Schema for xenoRefGene
  Database: droVir2    Primary Table: xenoRefGene    Row Count: 277,208   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 673smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001080624varchar(255) values Name of gene (usually transcript_id from GTF)
chrom scaffold_12875varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 11621015int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 11621183int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 11621015int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 11621183int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 11621015,11621147,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 11621117,11621183,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 sacm1lbvarchar(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 0,0,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
        droVir2.all_est.qName (via xenoRefGene.name)
      droVir2.all_mrna.qName (via xenoRefGene.name)
      droVir2.xenoMrna.qName (via xenoRefGene.name)
      droVir2.xenoRefFlat.name (via xenoRefGene.name)
      droVir2.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
673NM_001080624scaffold_12875+11621015116211831162101511621183211621015,11621147,11621117,11621183,0sacm1lbincmplincmpl0,0,
585NR_003280scaffold_10001+1492312312311149,231,0Rs5-8s1unkunk-1,
588NM_001009815scaffold_12823+4097614100224097614100221409761,410022,0TGIF1incmplincmpl0,
585NR_045133scaffold_10001+1492312312311149,231,0Rn5-8sunkunk-1,
585NR_076642scaffold_10001+7101078107810782710,1036,785,1078,0unkunk-1,-1,
585NR_076255scaffold_10001+7401078107810782740,1036,785,1078,0unkunk-1,-1,
585NR_076561scaffold_10001+7401078107810782740,1036,788,1078,0unkunk-1,-1,
585NR_076641scaffold_10001+7401078107810782740,1036,785,1078,0unkunk-1,-1,
585NR_076986scaffold_10001+7401078107810782740,1036,785,1078,0unkunk-1,-1,
585NR_103992scaffold_10001+7401078107810782740,1036,788,1078,0unkunk-1,-1,

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