Schema for xenoRefGene
  Database: galVar1    Primary Table: xenoRefGene    Row Count: 568,133   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 587smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001091497varchar(255) Name of gene (usually transcript_id from GTF)
chrom NW_007726394v1varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 289634int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 291047int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 289634int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 291032int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned Number of exons
exonStarts 289634,290307,290377,290691...longblob Exon start positions (or end positions for minus strand item)
exonEnds 289715,290367,290380,290817...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 anapc15.Svarchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,0,longblob Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        galVar1.xenoRefFlat.name (via xenoRefGene.name)
      galVar1.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
587NM_001091497NW_007726394v1+2896342910472896342910325289634,290307,290377,290691,290987,289715,290367,290380,290817,291047,0anapc15.Scmplcmpl0,0,0,0,0,
585NR_073064NW_007748720v1-654866716671667116548,6671,0EXOC2unkunk-1,
73NM_001082442NW_007727671v1+22012427699722017227601912220124,228450,238215,240952,243813,248598,254331,255069,261289,275851,276716,276943,220248,228534,238449,241280,243884,248735,254410,255146,261409,276209,276917,276997,0ATG4Ccmplcmpl0,1,1,1,2,1,0,1,0,0,-1,-1,
585NM_001135109NW_007730876v1+209462604320946213923020946,22015,22238,22295,22593,22648,22832,22925,23068,23234,23274,23306,23895,23968,24202,24255,24314,24415,24628,24802,24909,25 ...21997,22211,22286,22479,22611,22821,22911,23058,23113,23255,23295,23349,23940,24186,24218,24285,24387,24520,24768,24893,24948,25 ...0RIC3incmplcmpl1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
591NM_001165932NW_007726291v1+8896489024888896489024832889648,902385,889746,902488,0Ucmaincmplcmpl2,1,
585NM_001166031NW_007727818v1-516974295169742925169,7304,5720,7429,0Mrps2incmplincmpl2,0,
585NM_194069NW_007730348v1-189630211896302131896,1971,2931,1953,1975,3021,0Ifi27incmplincmpl0,2,2,
585NM_194069NW_007742797v1+706972167069721627069,7195,7180,7216,0Ifi27incmplincmpl0,2,
585NM_194068NW_007730348v1-189630211896302131896,1971,2931,1953,1975,3021,0Ifi27incmplincmpl0,2,2,
585NM_194068NW_007742797v1+706972167069721627069,7195,7180,7216,0Ifi27incmplincmpl0,2,

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