Schema for xenoRefFlat
  Database: caeRem2    Primary Table: xenoRefFlat    Row Count: 271,110   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName ZK355.2varchar(255) values Name of gene as it appears in genome browser.
name NM_061999varchar(255) values Name of gene
chrom chrUnvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 138394999int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 138397025int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 138397025int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 138397025int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 138394999,138396021,1383967...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 138395017,138396029,1383967...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        caeRem2.xenoMrna.qName (via xenoRefFlat.name)
      caeRem2.xenoRefGene.name (via xenoRefFlat.name)
      caeRem2.xenoRefSeqAli.qName (via xenoRefFlat.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
ZK355.2NM_061999chrUn-1383949991383970251383970251383970255138394999,138396021,138396756,138396872,138396992,138395017,138396029,138396767,138396889,138397025,
FlncNM_001081185chrUn-641651616417738064165161641773801064165161,64165684,64166005,64166704,64166800,64175022,64176199,64176538,64177105,64177317,64165365,64165786,64166191,64166725,64166851,64175035,64176313,64176622,64177150,64177380,
MRPS31P5NR_002816chrUn-1556726981556728311556728311556728311155672698,155672831,
VvlNM_001145913chrUn+16349799163503751634979916350375216349799,16350267,16349852,16350375,
VvlNM_001145913chrUn+62374506623762876237450662376287562374506,62374580,62375332,62375559,62376242,62374560,62374583,62375431,62375634,62376287,
Syt1NM_001145912chrUn+13974444139761581397444413976158513974444,13974753,13974948,13975433,13976098,13974684,13974867,13975066,13975570,13976158,
SrfNM_001145911chrUn-62442422624427346244242262442734262442422,62442626,62442575,62442734,
Supt16hNM_001107261chrUn+11497073114972711149707311497271111497073,11497271,
R05D7.8NR_050637chrUn+22025151220253532202535322025353122025151,22025353,
PkcdeltaNM_001144719chrUn+1403816941403820091403816941403820092140381694,140381805,140381769,140382009,

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