I'm looking at the sequence of a flavivirus virus genome (mRNA). Kindly see the link MH900227.1. How can I identify the Guanine nucleotide that is methylated in the capping process?
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Why do you think the methylated G is present in these sequences?
I have two reasons for thinking your question isn't answerable.
1) As I said in my comment, based on BLAST results I don't think your sequence is complete — it appears to be missing the 5' end.
If the 5 end is missing then the end that gets capped is missing.
2) The 5' cap gets added post-transcriptionally and has a linkage that will prevent it from being sequenced.
That means you will never see the G that gets methylated in any sequence.
This is why I suggest that you make sure you understand the capping process.