Schema for xenoRefFlat
  Database: oreNil2    Primary Table: xenoRefFlat    Row Count: 461,652   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName HNRNPH1varchar(255) values Name of gene as it appears in genome browser.
name NM_001364240varchar(255) values Name of gene
chrom chrLG2varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 22322395int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 22325892int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 22322395int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 22325892int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 22322395,22322552,22322821,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 22322468,22322707,22322945,...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)
      oreNil2.xenoRefGene.name (via xenoRefFlat.name)
      oreNil2.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
HNRNPH1NM_001364240chrLG2+22322395223258922232239522325892822322395,22322552,22322821,22324065,22324991,22325349,22325577,22325802,22322468,22322707,22322945,22324204,22325172,22325463,22325712,22325892,
HNRNPH1NM_001364239chrLG2+22322395223258922232239522325892822322395,22322552,22322821,22324065,22324991,22325346,22325577,22325799,22322468,22322707,22322945,22324204,22325172,22325463,22325712,22325892,
Dclk3NM_001191800chrLG6-963522796359749635227963597449635227,9635601,9635821,9635947,9635303,9635705,9635860,9635974,
diras2NM_001173657GL831251-1-124140512427651241405124276541241405,1241553,1241935,1242627,1241523,1241631,1242109,1242765,
GLIS2NM_001318918GL831359-1-3648613689513648613689513364861,368038,368816,365055,368162,368951,
H2ac21NM_001111341GL831231-1+133270913330721332709133307211332709,1333072,
Pcbp2NM_001013223chrLG5+342345773424135834234620342413581334234577,34234620,34235916,34236033,34236100,34236197,34236410,34236658,34237045,34238447,34239657,34240210,34241157,34234592,34234689,34235940,34236066,34236103,34236311,34236542,34236787,34237123,34238477,34239726,34240264,34241358,
PKDNM_001275775chrLG19-164789261648916016478926164891601216478926,16479425,16479770,16480700,16480891,16480967,16481162,16485612,16485868,16487271,16488463,16489060,16479022,16479680,16479872,16480853,16480895,16481059,16481222,16485657,16485988,16487367,16488516,16489160,
ACVR2ANM_205367GL831181-1+2592423266331925924292663319122592423,2624759,2635396,2637992,2654379,2656671,2660897,2661152,2662385,2662618,2662790,2663124,2592484,2624968,2635544,2638000,2654520,2656815,2661043,2661267,2662524,2662746,2662793,2663319,
SLC43A3NM_001278206chrLG6-31611232316137493161123231613749531611232,31611427,31612619,31613572,31613659,31611286,31611556,31612758,31613574,31613749,

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