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Direct repeats in the flavivirus 3' untranslated region; a strategy for survival in the environment?

Gritsun, T. S.; Gould, E. A.. 2006 Direct repeats in the flavivirus 3' untranslated region; a strategy for survival in the environment? Virology, 358. 258-265. 10.1016/j.virol.2006.09.033

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Abstract/Summary

Previously, direct repeats (DRs) of 20–70 nucleotides were identified in the 3′ untranslated regions (3′UTR) of flavivirus sequences. To address their functional significance, we have manually generated a pan-flavivirus 3′UTR alignment and correlated it with the corresponding predicted RNA secondary structures. This approach revealed that intra-group-conserved DRs evolved from six long repeated sequences (LRSs) which, as 200-nucleotide domains were preserved only in the genomes of the slowly evolving tick-borne flaviviruses. We propose that short DRs represent the evolutionary remnants of LRSs rather than distinct molecular duplications. The relevance of DRs to virus replication enhancer function, and thus survival, is discussed.

Item Type: Publication - Article
Digital Object Identifier (DOI): 10.1016/j.virol.2006.09.033
Programmes: CEH Programmes pre-2009 publications > Biodiversity
CEH Sections: _ Molecular Virology & Parasitology
ISSN: 0042-6822
Additional Keywords: flaviviruses, alignment “by eye”, direct repeats, 3′UTR, promoter, enhancer
NORA Subject Terms: Biology and Microbiology
Ecology and Environment
Health
Date made live: 01 May 2008 09:36
URI: http://nora.nerc.ac.uk/id/eprint/2856

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