title: A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product.
abstract: The genus Torovirus (order Nidovirales) includes a number of species that infect livestock. These viruses have a linear positive-sense ssRNA genome of approximately 25-30 kb, encoding a large polyprotein that is expressed from the genomic RNA, and several additional proteins expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the polyprotein coding sequence, ORF1a, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF1a. We propose that the new ORF utilizes a non-AUG initiation codon--namely a conserved CUG codon in a strong Kozak context--upstream of the ORF1a AUG initiation codon, resulting in a novel 258 amino acid protein, dubbed '30K'.
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: D000595:Amino Acid Sequence; D001483:Base Sequence; D018387:Codon, Initiator; D008969:Molecular Sequence Data; D008970:Molecular Weight; D016366:Open Reading Frames; D020815:Polyproteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D017003:Torovirus / Q000737:chemistry / Q000235:genetics*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: D018387:Codon, Initiator; D020815:Polyproteins; D014764:Viral Proteins