Schema for refFlat
  Database: rheMac3    Primary Table: refFlat    Row Count: 6,662   Data last updated: 2020-08-23
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName COX7A1varchar(255) values Name of gene as it appears in genome browser.
name NM_001040278varchar(255) values Name of gene
chrom chr19varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 42758975int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 42760566int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 42759037int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 42760476int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 42758975,42759510,42759715,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 42759090,42759595,42759802,...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)
      rheMac3.mrnaOrientInfo.name (via refFlat.name)
      rheMac3.refGene.name (via refFlat.name)
      rheMac3.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
COX7A1NM_001040278chr19-42758975427605664275903742760476442758975,42759510,42759715,42760461,42759090,42759595,42759802,42760566,
DAPK1NM_001257788chr15+969476229715888696947731971576082596947622,97053287,97086475,97088286,97088582,97088721,97089235,97089740,97090886,97092634,97095180,97095744,97096586,97098044,97 ...96947793,97053509,97086614,97088416,97088631,97088748,97089388,97089786,97090976,97092727,97095300,97095843,97096685,97098143,97 ...
CA12NM_001257824chr7-413568214141645241358365414164191141356821,41356888,41359228,41372047,41373512,41373945,41375200,41379242,41380295,41410520,41416334,41356857,41358438,41359313,41372174,41373670,41374009,41375296,41379385,41380475,41410541,41416452,
DDX5NM_001258162chr16-620549086206276862056575620626621362054908,62057202,62058663,62058811,62059085,62059551,62059810,62060052,62060430,62060607,62060849,62061301,62062629,62056979,62057427,62058723,62058873,62059196,62059724,62059971,62060194,62060496,62060741,62060946,62061468,62062768,
SMARCD3NM_001260684chr3-19018919519019883919018930019019875313190189195,190189595,190189823,190190310,190190624,190191682,190192067,190192327,190192673,190192913,190193855,190195656,19019867 ...190189354,190189697,190189946,190190446,190190722,190191844,190192169,190192423,190192796,190193036,190193898,190195868,19019883 ...
PDE4BNM_001265964chr1+693825716974874569382773697468281569382571,69619450,69629967,69630113,69638371,69706590,69729356,69735628,69737170,69737408,69739653,69741686,69741932,69742778,69 ...69383009,69619645,69630004,69630184,69638421,69706703,69729450,69735807,69737269,69737573,69739753,69741841,69742055,69742961,69 ...
PSKH1NM_001265966chr20+66208862662490666622667566247010366208862,66226605,66246692,66208948,66227632,66249066,
SLC1A3NM_001266066chr6+368778063696232636879652369603271036877806,36879557,36902679,36944739,36947771,36950613,36953326,36954094,36957921,36960122,36877939,36879833,36902817,36944944,36947814,36950906,36953560,36954289,36958056,36962326,
CXXC1NM_001266065chr18-443501094435548044350352443553091544350109,44350613,44351025,44351263,44351452,44351641,44352122,44352464,44352746,44353069,44353491,44353764,44354285,44354486,44 ...44350499,44350766,44351122,44351313,44351563,44351849,44352307,44352584,44352992,44353096,44353671,44354000,44354386,44354605,44 ...
MAMDC2NM_001265965chr15+797118367988147679712004798811051479711836,79712384,79775050,79776589,79779958,79793065,79798348,79806143,79809634,79835044,79836824,79868114,79880825,79881040,79712038,79712498,79775322,79776674,79780096,79793322,79798442,79806287,79809900,79835138,79836977,79868374,79880910,79881476,

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