Schema for xenoRefGene
  Database: loxAfr3    Primary Table: xenoRefGene    Row Count: 359,460   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 920smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_149025varchar(255) values Name of gene (usually transcript_id from GTF)
chrom scaffold_12varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 43973634int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 43974367int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 43974367int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 43974367int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 43973634,43973822,43973894,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 43973706,43973882,43974036,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LOC100130207varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -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
        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)
      loxAfr3.all_mrna.qName (via xenoRefGene.name)
      loxAfr3.refGene.name (via xenoRefGene.name)
      loxAfr3.refSeqAli.qName (via xenoRefGene.name)
      loxAfr3.xenoMrna.qName (via xenoRefGene.name)
      loxAfr3.xenoRefFlat.name (via xenoRefGene.name)
      loxAfr3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
920NR_149025scaffold_12+43973634439743674397436743974367643973634,43973822,43973894,43974124,43974246,43974325,43973706,43973882,43974036,43974231,43974279,43974367,0LOC100130207unkunk-1,-1,-1,-1,-1,-1,
890NM_001044902scaffold_21-40096586401056704009658640105670540096586,40097586,40104106,40104691,40105631,40096710,40097676,40104229,40104832,40105670,0wee2incmplincmpl2,0,0,0,0,
74NM_001044902scaffold_83-157054315796741570543157967451570543,1571423,1572406,1578264,1579536,1570669,1571510,1572496,1578381,1579674,0wee2incmplincmpl0,0,0,0,0,
1168NM_001192084scaffold_9-764465597653971776446798765164571776446559,76446606,76446792,76449435,76449903,76452546,76452699,76454429,76457081,76459608,76460363,76460504,76462252,76465444,76 ...76446597,76446706,76446836,76449497,76449966,76452609,76452768,76454479,76457142,76459730,76460460,76460567,76462273,76465510,76 ...0EVLincmplcmpl-1,-1,1,2,2,2,2,0,2,0,2,0,2,2,0,2,-1,
73NM_001360951scaffold_94-47638279580479892795802147638,47716,47968,47989,48263,48989,102383,102754,134423,134462,134714,134882,161969,162232,179483,179528,180032,206954,259724,2 ...47692,47764,47986,48095,48355,49025,102469,102799,134431,134516,134774,135009,162081,162284,179505,179585,180074,207368,259784,2 ...0Gm21814incmplincmpl-1,-1,-1,2,0,2,0,0,1,0,0,2,1,0,2,0,0,0,0,1,2,
756NM_001099738scaffold_13+22476129224770352247612922477035322476129,22476381,22476573,22476378,22476543,22477035,0Dnajc28incmplincmpl0,0,0,
75NM_001107227scaffold_18+2990811306716929908113065911172990811,3004161,3006788,3008858,3017099,3021154,3021713,3022031,3051966,3052018,3052025,3053157,3056931,3065050,3065779,3066904, ...2990952,3004299,3006991,3008949,3017202,3021575,3021955,3022110,3052017,3052024,3052050,3053274,3057036,3065154,3065911,3067011, ...0Zfyve28incmplcmpl0,0,0,2,1,2,0,0,0,0,0,1,1,1,0,-1,-1,
77NM_001110823scaffold_84+5075627512514550761695124315275075627,5075844,5075992,5076065,5076944,5077046,5084698,5088407,5104733,5106371,5107608,5111264,5111825,5112911,5117580,5117798, ...5075724,5075865,5076046,5076208,5076963,5077129,5084803,5088546,5104814,5106457,5108073,5111355,5111924,5113043,5117703,5118017, ...0Atp2a2cmplcmpl-1,-1,-1,0,0,1,0,0,1,1,0,0,0,0,0,0,0,0,2,1,0,2,2,0,-1,-1,-1,
1139NM_001109850scaffold_5+72631940726321237263194072632123172631940,72632123,0zgc:173915incmplincmpl0,
821NM_001109850scaffold_6+31053227310550833105322731055083231053227,31055023,31053281,31055083,0zgc:173915incmplincmpl0,0,

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