SEA-PHAGES | Overlapping Forward and Reverse Genes

Link to this post \| posted 11 Feb, 2022 18:40
aahowel3@asu.edu	Hello, we are looking at genes 70 (F) and 71 (R) in BiggityBass and they appear way too overlapping for genes going opposite directions. Looking at Yago84, AnClar, and Sour (the other cluster DRs most similar to BB in this region) it looks like we could either remove 70 entirely as it seems is done with Yago84 and AnClar or keep it as is the case with Sour. However we don't see any other frame that would accommodate 70 and no coding potential in other frames to support keeping it either, though there is plenty of coding potential in the frame its currently in. The large gap between 69 and 71 is still supported by Yago84 and AnClar. Its odd that the blast result returns a hit in BB 71 to the AnClar 71, and BB 70 to AnClar 70 when looking at the phamerator alignment BB 71 is AnClar's 70 and BB's 70 does not seem to exist in AnClar. Any guidance would be much appreciated! Supporting images in attached document. 831Kb

Link to this post | posted 11 Feb, 2022 18:40

Hello, we are looking at genes 70 (F) and 71 (R) in BiggityBass and they appear way too overlapping for genes going opposite directions. Looking at Yago84, AnClar, and Sour (the other cluster DRs most similar to BB in this region) it looks like we could either remove 70 entirely as it seems is done with Yago84 and AnClar or keep it as is the case with Sour. However we don't see any other frame that would accommodate 70 and no coding potential in other frames to support keeping it either, though there is plenty of coding potential in the frame its currently in. The large gap between 69 and 71 is still supported by Yago84 and AnClar. Its odd that the blast result returns a hit in BB 71 to the AnClar 71, and BB 70 to AnClar 70 when looking at the phamerator alignment BB 71 is AnClar's 70 and BB's 70 does not seem to exist in AnClar. Any guidance would be much appreciated! Supporting images in attached document.

Link to this post \| posted 11 Feb, 2022 18:48
debbie	Hi all, If what you are worried about is the the overlappedness (I just made that word up, I think) between the C terminus of the forward facing gene and the C terminus of the reverse facing gene, I would suggest that that will have no bearing on whether these two genes get expressed. Where this does matter is at the N terminus, and its possible DNA binding sequences/promoters and such. We try to make sure there is room for the 'stuff' that genes need to get transcribed and translated. We have many examples of this in the database. debbie

Link to this post | posted 11 Feb, 2022 18:48

debbie

Hi all,
If what you are worried about is the the overlappedness (I just made that word up, I think) between the C terminus of the forward facing gene and the C terminus of the reverse facing gene, I would suggest that that will have no bearing on whether these two genes get expressed. Where this does matter is at the N terminus, and its possible DNA binding sequences/promoters and such. We try to make sure there is room for the 'stuff' that genes need to get transcribed and translated. We have many examples of this in the database.
debbie

Link to this post \| posted 11 Feb, 2022 21:39
aahowel3@asu.edu	Thank you so much for clarifying we appreciate it!

Link to this post \| posted 11 Feb, 2022 22:40
debbie	Welcome!

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Overlapping Forward and Reverse Genes