Schema for xenoRefGene
  Database: criGriChoV1    Primary Table: xenoRefGene    Row Count: 463,610   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001085450varchar(255) values Name of gene (usually transcript_id from GTF)
chrom NW_003614216v1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 313587int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 369943int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 315602int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 341216int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 33int(10) unsigned range Number of exons
exonStarts 313587,313708,313768,313948...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 313641,313753,313910,314060...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Ctnnd1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-1,-1,-1,-1,-1,-1,-1,...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
        criGriChoV1.all_est.qName (via xenoRefGene.name)
      criGriChoV1.all_mrna.qName (via xenoRefGene.name)
      criGriChoV1.refGene.name (via xenoRefGene.name)
      criGriChoV1.refSeqAli.qName (via xenoRefGene.name)
      criGriChoV1.xenoRefFlat.name (via xenoRefGene.name)
      criGriChoV1.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_001085450NW_003614216v1-31358736994331560234121633313587,313708,313768,313948,314192,314515,314685,314756,314814,314850,315177,315302,315421,315582,316382,318148,321683,322325,32 ...313641,313753,313910,314060,314374,314617,314746,314805,314839,315135,315270,315390,315543,315612,316486,318211,321771,322440,32 ...0Ctnnd1cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,1,1,0,2,1,0,2,1,1,2,0,1,2,0,1,0,0,-1,-1,
585NM_003708NW_003614393v1-787660278765694787,880,2176,6266,847,955,2332,6602,0RDH16cmplincmpl2,2,2,0,
585NM_003708NW_003614393v1-88341526288381525068834,10366,10447,12102,13443,14947,9035,10398,10520,12363,13451,15262,0RDH16cmplcmpl1,1,2,2,0,0,
585NM_018156NW_003654420v1-2563902563901256,390,0VPS13Dincmplincmpl0,
585NM_018156NW_003617407v1-10891901010891422261089,4447,4639,6321,14125,18974,1209,4522,4833,6396,14293,19010,0VPS13Dcmplincmpl0,0,1,1,0,-1,
587NR_002989NW_003614504v1-3688573690353690353690351368857,369035,0SNORA81unkunk-1,
587NM_001300015NW_003614938v1-3763533783793763533783793376353,378068,378289,376488,378164,378379,0Alp9incmplincmpl0,0,0,
603NR_040566NW_003613671v1+247756424777082477708247770822477564,2477632,2477609,2477708,04930542D17Rikunkunk-1,-1,
594NM_001368389NW_003614050v1+129626812964241296424129642411296268,1296424,0Gfod2unkunk-1,
73NM_001368389NW_003614552v1-64269665598064509964940014642696,642801,643752,643832,643920,643964,644246,644403,644635,644680,644918,645088,649356,655634,642758,642905,643806,643863,643947,644021,644335,644550,644648,644860,645022,646000,649407,655980,0Gfod2cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,2,0,-1,

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