Journal
VIROLOGY
Volume 358, Issue 2, Pages 258-265Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.virol.2006.09.033
Keywords
flaviviruses; alignment by eye; direct repeats; 3'UTR; promoter; enhancer
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Funding
- Natural Environment Research Council [CEH010021] Funding Source: researchfish
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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 similar to 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. (c) 2006 Elsevier Inc. All rights reserved.
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