Schema for xenoRefGene
  Database: droMoj1    Primary Table: xenoRefGene    Row Count: 336,922   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001256171varchar(255) values Name of gene (usually transcript_id from GTF)
chrom contig_5874varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 24451int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 24658int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 24451int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 24658int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 24451,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 24658,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ZNF85varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 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
        droMoj1.all_mrna.qName (via xenoRefGene.name)
      droMoj1.xenoMrna.qName (via xenoRefGene.name)
      droMoj1.xenoRefFlat.name (via xenoRefGene.name)
      droMoj1.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
585NM_001256171contig_5874-24451246582445124658124451,24658,0ZNF85incmplincmpl0,
585NR_164948contig_12477-2443453453452244,303,286,345,0unkunk-1,-1,
585NR_164949contig_12477-2443453453452244,303,286,345,0unkunk-1,-1,
585NR_136715contig_2393-176041924192419251760,1971,2163,2405,4123,1904,2101,2340,2497,4192,0PANK2unkunk-1,-1,-1,-1,-1,
586NM_001310177contig_1804+1421591440911421591440915142159,142291,142657,143668,144043,142246,142609,143272,143827,144091,0LOC101669961incmplincmpl0,0,0,0,0,
585NM_001321354contig_3935-643893126438931296438,7637,7766,8153,8288,8342,8848,9064,9232,7059,7748,8099,8255,8303,8444,9037,9187,9312,0LOC100381789incmplincmpl0,0,0,0,0,0,0,0,1,
585NM_001321351contig_5874-24499246342449924634124499,24634,0ZNF529incmplincmpl0,
585NM_001321362contig_2433+201640812016408142016,2307,2658,4066,2286,2547,2724,4081,0NRBP1incmplincmpl0,0,0,0,
585NM_001321361contig_2433+201640812016408142016,2307,2622,4066,2286,2538,2724,4081,0NRBP1incmplincmpl0,0,0,0,
585NM_001321359contig_2433+201640812016408142016,2307,2622,4066,2286,2538,2724,4081,0NRBP1incmplincmpl0,0,0,0,

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