Schema for refFlat
  Database: gasAcu1    Primary Table: refFlat    Row Count: 65   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName LOC100190878varchar(255) values Name of gene as it appears in genome browser.
name NM_001267687varchar(255) values Name of gene
chrom chrIvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 717456int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 724541int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 717456int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 724541int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 717456,718511,719636,724415,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 717597,718559,719789,724541,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      gasAcu1.mrnaOrientInfo.name (via refFlat.name)
      gasAcu1.refGene.name (via refFlat.name)
      gasAcu1.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
LOC100190878NM_001267687chrI+7174567245417174567245414717456,718511,719636,724415,717597,718559,719789,724541,
socs9NM_001267680chrI-11579499115811821157949911581182211579499,11580321,11580240,11581182,
cacnb4.1NM_001267653chrI-228167282283012422816728228301241422816728,22817099,22817593,22818725,22819114,22819500,22820101,22821375,22821841,22823937,22824178,22824414,22828354,22830061,22816989,22817285,22817689,22818877,22819224,22819559,22820182,22821395,22821918,22824065,22824301,22824585,22828438,22830124,
rhcgNM_001267646chrII+118426091184789111842656118473961111842609,11844431,11844951,11845214,11845481,11845733,11846329,11846632,11847003,11847197,11847362,11842885,11844624,11845102,11845362,11845648,11845871,11846466,11846757,11847077,11847271,11847891,
spg1NM_001267628chrIV+210183132102919221018340210275793221018313,21019011,21019564,21020298,21020582,21020838,21021138,21021420,21021646,21021908,21022123,21022307,21022524,21022833,21 ...21018389,21019056,21019790,21020428,21020646,21020921,21021331,21021546,21021767,21022044,21022201,21022377,21022662,21022983,21 ...
socs4NM_001267676chrII+21769056217702442176905621770244121769056,21770244,
LOC100174897NM_001267650chrVI+15261700152635361526203215263443415261700,15262031,15262845,15263209,15261718,15262126,15262964,15263536,
il-2NM_001267682chrIV-330480633057653304806330576543304806,3305032,3305517,3305654,3304917,3305179,3305556,3305765,
LOC100190874NM_001267683chrIV-330792833086033307928330860343307928,3308110,3308338,3308480,3308036,3308236,3308374,3308603,
il-21NM_001267686chrIV-331420433167343314204331673463314204,3314371,3314557,3314674,3316448,3316584,3314231,3314449,3314590,3314779,3316490,3316734,

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