Schema for refFlat
  Database: vicPac2    Primary Table: refFlat    Row Count: 17   Data last updated: 2020-02-05
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName MIFvarchar(255) values Name of gene as it appears in genome browser.
name NM_001287197varchar(255) values Name of gene
chrom KB632605varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 770726int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 771476int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 770825int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 771400int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 770726,770973,771292,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 770892,771146,771476,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)
      vicPac2.mrnaOrientInfo.name (via refFlat.name)
      vicPac2.refGene.name (via refFlat.name)
      vicPac2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MIFNM_001287197KB632605-7707267714767708257714003770726,770973,771292,770892,771146,771476,
PRLNM_001287199KB632446+256073125668242560731256674652560731,2561983,2564135,2566478,2566520,2560915,2562091,2564315,2566520,2566824,
GH1NM_001287198KB632449-311157231132963111666311323753111572,3112143,3112491,3112823,3113227,3111867,3112305,3112608,3112984,3113296,
CDK5NM_001287200KB632560+5058739506256050587395062560125058739,5059442,5059622,5059828,5059986,5060738,5060975,5061210,5061490,5062133,5062306,5062473,5058776,5059531,5059690,5059889,5060043,5060834,5061050,5061307,5061560,5062194,5062387,5062560,
TGFB1NM_001290071KB632637+2536122664092536322662657253612,256887,258300,260041,260403,265455,266106,253987,257048,258418,260119,260551,265609,266409,
ASIPNM_001287858KB632468-10005200100091181000520010009118310005200,10007602,10008958,10005320,10007667,10009118,
AZIN2NM_001293786KB632436+234572982348903823458364234887001123457298,23457541,23458297,23460005,23463738,23464892,23465783,23467497,23468831,23485116,23488561,23457445,23457659,23458469,23460179,23463911,23465027,23465949,23467660,23468944,23485331,23489038,
AZIN1NM_001291757KB632582+1804448183161818204741829408131804448,1808535,1815117,1820378,1822065,1823040,1824687,1826217,1826732,1827400,1828414,1828853,1829296,1804804,1808673,1815263,1820576,1822239,1823213,1824822,1826299,1826807,1827563,1828530,1829068,1831618,
PEG10NM_001291338KB632506-573914957521085744283575189125739149,5751886,5745511,5752108,
PEG10NM_001291337KB632506-573914957521085743138575189125739149,5751886,5745511,5752108,

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