Schema for xenoRefFlat
  Database: papHam1    Primary Table: xenoRefFlat    Row Count: 635,835   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName HENMT1varchar(255) Name of gene as it appears in genome browser.
name NM_144584varchar(255) Name of gene
chrom scaffold20722varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 19704int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 35085int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 19994int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 33738int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned Number of exons
exonStarts 19704,21603,22415,28580,294...longblob Exon start positions (or end positions for minus strand item)
exonEnds 20420,21781,22595,28715,295...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)
      papHam1.xenoRefGene.name (via xenoRefFlat.name)
      papHam1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
HENMT1NM_144584scaffold20722-19704350851999433738819704,21603,22415,28580,29454,31321,33717,34739,20420,21781,22595,28715,29567,31450,33816,35085,
VAMP4NM_001244707scaffold3142+158775052919612499371215877,16010,19612,27025,34812,43307,44373,48032,49908,50305,50396,50449,15996,16039,19678,27072,34863,43408,44453,48084,50287,50344,50435,50529,
CRABP1NM_001128492scaffold10196-59380684045946368404459380,64631,67607,68334,59514,64745,67786,68404,
CXCL11NM_001128491scaffold4924+78788797267878879726378788,79419,79657,78835,79555,79726,
SH3KBP1NM_001128500scaffold10053+22864376272286436616722864,26934,30847,35261,36574,37102,37351,22975,27063,31116,35325,37070,37311,37627,
MGAT4BNM_001266822scaffold7426+818639084981918904241581863,86498,86773,87001,87516,87870,88206,88377,88806,89135,89324,89850,90008,90191,90400,82015,86684,86914,87135,87563,87984,88282,88492,88937,89243,89518,89929,90096,90304,90849,
GPR85NM_001266820scaffold1298-29041332453070331816229041,33081,31986,33245,
PRELPNM_001266819scaffold8890-20642330702086824536320642,23563,32930,21044,24552,33070,
ADNPNM_001266818Contig613624+5878938938932587,842,686,893,
LINC00623NR_109754Contig458615+017261726172650,524,561,678,964,21,546,627,943,1726,

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