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?


  • $\begingroup$ You might give us a link to the sequence you are looking at. If it is a GenBank file the annotation might help. You might also tell us what relevant papers you have retrieved from the literature that discuss the topic and why they don't help you. See the Help on Asking Good Questions. $\endgroup$ – David Aug 21 '19 at 16:17
  • $\begingroup$ I've added the like to the sequence. I think it's a general question for biologist/virologist so I did not ask the authors. $\endgroup$ – SHAD Aug 21 '19 at 17:16
  • $\begingroup$ What else do you know about this sequence? How was it generated? A quick blast search suggests that it is not a complete sequence and that it is missing the 5' end — do you have some reason to believe that this is a complete genome sequence? ——— Also, are you familiar with how 5' capping occurs — if not looking into that may help you better formulate your question. $\endgroup$ – tyersome Aug 21 '19 at 17:50
  • $\begingroup$ Hi tyersome, The cap (GpppA) should be at the 5' end. However, the mRNA deposited in database showed different nucleotides in the 5' end. I did Blast search for all mRNA sequences available but it shows no (GA) in the beginning of the sequence. Since there are serveral "GA" nucleotides in the sequence , I wrote my question about how to identify the guanine that is in the cap and will be methylated in the capping process. Here is the other sequences of mRNA LQ868304.1 LQ868303.1 LQ868302.1 LQ868301.1 LQ868300.1 LQ868299.1 $\endgroup$ – SHAD Aug 22 '19 at 12:15

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.

  • $\begingroup$ Thank you tyersome for your reply. (1) for the first reason, you are right. I updated the link in the question to a sequence which should be a complete one . (2) for the second reason, I suppose that the 5' cap will appear in the sequence, even-though if it added post-transcriptionally, in case the mRNA was directly isolated from the bacteria and not from the DNA. Please correct me if I 'm wrong. $\endgroup$ – SHAD Aug 23 '19 at 11:30
  • $\begingroup$ I encourage you to make sure you understand how sequencing reactions work. If you review that and look at the structure of the 5' cap I think you will understand my second point. (You could also look at the sequences of a few eukaryotic mRNAs — you will find that they don't always start with a G.) $\endgroup$ – tyersome Aug 23 '19 at 18:42
  • $\begingroup$ That's a bit extreme. Ask yourself, how did they ever identify and characterize mRNA caps? The review I cite in my answer indicates there is a capped mRNA (Figure 1). $\endgroup$ – David Sep 23 '19 at 13:51


“How can I identify the Guanine nucleotide that is methylated in the capping process?”


Not from the genome sequence MH900227.1 mentioned in the question. It is the sequence of the genomic RNA (given as DNA), it starts with an A and even the full Genbank entry lacks any annotation of whether there is a separate capped mRNA and, if so, where it starts.

To answer your question you will have to search the literature. There is a 2018 review by Göertz et al. entitled Functional RNA during Zika virus infection which should have (or lead to) the answer. It does appear from Figure 1 of that review that Zika virus polyprotein mRNA is capped, although the position is not immediately apparent just skimming the paper. Some hours of work and access to a university library is probably required to track it down.


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