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short introns in tRNAs in cluster E

| posted 24 May, 2021 19:11

So I've got 2 predicted tRNAs by both tRNAScanSE and Aragorn, in cluster E phage, Filch. One of them is canonical and easy to call (tRNA-Gly(tcc)). The other, just upstream, has a 3bp intron (gcc) according to Aragorn. According to tRNAScanSE (Infernal score = 36.3), it can't determine the anticodon. I would simply leave it out, except it seems that several other phages have called this one, BUT haven't used the anti-codon specified by Aragorn, though they have kept the coordinates. according to Aragorn's prediction. For example, like Filch, CrystalP's Aragorn output predicts an 84bp tRNA (81+3bp intron)at coordinates 63089-63172: tRNA-Lys(ctt). But in GenBank, at these same coordinates it's "tRNA-Arg (cct)"

What is happening, and what should I do? Note that CrystalP is the most recently annotated phage in this cluster to call tRNAs at all. Other phages in this cluster, annotated more recently (like Quallification) have tRNAs in the same region (according to online Aragorn), but were never called (even the canonical one).

I've attached the Aragorn output for Filch (note that the very first one it calls isn't real, as it's in the middle of an ORF).
| posted 25 May, 2021 17:28
Hi Nikki,
I am sure I called CrystalP, and now want to disagree with the intron part of that call. According to the literature, the introns have to be self-splicing in a prokaryote. So it has to be ~200-ish nucleotides.
As for whether that second tRNA is worth calling, the argument has persisted for 17 years. I need to investigate further. Give me a bit of time for this one.
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