title: Conserved RNA secondary structures in Picornaviridae genomes.
abstract: 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 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry site (IRES) region towards 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: (i) that only smaller sections of the IRES region than previously reported are conserved at single base-pair resolution and (ii) that there is a number of significant structural elements in the coding region. Furthermore, we identify potential cis-acting replication elements in four genera where this feature has not been reported so far.
authors.affiliation: Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstrasse 17, A-1090 Wien, Austria.
authors.forename: C
authors.initials: C
authors.lastname: Witwer
authors.forename: S
authors.initials: S
authors.lastname: Rauscher
authors.forename: I L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: P F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D020121:5' Untranslated Regions / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010849:Picornaviridae / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral