ArticleNucleic acids research2005
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Transposable Elements Drive Regulatory and Functional Innovation of F-box Genes.Molecular biology and evolution · 2025Article
- Retention of duplicated genes in evolution.Trends in genetics : TIG · 2022Review
- Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots.BioMed research international · 2016Article
- Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!Nucleic acids research · 2014Article
- Constraint and opportunity in genome innovation.RNA biology · 2014Review
- Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins.The Journal of biological chemistry · 2013Article
- Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective.Molecular biology and evolution · 2013Article
- Turning gold into 'junk': transposable elements utilize central proteins of cellular networks.Nucleic acids research · 2013Article
- Somatic transposition in the brain has the potential to influence the biosynthesis of metabolites involved in Parkinson's disease and schizophrenia.Biology direct · 2012Article
- A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana.PLoS genetics · 2012Article
- Genetic innovation in vertebrates: gypsy integrase genes and other genes derived from transposable elements.International journal of evolutionary biology · 2012Article
- Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomes.BMC genomics · 2009Article
- Transposable elements and the evolution of regulatory networks.Nature reviews. Genetics · 2008Review
- Transposable elements as drivers of genomic and biological diversity in vertebrates.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2008Review
- Evaluating the protein coding potential of exonized transposable element sequences.Biology direct · 2007Article
- Automated recognition of retroviral sequences in genomic data--RetroTector.Nucleic acids research · 2007Article
- DNA transposons and the evolution of eukaryotic genomes.Annual review of genetics · 2007Review
- Birth of a chimeric primate gene by capture of the transposase gene from a mobile element.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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