Schema for refFlat
  Database: galGal5    Primary Table: refFlat    Row Count: 7,730   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 LOC117654556varchar(255) values Name of gene as it appears in genome browser.
name NM_001382582varchar(255) values Name of gene
chrom chr22varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 2259178int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 2261236int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 2259864int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 2261089int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 2259178,2260111,2260381,226...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 2259962,2260205,2260501,226...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      galGal5.mrnaOrientInfo.name (via refFlat.name)
      galGal5.refGene.name (via refFlat.name)
      galGal5.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
LOC117654556NM_001382582chr22-225917822612362259864226108952259178,2260111,2260381,2260585,2260794,2259962,2260205,2260501,2260668,2261236,
BRD8NM_001006148chr13+100652881008001810065324100796712110065288,10065607,10066350,10067327,10067492,10067770,10068300,10068864,10069428,10070879,10072254,10072849,10073542,10074354,10 ...10065343,10065704,10066420,10067377,10067615,10067851,10068365,10069001,10069644,10071024,10072464,10073130,10073998,10074448,10 ...
IRF7NM_205372chr5+158458761584934415845917158488621015845876,15846008,15846753,15846993,15847179,15847372,15847571,15847921,15848409,15848715,15845940,15846171,15846916,15847055,15847225,15847495,15847829,15848293,15848528,15849344,
CTSBNM_205371chr3-10782933910783842610782948910783391910107829339,107829675,107830221,107830961,107831661,107832312,107832675,107833589,107833793,107838382,107829587,107829804,107830338,107831108,107831747,107832431,107832790,107833675,107833945,107838426,
KCNJ2NM_205370chr18+825905482657978263995826527928259054,8263779,8259157,8265797,
C5H14orf166NM_205369chr5+58218720582313775821876458231187858218720,58221000,58222428,58223722,58224463,58227204,58230259,58231032,58218825,58221125,58222528,58223809,58224553,58227240,58230308,58231377,
EEF2NM_205368chr28+1449755145768814497721457160161449755,1450348,1451537,1451804,1452698,1453075,1453493,1453802,1454374,1454685,1455276,1455594,1456301,1456568,1456966,1457318,1449775,1450563,1451719,1452016,1452877,1453181,1453607,1453941,1454570,1454944,1455384,1455948,1456484,1456701,1457300,1457688,
ACVR2ANM_205367chr7+346870343474155834688242347411871134687034,34718330,34720765,34722184,34733220,34734432,34735802,34736399,34737771,34739855,34740992,34688297,34718538,34720875,34722339,34733364,34734576,34735948,34736514,34737910,34739986,34741558,
AKTIPNM_001005838chr11+5078317508969950814615088882105078317,5081401,5082696,5084665,5084812,5086184,5086344,5086657,5087151,5088771,5078398,5081503,5082902,5084730,5084913,5086273,5086443,5086765,5087212,5089699,
CELF1NM_001012521chr5+228047582285243922832826228495541422804758,22817937,22832816,22833598,22834068,22835892,22836209,22836614,22838140,22840985,22846244,22846513,22847611,22849426,22804905,22817976,22833004,22833681,22834117,22836027,22836289,22836776,22838210,22841114,22846358,22846699,22847755,22852439,

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