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Published 20 hours ago • verified publisher icon RNAcentral

5.8S sequences folded differently

Open nawrockie opened this issue 3 years ago • 2 comments

URS000075D341_9606 and URS00021ED94B_9606 are both human 5.8S rRNA sequences that differ only by a single nt (the first is 1nt longer than the second) but their secondary structure diagrams look very different.

URS00021ED94B is a PDB sequence. Its secondary structure looks 'good', and URS000075D341_9606 and many other 5.8S rRNAs have structures that look 'bad'.

This issue was raised by Anton S. Petrov at the RNAcentral consortium meeting today (11/19/2021).

There are actually 2 issues:

  1. both sequences match best to the HS_LSU_3D template (so full LSU template which must include 5.8S) as opposed to a dedicated 5.8S-only template. Do we want to have these sequences match best and get folded against a dedicated 5.8S template?

  2. why do the secondary structures of these two sequences look so different despite the sequences being so similar?

nawrockie avatar Nov 19 '21 17:11 nawrockie