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Allow intron in GG cluster tRNA?
| Link to this post | posted 13 Apr, 2023 14:41 | |
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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? |
| Link to this post | posted 13 Apr, 2023 15:42 | |
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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 |