Schema for Vega Genes - Vega Annotations
  Database: hg19    Primary Table: vegaGene    Row Count: 103,437   Data last updated: 2010-08-25
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 OTTHUMT00000002840varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 29553int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 31097int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 31097int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 31097int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 29553,30563,30975,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 30039,30667,31097,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 RP11-34P13.3varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -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
        hg19.vegaGtp.transcript (via vegaGene.name)
      hg19.vegaPep.name (via vegaGene.name)
      hg19.vegaPseudoGene.name (via vegaGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585OTTHUMT00000002840chr1+29553310973109731097329553,30563,30975,30039,30667,31097,0RP11-34P13.3nonenone-1,-1,-1,
585OTTHUMT00000002841chr1+30266311093110931109230266,30975,30667,31109,0RP11-34P13.3nonenone-1,-1,
585OTTHUMT00000002842chr1-34553360813513735736334553,35276,35720,35174,35481,36081,0FAM138Acmplcmpl2,1,0,
585OTTHUMT00000002843chr1-35244360733607336073235244,35720,35481,36073,0FAM138Anonenone-1,-1,
585OTTHUMT00000003223chr1+69090700086909070008169090,70008,0OR4F5cmplcmpl0,
585OTTHUMT00000003225chr1-89294120932120932120932489294,92090,112699,120774,91629,92240,112804,120932,0RP11-34P13.7nonenone-1,-1,-1,-1,
585OTTHUMT00000003226chr1-89550911059110591105289550,90286,90050,91105,0RP11-34P13.8nonenone-1,-1,
585OTTHUMT00000003688chr1-92229129217129217129217492229,112699,120720,129054,92240,112804,120932,129217,0RP11-34P13.7nonenone-1,-1,-1,-1,
585OTTHUMT00000003687chr1-1109521291731291731291733110952,112699,129054,111357,112804,129173,0RP11-34P13.7nonenone-1,-1,-1,
73OTTHUMT00000003689chr1-1290801335661335661335662129080,133373,129223,133566,0RP11-34P13.7nonenone-1,-1,

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

Vega Genes (vegaGeneComposite) Track Description
 

Description and Methods

This track shows gene annotations from the Vertebrate Genome Annotation (Vega) database. Annotations are divided into two subtracks from the Vega Human Genome Annotation project:

  • Vega Protein-Coding and Non-Coding Gene Annotations
  • Vega Annotated Pseudogenes and Immunoglobulin Segments

The following information is an excerpt from the Vertebrate Genome Annotation home page:

"The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidence only."

"In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery."

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. Transcript type (and other details) may be found by clicking on the transcript identifier which forms the outside link to the Vega transcript details page. Further information on the gene and transcript classification may be found here.

Credits

Thanks to Steve Trevanion at the Wellcome Trust Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega acknowledgements and publications are listed here.