Schema for refFlat
  Database: canFam6    Primary Table: refFlat    Row Count: 2,261   Data last updated: 2021-05-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName CYB5Avarchar(255) values Name of gene as it appears in genome browser.
name NM_001193298varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 6078220int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 6113929int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 6078252int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 6113906int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 6078220,6106054,6108031,611...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 6078381,6106183,6108061,611...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      canFam6.mrnaOrientInfo.name (via refFlat.name)
      canFam6.refGene.name (via refFlat.name)
      canFam6.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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
CYB5ANM_001193298chr1+607822061139296078252611390656078220,6106054,6108031,6112084,6113824,6078381,6106183,6108061,6112119,6113929,
BCL2NM_001002949chr1+14699876148666891470053114866486414699876,14700249,14700747,14866351,14700023,14700747,14701107,14866689,
PPIAP1NR_036669chr1-15634385156351141563511415635114115634385,15635114,
CDH20NM_001286988chr1-161509071620243216152048162021571116150907,16156755,16161328,16166678,16169523,16175891,16185398,16189867,16192522,16193173,16201911,16152554,16157007,16161446,16166800,16169660,16176145,16185586,16190035,16192642,16193468,16202432,
MC4RNM_001080724chr1+17102320171033181710232017103318217102320,17103096,17103096,17103318,
PMAIP1NM_001195771chr1-17446016174493251744601717449323217446016,17449265,17446124,17449325,
SEC11CNM_001003312chr1-17995617180111611799565018011091617995617,17996316,17998421,18000665,18004574,18011004,17995704,17996374,17998541,18000815,18004684,18011161,
MIR122NR_049246chr1-18577762185778201857782018577820118577762,18577820,
TCF4NM_001003268chr1+210449562140158421049703214011711921044956,21049703,21166184,21169295,21225181,21276427,21277034,21349942,21353628,21359624,21367569,21368761,21371634,21374456,21 ...21045483,21049776,21166246,21169392,21225246,21276554,21277084,21350048,21353762,21359757,21367637,21368840,21371711,21374660,21 ...
CUPIN1NM_001371796chr1-22052251220653102205382822065286922052251,22054766,22056300,22057195,22059217,22060520,22063541,22064289,22065202,22053963,22054913,22056414,22057305,22059371,22060751,22063748,22064523,22065310,

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