Schema for refFlat
  Database: danRer4    Primary Table: refFlat    Row Count: 19,100   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 zgc:114130varchar(255) values Name of gene as it appears in genome browser.
name NM_001030247varchar(255) values Name of gene
chrom chr15varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 55892635int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 55896543int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 55894187int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 55895177int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 55892635,55894046,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 55892763,55896543,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      danRer4.mrnaOrientInfo.name (via refFlat.name)
      danRer4.refGene.name (via refFlat.name)
      danRer4.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
zgc:114130NM_001030247chr15+55892635558965435589418755895177255892635,55894046,55892763,55896543,
LOC100001444NM_001161602chr8-517751855177994351775521517788921151775185,51776358,51776575,51776910,51777413,51777826,51778160,51778556,51778810,51779388,51779910,51775842,51776486,51776762,51777246,51777507,51777963,51778306,51778697,51778914,51779467,51779943,
myh7NM_001112733chr2-215349902154838321535095215480083921534990,21536131,21536347,21536728,21536919,21537305,21537587,21538812,21539139,21539390,21539822,21540101,21540302,21540520,21 ...21535116,21536266,21536443,21536833,21537216,21537509,21537896,21538937,21539305,21539574,21540019,21540220,21540429,21540910,21 ...
aurkaip1NM_001105695chrNA_random+74861454748622777486145474862140274861454,74862029,74861921,74862277,
gpank1NM_001105703chr1+34950390349568413495101334956214434950390,34950948,34953039,34956052,34950465,34951206,34953311,34956841,
map3k22NM_001105691chr24-140482761413951614048516141076181314048276,14050334,14054562,14059986,14063955,14070297,14071361,14072401,14078963,14083048,14100812,14107614,14139393,14048542,14050406,14054624,14060060,14064089,14070412,14071478,14072501,14079001,14083164,14100857,14107677,14139516,
taco1NM_001082873chr12+912202091320009122223913179659122020,9124129,9125969,9126181,9131586,9122539,9124236,9126100,9126344,9132000,
sars2NM_201179chr20+9353451937790693535059377742169353451,9354377,9359426,9359799,9360652,9362371,9362511,9365248,9370707,9371423,9371557,9375161,9376529,9376990,9377221,9377625,9353772,9354473,9359456,9359940,9360707,9362435,9362617,9365296,9370816,9371469,9371645,9375274,9376623,9377086,9377284,9377906,
luzp2NM_001099255chr18-39123865391577253912386539157725539123865,39124275,39134421,39136453,39157663,39124035,39124349,39134484,39136516,39157725,
kdm8NM_001109869chr3-51749788517626605174981851762363851749788,51750356,51750562,51757143,51757274,51757677,51761904,51762534,51749983,51750449,51750712,51757191,51757407,51757850,51762410,51762660,

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