773,25643,26711,27289,34295,35475,70936,77793,82838,84003,85283,
tmem165NM_001017260GL172743+119045911987811192408119771041190459,1192405,1193856,1197632,1190532,1192631,1194032,1198781,
fntbNM_001017258GL172882-1589576160091215899211600870121589576,1590497,1590693,1591981,1592542,1593356,1594191,1595332,1595750,1597156,1597583,1600771,1590029,1590612,1590805,1592114,1592672,1593443,1594275,1595479,1595842,1597229,1597648,1600912,
glyr1NM_001030494GL173338+27914730669327918930418716279147,288421,288553,290531,290909,292814,296145,296350,296500,298409,299329,301590,301797,302060,302714,304112,279227,288458,288633,290682,291068,292901,296217,296401,296574,298509,299440,301692,301960,302181,302839,306693,
pls3NM_001030528GL173154-72556077949872745975402117725560,728636,729198,731190,731513,731761,733611,734579,737599,738246,738718,739248,740522,743041,753954,756277,779423,727592,728764,729322,731324,731628,731840,733807,734675,737742,738412,738800,739381,740652,743205,754040,756322,779498,
serpina3mNM_001030522GL172821+199613920033281997389200189661996139,1996778,1997370,1999257,1999697,2001704,1996221,1996860,1998020,1999528,1999845,2003328,
ncf4NM_001030521GL172724-1615527163872516162991636984121615527,1616310,1625281,1625436,1626737,1627043,1627547,1628234,1628604,1635206,1636952,1638615,1616310,1616492,1625347,1625567,1626836,1627092,1627675,1628305,1628758,1635291,1637057,1638725,

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