Schema for refFlat
  Database: ponAbe2    Primary Table: refFlat    Row Count: 3,599   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 CD74varchar(255) values Name of gene as it appears in genome browser.
name NM_001131158varchar(255) values Name of gene
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 152369072int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 152382850int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 152369673int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 152382848int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 152369072,152369996,1523721...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 152369684,152370059,1523721...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)
      ponAbe2.mrnaOrientInfo.name (via refFlat.name)
      ponAbe2.refGene.name (via refFlat.name)
      ponAbe2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
CD74NM_001131158chr5-1523690721523828501523696731523828488152369072,152369996,152372109,152372514,152373678,152374300,152374583,152382723,152369684,152370059,152372197,152372610,152373741,152374380,152374756,152382850,
TBC1D15NM_001131200chr12+721875287226998472187545722695271872187528,72219774,72220630,72228505,72232853,72240979,72242066,72242425,72244003,72244717,72245894,72255090,72260072,72263992,72 ...72187575,72219873,72220705,72228644,72233064,72241082,72242117,72242623,72244132,72244821,72245989,72255207,72260173,72264092,72 ...
CNN2NM_001131129chr19+9351989475279352249463867935198,939108,941517,941684,944547,944833,946110,935287,939230,941584,941822,944664,944980,947527,
CCNDBP1NM_001131130chr15+396388513964872839638915396483681139638851,39639213,39639547,39642731,39643587,39643857,39644506,39644926,39646273,39647941,39648253,39639024,39639273,39639627,39642813,39643684,39643931,39644583,39645207,39646334,39647988,39648728,
SH3BGRLNM_001131128chrX+79159857792677427915993879266425479159857,79245200,79246552,79266392,79159983,79245386,79246633,79267742,
DHX58NM_001131127chr17+473343294734597247335109473456173347334329,47334811,47335108,47335506,47335634,47335676,47335709,47336093,47336194,47336268,47337682,47339009,47339047,47339387,47 ...47334370,47334889,47335277,47335633,47335675,47335708,47335711,47336193,47336267,47336289,47337799,47339035,47339139,47339502,47 ...
COG4NM_001132812chr16+613467406138994761346750613895081961346740,61350608,61352225,61355447,61357529,61360200,61360836,61361760,61368858,61371938,61372627,61373583,61379322,61386558,61 ...61346909,61350691,61352340,61355622,61357723,61360306,61360994,61361819,61368992,61372057,61372794,61373749,61379385,61386675,61 ...
IKZF2NM_001132858chr2b-1045828761047271321045842181047241539104582876,104590663,104598970,104627181,104634323,104723236,104724119,104725661,104726941,104584943,104590807,104599108,104627349,104634590,104723341,104724168,104725765,104727132,
RSPRY1NM_001132707chr16+444343074448623644450420444847601544434307,44450265,44453820,44454825,44458714,44459631,44461868,44462661,44466164,44466709,44472764,44476237,44476692,44480886,44 ...44434447,44450770,44453873,44454938,44458841,44459690,44461935,44462793,44466280,44466853,44472876,44476340,44476845,44480991,44 ...
PPP1R7NM_001131107chr2b+13390231213393676413390231913393593510133902312,133905308,133909781,133910460,133911187,133912299,133914680,133918331,133922064,133935758,133902371,133905424,133909839,133910526,133911318,133912462,133914797,133918436,133922151,133936764,

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