Schema for xenoRefFlat
  Database: oryCun2    Primary Table: xenoRefFlat    Row Count: 345,704   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName OTUB1varchar(255) values Name of gene as it appears in genome browser.
name NM_001034719varchar(255) values Name of gene
chrom chr11varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 20499382int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 20500282int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 20499557int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 20500282int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 20499382,20499433,20499554,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 20499412,20499478,20499727,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)
      oryCun2.xenoMrna.qName (via xenoRefFlat.name)
      oryCun2.xenoRefGene.name (via xenoRefFlat.name)
      oryCun2.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
OTUB1NM_001034719chr11-20499382205002822049955720500282820499382,20499433,20499554,20499731,20499792,20499965,20500075,20500192,20499412,20499478,20499727,20499779,20499965,20500043,20500124,20500282,
ORNANAV1R3065NM_001253457chr9-868961887064118689618870641128689618,8706363,8689720,8706411,
PSME3IP1NM_001354086chrX-98699217987011099869937498700441998699217,98699296,98699358,98699532,98699569,98700299,98700334,98700420,98701055,98699247,98699320,98699460,98699545,98699705,98700334,98700419,98700490,98701109,
DAB1NM_001353985chr13+10942145210987289610955389610985412827109421452,109421655,109553756,109712564,109722354,109791078,109791797,109792351,109793826,109800664,109838594,109840806,10984940 ...109421515,109421680,109553963,109712704,109722453,109791210,109791917,109792390,109793892,109800724,109838657,109840915,10984995 ...
bccipNM_001140316chr15-80358149803589358035815280358935380358149,80358422,80358647,80358371,80358593,80358935,
SCN11ANM_014139chrUn0071+1034346115169410343911151214341034346,1034533,1037949,1039147,1072476,1073669,1074465,1079657,1088724,1089432,1090476,1094399,1094604,1095997,1099916,1100071, ...1034524,1034667,1038068,1039251,1072601,1073763,1074468,1079792,1088865,1089631,1090637,1094527,1094607,1096198,1100043,1100087, ...
SMARCAL1NM_014140chr7+15784948515791225815785169115791224219157849485,157851628,157852051,157852285,157853215,157857748,157860707,157865710,157870622,157872191,157875064,157885331,15788801 ...157849536,157851969,157852151,157852502,157853297,157857926,157860758,157865889,157870773,157872353,157875130,157885474,15788823 ...
IDH1NM_001195527chr7-1491342831491492131491342831491492138149134283,149135700,149136507,149139275,149140421,149142462,149146342,149149094,149134373,149135863,149136648,149139427,149140599,149142568,149146637,149149213,
FGF8NM_033164chr3+52655204526755525265520452675552352655204,52667539,52675381,52655270,52667638,52675552,
FGF8NM_033164chr18-49826404498298644982640449829864349826404,49829348,49829750,49826512,49829496,49829864,

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