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Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria
Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria
Author to whom correspondence should be addressed.
Viruses 2019, 11(3), 298;
Received: 1 March 2019 / Revised: 19 March 2019 / Accepted: 20 March 2019 / Published: 24 March 2019
(This article belongs to the Special Issue Virus Bioinformatics)
PDF [745 KB, uploaded 24 March 2019]


Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3 UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs. View Full-Text
Keywords: flavivirus; non-coding RNA; secondary structure flavivirus; non-coding RNA; secondary structure

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

  • Externally hosted supplementary file 1
    Description: Supporting data for Ochsenreiter et al. (2019), including xrRNA covariance models, seed alignments and xrRNA coordinates

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Ochsenreiter, R.; Hofacker, I.L.; Wolfinger, M.T. Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses. Viruses 2019, 11, 298.

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