Schema for refFlat
  Database: galGal4    Primary Table: refFlat    Row Count: 7,567   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 ACO1varchar(255) values Name of gene as it appears in genome browser.
name NM_001030536varchar(255) values Name of gene
chrom chrZvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 70787482int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 70824265int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 70799716int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 70823606int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 21int(10) unsigned range Number of exons
exonStarts 70787482,70799692,70802087,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 70787511,70799813,70802256,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      galGal4.mrnaOrientInfo.name (via refFlat.name)
      galGal4.refGene.name (via refFlat.name)
      galGal4.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
ACO1NM_001030536chrZ+707874827082426570799716708236062170787482,70799692,70802087,70804964,70806071,70806245,70807052,70808101,70808721,70809851,70811242,70816000,70816638,70816955,70 ...70787511,70799813,70802256,70805102,70806141,70806429,70807192,70808273,70808822,70809968,70811402,70816136,70816723,70817112,70 ...
TGFBR2NM_205428chr2+40385524404476324038555140447316740385524,40412388,40414056,40429676,40434735,40443590,40447136,40385633,40412539,40414247,40430476,40434877,40443718,40447632,
IFNA3NM_205427chrZ+723646772372307236521723710317236467,7237230,
IFNA3NM_205427chrZ+724043972412027240493724107517240439,7241202,
IFNA3NM_205427chrZ+724441172451747244465724504717244411,7245174,
IFNA3NM_205427chrZ+724622072469837246274724685617246220,7246983,
IFNA3NM_205427chrZ+725416972549327254223725480517254169,7254932,
IFNA3NM_205427chrZ+726020772609707260261726084317260207,7260970,
LHX9NM_205426chr8-226965522794022269663227899752269655,2271049,2276067,2277183,2278880,2269921,2271252,2276423,2277386,2279402,
CSKNM_205425chr10-1926023192958419260231929584121926023,1926308,1926479,1927091,1927381,1927604,1927856,1927996,1928613,1928920,1929334,1929569,1926206,1926395,1926675,1927165,1927472,1927704,1927922,1928090,1928833,1929033,1929448,1929584,

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