Schema for refFlat
  Database: cavPor3    Primary Table: refFlat    Row Count: 491   Data last updated: 2020-08-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName Cxcr2varchar(255) values Name of gene as it appears in genome browser.
name NM_001172875varchar(255) values Name of gene
chrom scaffold_153varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 309974int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 311033int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 309974int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 311033int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 309974,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 311033,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      cavPor3.mrnaOrientInfo.name (via refFlat.name)
      cavPor3.refGene.name (via refFlat.name)
      cavPor3.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
Cxcr2NM_001172875scaffold_153-3099743110333099743110331309974,311033,
Hrh3NM_001172737scaffold_119+183009218324671830092183246621830092,1831548,1830260,1832467,
Hsd11b1NM_001172857scaffold_13+14260174142812601426022114281141614260174,14261082,14261621,14261862,14279315,14280899,14260309,14261213,14261733,14262048,14279459,14281260,
Tnnt2NM_001172868scaffold_12+210625022107401021062502210740101321062502,21063381,21068145,21068873,21069906,21070121,21070979,21071568,21072302,21072826,21073212,21073562,21073964,21062520,21063392,21068181,21068907,21069967,21070238,21071057,21071679,21072308,21072939,21073303,21073603,21074010,
LOC100379225NM_001173099scaffold_117-31202642339431204442335518312026,325103,325605,333989,340556,349326,350378,355926,358434,368125,376836,417544,418484,419460,419810,421327,422358,423300,312096,325154,325783,334101,340640,349549,350469,356125,358530,368324,376974,417610,418662,419537,419889,421383,422438,423394,
Pex5NM_001172998scaffold_107-10272811213010278511213011102728,103164,103613,104059,104600,104832,110135,110603,110950,111439,112021,102987,103322,103779,104272,104671,104976,110255,110696,111061,111530,112130,
GapdhNM_001172951scaffold_107-69163269583869182369560012691632,692003,692186,692358,692516,692769,692926,693118,693294,693479,695577,695799,691893,692101,692270,692437,692668,692851,693042,693209,693401,693579,695617,695838,
Gabarapl1NM_001172950scaffold_28-435666143651254357915436481344356661,4359283,4360446,4364723,4357981,4359402,4360525,4365125,
Scnn1bNM_001173063scaffold_4+397800373980225539780037398022551339780037,39782102,39784127,39791710,39793781,39794251,39796786,39796858,39797951,39798123,39800272,39801575,39801875,39780348,39782379,39784318,39791814,39793945,39794359,39796858,39796903,39798027,39798181,39800334,39801651,39802255,
NrlNM_001173050scaffold_13+16749197167526011675078916752263316749197,16750762,16751930,16749304,16751170,16752601,

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