Preprint 01-08-040

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Conserved RNA Secondary Structures in Picornaviridae Genomes

Christina Witwer, Susanne Rauscher, Ivo L. Hofacker, Peter F. Stadler.

The family Picornaviridae contains important pathogens including, for example, Hepatitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200 to 8500nts. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an IRES region toward the 5'end.
This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family Picornaviridae. Compared with previous studies we find: (1) that only smaller sections of the IRES region than previously reported are conserved at single-base-pair resolution, and (2) that there is a number of significant structural elements in the coding region. Furthermore we identify potential CREs in four genera where this feature has not been reported so far.

Picornaviridae, RNA secondary structure, IRES, CRE

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