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Nucleic Acids Research 2005 33(3):946-954; doi:10.1093/nar/gki236
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Published online 16 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes

Evgeny M. Zdobnov1, Mónica Campillos1, Eoghan D. Harrington1, David Torrents1 and Peer Bork1,2,*

1 EMBL Meyerhofstrasse 1, 69117 Heidelberg, Germany 2 MDC Berlin-Buch Robert-Roessle-Strasse 10, Germany

*To whom correspondence should be addressed at EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany. Tel: +49 6221 387 526; Fax: +49 6221 387 517; Email: bork{at}embl.de

Received September 21, 2004. Revised November 29, 2004. Accepted January 20, 2005.

We suggest an annotation strategy for genes encoded by retroviruses and transposable elements (RETRA genes) based on a set of marker protein domains. Usually RETRA genes are masked in vertebrate genomes prior to the application of automated gene prediction pipelines under the assumption that they provide no selective advantage to the host. Yet, we show that about 1000 genes in four vertebrate gene sets analyzed contain at least one RETRA gene marker domain. Using the conservation of genomic neighborhood (synteny), we were able to discriminate between RETRA genes with putative functionality in the vertebrates and those that probably function only in the context of mobile elements. We identified 35 such genes in human, along with their corresponding mouse and rat orthologs; which included almost all known human genes with similarity to mobile elements. The results also imply that the vast majority of the remaining RETRA genes in current gene sets are unlikely to encode vertebrate functions. To automatically annotate RETRA genes in other vertebrate genomes, we provide as a tool a set of marker protein domains and a manually refined list of domesticated or ancestral RETRA genes for rescuing genes with vertebrate functions.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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