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Identification of the full complement of genes in SARS-CoV-2 is a crucial step towards gaining a fuller understanding of its molecular biology. However, short and/or overlapping genes can be difficult to detect using conventional computational approaches, whereas high throughput experimental approaches – such as ribosome profiling – cannot distinguish translation of functional peptides from regulatory translation or translational noise. By studying regions showing enhanced conservation at synonymous sites in alignments of SARS-CoV and related viruses (subgenus Sarbecovirus), and correlating with the conserved presence of an open reading frame and plausible translation mechanism, we identified a putative new gene, ORF3a*, overlapping ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3a* is indeed translated during infection. ORF3a* is conserved across the subgenus Sarbecovirus, and encodes a 40–41 amino acid predicted transmembrane protein.
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?:doi
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10.1101/2020.05.12.088088
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document_parses/pdf_json/6601a2bd784dda7c93325c17ec89e38100aeabe2.json
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?:title
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A putative new SARS-CoV protein, 3a*, encoded in an ORF overlapping ORF3a
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