Burnham AJ, Miller JR, Singh I, Billings EA, Rush. Novel isoforms of influenza virus PA-X and PB1-F2 indicated by automatic annotation. Virus Res. 2021 Aug 12:198545
The influenza A virus genome contains 8 gene segments encoding 10 commonly recognized proteins. Additional protein products have been identified including PB1-F2 and PA-X. We report in-silico identification of novel isoforms of PB1-F2 and PA-X in influenza virus genomes sequenced from avian samples. The isoform observed in PA-X includes a mutated stop codon that should extend the protein product by 8 amino acids. The isoform observed in PB1-F2 includes two nonsense mutations that should truncate the N-terminal region of the protein product and remove the entire mitochondrial targeting domain. Both isoforms were uncovered during automatic annotation of CEIRS sequence data. Nominally termed PA-X8 and PB1-F2-Cterm, both predicted isoforms were subsequently found in other annotated influenza genomes previously deposited in GenBank. Both isoforms were noticed due to discrepant annotations output by two annotation engines, indicating a benefit of incorporating multiple algorithms during gene annotation.
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