Schema for xenoRefFlat
  Database: ochPri2    Primary Table: xenoRefFlat    Row Count: 666,260   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName DZANK1varchar(255) Name of gene as it appears in genome browser.
name NM_001076838varchar(255) Name of gene
chrom scaffold_1739varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 77091int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 112596int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 77091int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 112587int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 15int(10) unsigned Number of exons
exonStarts 77091,77573,80540,82104,836...longblob Exon start positions (or end positions for minus strand item)
exonEnds 77206,77648,80668,82191,837...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)
      ochPri2.xenoRefGene.name (via xenoRefFlat.name)
      ochPri2.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
DZANK1NM_001076838scaffold_1739-77091112596770911125871577091,77573,80540,82104,83688,84740,86876,89675,95704,96988,98410,101692,107422,108730,112478,77206,77648,80668,82191,83785,84815,86980,89883,95770,97102,98528,101775,107480,108884,112596,
chd4.LNM_001087035scaffold_1100-211994191421199419143521199,21484,21530,23840,24061,24243,24414,29658,29725,29791,30023,30550,34201,34444,34666,34694,35143,35412,35444,35831,36155,36 ...21234,21524,21590,23962,24148,24330,24592,29661,29791,29895,30264,30675,34319,34576,34693,34809,35316,35415,35564,35969,36356,36 ...
Olfr1432NM_001011788scaffold_3655-1154861162481154861162483115486,115948,116197,115594,116059,116248,
CRIP2NR_073082scaffold_156732+5818128128122581,752,677,812,
PALM2AKAP2NM_007203scaffold_8+7594511070266759704104491914759451,759659,852610,878553,884840,1044672,1068849,1069028,1069186,1069325,1069482,1069507,1069711,1070095,759590,759754,852743,878656,884962,1044919,1068906,1069049,1069204,1069446,1069496,1069515,1070052,1070266,
SEC63NM_007214scaffold_52427-162157721621577261621,1665,3513,3589,5462,5677,1665,1769,3585,3637,5596,5772,
SEC63NM_007214scaffold_68665-748418374841833748,4072,4127,906,4127,4183,
SEC63NM_007214scaffold_91391-415643304156428114156,4330,
PRAF2NM_007213scaffold_2327-537365706103656755373,6102,6162,6350,6369,5409,6133,6336,6359,6570,
RNF2NM_007212scaffold_5595+55811559015581455901155811,55901,

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