title: Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene.
abstract: The genus Okavirus (order Nidovirales) includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of approximately 26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are 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 envelope glycoprotein encoding sequence, ORF3, 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 ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.
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; D000818:Animals; D001483:Base Sequence; D018387:Codon, Initiator / Q000235:genetics; D019295:Computational Biology; D005807:Genes, Overlapping; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D033561:Penaeidae / Q000821:virology; D012367:RNA, Viral / Q000235:genetics; D046828:Roniviridae / Q000235:genetics*; D016415:Sequence Alignment; D014759:Viral Envelope Proteins / Q000235:genetics*
chemical_list: D018387:Codon, Initiator; D012367:RNA, Viral; D014759:Viral Envelope Proteins