Schema for refFlat
  Database: xenTro7    Primary Table: refFlat    Row Count: 8,995   Data last updated: 2020-09-02
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName dmap1varchar(255) values Name of gene as it appears in genome browser.
name NM_001005440varchar(255) values Name of gene
chrom KB021653varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 100813326int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 100846244int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 100813775int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 100844901int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 100813326,100823031,1008244...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 100813835,100823318,1008245...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)
      xenTro7.mrnaOrientInfo.name (via refFlat.name)
      xenTro7.refGene.name (via refFlat.name)
      xenTro7.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
dmap1NM_001005440KB021653-10081332610084624410081377510084490111100813326,100823031,100824439,100832352,100835094,100836740,100838196,100842230,100843497,100844799,100846211,100813835,100823318,100824512,100832424,100835280,100836908,100838355,100842426,100843589,100844909,100846244,
ube2kNM_001005662KB021649-1192776661192980771192790191192979667119277666,119280776,119282373,119284720,119285015,119288462,119297903,119279094,119280905,119282473,119284803,119285074,119288556,119298077,
unc119bNM_001016815KB021649-56075618560901845607839256090182756075618,56076926,56077458,56078868,56085850,56088779,56089959,56076878,56077429,56078505,56079041,56085956,56088890,56090184,
smg8NM_001078823KB021650-26602677266087062660291826608636526602677,26603847,26605843,26605877,26607114,26603116,26604729,26605876,26605990,26608706,
sin3bNM_001078821KB021649+11883484211885687511883726911885672920118834842,118837114,118840872,118841065,118841329,118841880,118842650,118842845,118843655,118845455,118846290,118846711,11884710 ...118834915,118837347,118840979,118841219,118841578,118842024,118842767,118842935,118843774,118845666,118846407,118846950,11884729 ...
smyd4NM_001078820KB021650+195210641953734319523564195370281119521064,19523549,19525324,19526868,19529630,19531630,19532246,19532476,19536383,19536668,19536883,19521248,19523698,19525469,19526958,19530627,19531813,19532398,19532609,19536500,19536792,19537343,
twist2NM_001103209KB021650+87808757878092468780875787809246187808757,87809246,
eftud2NM_001030366KB021662-187712291879287118771594187910292718771229,18772204,18772608,18772839,18773150,18773381,18774729,18775210,18775948,18776114,18776302,18777714,18778417,18779277,18 ...18771690,18772312,18772762,18772934,18773269,18773469,18774856,18775297,18776031,18776216,18776443,18777826,18778611,18779405,18 ...
ttc37NM_001127981KB021649+362141953626627236216811362661314136214195,36216804,36220038,36220857,36221487,36223199,36224654,36227178,36228833,36229071,36229397,36233837,36235363,36235675,36 ...36214335,36216901,36220182,36220949,36221563,36223340,36224753,36227287,36228974,36229173,36229537,36233924,36235467,36235802,36 ...
LOC100145162NM_001278435KB021649+513293875139362451330784513922345351329387,51330748,51336498,51337537,51338568,51339520,51340791,51341316,51341666,51343523,51343659,51344566,51345473,51346498,51 ...51329446,51332101,51336562,51337624,51338879,51339802,51340977,51341457,51341745,51343561,51343755,51344624,51345652,51346676,51 ...

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