Schema for xenoRefGene
  Database: speTri2    Primary Table: xenoRefGene    Row Count: 446,239   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 106smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001082866varchar(255) values Name of gene (usually transcript_id from GTF)
chrom JH393281varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 35237325int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 35263531int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 35237337int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 35263531int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 35237325,35237434,35250351,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 35237400,35237437,35250546,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 tspan3bvarchar(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 0,0,0,0,0,0,0,2,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)
      speTri2.all_est.qName (via xenoRefGene.name)
      speTri2.all_mrna.qName (via xenoRefGene.name)
      speTri2.xenoRefFlat.name (via xenoRefGene.name)
      speTri2.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
106NM_001082866JH393281+35237325352635313523733735263531835237325,35237434,35250351,35250775,35252593,35256272,35256723,35263434,35237400,35237437,35250546,35250838,35252695,35256425,35256803,35263531,0tspan3bcmplcmpl0,0,0,0,0,0,0,2,
674NM_001201140JH393319+11684320117267391168432011726739511684320,11687743,11723200,11724012,11726661,11684434,11687866,11723275,11724141,11726739,0nup35incmplcmpl0,0,0,0,0,
586NM_001256453JH393771+1403901412871403901412871140390,141287,0COR52A16incmplincmpl0,
780NM_001197972JH393286-25645428256455092564542825645509125645428,25645509,0RING1Bincmplincmpl0,
656NR_024320JH393340-940979894128289412828941282839409798,9409943,9412675,9409882,9410058,9412828,0LITAFunkunk-1,-1,-1,
9NM_001371531JH393369-2860195319474928640413194743152860195,2864041,2874577,2889850,2890165,2890540,2891062,2891221,2891446,2891788,3038298,3073780,3111062,3115925,3194698,2860288,2864119,2874760,2890033,2890201,2890762,2891131,2891431,2891581,2891905,3038316,3073897,3111068,3116048,3194749,0palm2cmplincmpl-1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,
602NM_001253542JH393474+233407923342832334079233428312334079,2334283,0ORNANAV1R3150incmplincmpl0,
604NM_001253542JH393481+254646525465882546465254658812546465,2546588,0ORNANAV1R3150incmplincmpl2,
73NM_001253542JH393711+9013041052190130410521290130,410473,90203,410521,0ORNANAV1R3150incmplincmpl1,2,
621NM_001105118JH393340+480402848063724804064480637234804028,4804635,4806291,4804115,4804722,4806372,0ubn1cmplincmpl0,0,0,

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