Description and Methods

This track shows pseudogene annotations from the Vertebrate Genome Annotation (Vega) database.

The following information is excerpted 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."

NOTE: VEGA annotations do not appear on every chromosome in this assembly.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks using the following color scheme to indicate the status of the gene annotation:

• Known (Dark blue): genes that are identical to known human complementary DNA or protein sequences and have an entry in the species-specific model organism database.
• Novel (Dark blue): genes that have an open reading frame (ORF) and are identical or homologous to human cDNAs, human ESTs, or proteins in all species. Novel transcripts are genes that fit the criteria of novel genes with the exception that an unambiguous ORF cannot be assigned.
• Putative (Medium blue): genes whose sequences are identical or homologous to human ESTs but do not contain an ORF.
• Predicted (Light blue): genes based on ab initio prediction and for which at least one exon is supported by biological data (unspliced ESTs, protein sequence similarity with mouse or tetraodon genomes, or expression data from Rosetta).
• Unclassified (Gray).

The details pages show the only the Vega gene type and not the transcript type. A single gene can have more than one transcript which can belong to different classes, so the gene as a whole is classified according to the transcript with the "highest" level of classification. 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 Searle at the Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega gene annotations are generated by manual annotation from the following groups:

Chromosome 6: The HAVANA group, Wellcome Trust Sanger Institute
Relevant publication: Mungall AJ et al., The DNA sequence and analysis of human chromosome 6. Nature. 2003 Oct 23;425:805-11.

Chromosome 7: Hillier et al., The Genome Institute at Washington University
Relevant publication: Hillier LW et al., The DNA sequence of human chromosome 7. Nature. 2003 Jul 10;424:157-64.

Chromosome 9: The HAVANA group, Wellcome Trust Sanger Institute
Relevant publication: Humphray SJ et al., The DNA sequence and analysis of human chromosome 9. Nature. 2004 May 27;429;369-74.

Chromosome 10: The HAVANA group, Wellcome Trust Sanger Institute
Relevant publication: Deloukas P et al., The DNA sequence and comparative analysis of human chromosome 10. Nature. 2004 May 27;429:375-81.

Chromosome 13: The HAVANA group, Wellcome Trust Sanger Institute
Relevant publication: Dunham A et al., The DNA sequence and analysis of human chromosome 13. Nature. 2001 Apr 1;428:522-8.

Chromosome 14: Genoscope
Relevant publication: Heilig R et al., The DNA sequence and analysis of human chromosome 14. Nature. 2003 Feb 6;421:601-7.

Chromosome 20: The HAVANA Group, Wellcome Trust Sanger Institute
Relevant publication: Deloukas P et al., The DNA sequence and comparative analysis of human chromosome 20. Nature. 2001 Dec 20;414:865-71.

Chromosome 22: Chromosome 22 Group, Wellcome Trust Sanger Institute
Relevant publications:
— Collins JE et al., Reevaluating Human Gene Annotation: A Second-Generation Analysis of Chromosome 22. Genome Research. 2003 Jan;13(1):27-36.
— Dawson E et al., A first-generation linkage disequilibrium map of human chromosome 22. Nature. 2002 Aug 1;418:544-8.
— Dunham I, et al., The DNA sequence of human chromosome 22. Nature. 1999 Dec 2;402:489-95.

Chromosome X: The HAVANA Group, Wellcome Trust Sanger Institute
Relevant publication: Ross MT et al., The DNA sequence and comparative analysis of human chromosome X. Nature 2005 Mar 17;434:325-37.