title: Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses.
abstract: The plant-infecting members of the genus Fijivirus (family Reoviridae) have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these - namely segment 5 - contains a second long ORF (approximately 200+ codons) that overlaps the 3' end of the major ORF (approximately 920-940 codons) in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed.
authors.affiliation: BioSciences Institute, University College Cork, Cork, Ireland. A.Firth@ucc.ie
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
mesh_terms: D001483:Base Sequence; D003062:Codon / Q000235:genetics; D005807:Genes, Overlapping / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D010944:Plants / Q000821:virology*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D012087:Reoviridae / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D003062:Codon; D012367:RNA, Viral