SEA-PHAGES | 4 bp overlaps

Link to this post \| posted 02 Mar, 2024 03:30
fbaliraine	We need further clarification about these small genes in subcluster F1: “The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.” Does this principle of calling them in F1 even without coding potential only apply to those “with 4bp overlaps at both ends,” or does it also apply to those with a 4 bp overlap at only one end? For example, FreddyB position 33967 – 34041bp (reverse) in the -2 frame has a potential small gene (75 bp) with a 4bp ATGA overlap with the start of the upstream gene, but there is a gap between it and the downstream gene. This potential gene has a strong RBS score (3.152), though its start is not part of an operon (only its stop is; see attached). Its amino acid sequence is MRMSRSDNASARKLATNTERPTTRZ. It currently has no significant blast hits. Thanks! Fred 119Kb

Link to this post | posted 02 Mar, 2024 03:30

We need further clarification about these small genes in subcluster F1:
“The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.”

Does this principle of calling them in F1 even without coding potential only apply to those “with 4bp overlaps at both ends,” or does it also apply to those with a 4 bp overlap at only one end? For example, FreddyB position 33967 – 34041bp (reverse) in the -2 frame has a potential small gene (75 bp) with a 4bp ATGA overlap with the start of the upstream gene, but there is a gap between it and the downstream gene. This potential gene has a strong RBS score (3.152), though its start is not part of an operon (only its stop is; see attached). Its amino acid sequence is MRMSRSDNASARKLATNTERPTTRZ. It currently has no significant blast hits.
Thanks!
Fred

Link to this post \| posted 03 Mar, 2024 20:46
debbie	Fred, I wold not look to fill this space in the same way I might be inclined to do so at the right end of the genome. This space is likely part of the immunity cassette, and is likely expressed during lysogeny. I would not call this gene. debbie

Link to this post \| posted 03 Mar, 2024 21:12
fbaliraine	Thank you, Debbie, for helping put this to rest! Fred

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4 bp overlaps