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How close can one pack protein and tRNA's genes

| posted 20 Mar, 2017 17:58
Thanks Welkin! I'll let the students know.

| posted 22 May, 2020 15:35
We have finished and our ready to send out our annotations but just want to double check about ORFs and tRNAs overlapping in Nanosmite (cluster M3, only member of the subcluster). I've attached a screen shot of the two ORFs in question. gp101 is an orpham (DNAmaster notes are visible in the screenshot for this gene) with no function and basically no coding potential so we are leaning towards deleting the ORF and keeping the tRNA. gp109 (not an orpham) overlaps with a downstream tRNA by 10 bps so just want to verify that we can keep both as they are transcribed in the same direction. Thanks for your help!
| posted 22 May, 2020 15:43
so with 101 I'd be inclined to root around a little in the ORFs in the forwards directions to see if there is an HNH in there somewhere. HNHs are frequently found associated with tRNA clusters, and sometimes give false positives with glimmer/genemark with a prediction in the opposite strand. If you don't find an HNH anywhere, I have no problem with the delete reverse 101 decision.
10bps should be fine for an overlap between 109 and a downstream tRNA.
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