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Allow intron in GG cluster tRNA?

| posted 13 Apr, 2023 14:41
tRNAScan-SE v 2.0 identifies a Ser tRNA in Huwbert (53324-53234). 90 nucleotides, so a tad big for comfort.

Aragorn v 1.2.41 identifies a Ser tRNA in Huwbert (53233,53324). 92 nucleotides–even worse.

But if we set Aragorn search parameters to allow introns, we instead get a Val tRNA (53233,53324) 88 nucleotides.

We are a bit stuck on 1.) is this a legitimate tRNA call (Triscuit did not call it), and if so, do we allow the intron?
| posted 13 Apr, 2023 15:42
Hi Eric,
I think I would call the Ser tRNA without the 4 base intron as Aragoron calls it.
tRNA-Val(gac)
88 bases, %GC = 62.5
Sequence c[53233,53324]

My rational is more practical than scientific. Adding the intron information into the record will not process easily. However, I would add a second note, as we did in Arthrobacter phage Bauer
gene 48444..48521
/gene="90"
/locus_tag="SEA_BAUER_90"
tRNA 48444..48521
/gene="90"
/locus_tag="SEA_BAUER_90"
/product="tRNA-His"
/note="tRNA-His(gtg); likely contains intron aaacac"

Let me know if you need further help with this,
debbie
 
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