A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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If you wanted to insert an FCS you would pick the AAs you wanted, pick the codons you wanted and then insert it.
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The alternative is that it was inserted in frame and then mutated to make it look out of frame
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Again, it depends on cloning strategy - if the use restriction enzymes and there would be an easy way to insert anFCS with PCR utilizing REs already present in the sequence, then it could be a way to do it. Not the optimal way, for sure, but sometimes ease trumps perfection.
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Would you pick CGG for example? Would you consider what codon to use for an R or just pick one arbitrarily.
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2021-09-21 08:21
Kristian G. Andersen
CGG would be an unusual choice IMO - not a 'optimized' R and sorta middle-of-the-pack as it comes to usage in human genomes. Very rare, of course, in viruses because it's a CpG.
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And you have 6 codons to chose from.
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Correct. Key here too is that if you were to 'optimize' the FCS sequence (as is commonly done for these types ofexperiments) you would _not_ end up with the FCS sequence we see, including the CGG codons. But again, itdoesn't really tell us much.
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What I think we have to look _very_ closely at are all the specific sites they talk about in the grant and then compare across our alignments - is SC2 unique in those positions compared to, say, the BANAL viruses? Does it flip back toSARS1 at some of these positions, etc.
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Yup.