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| posted 11 Feb, 2023 22:52
We are annotating phage Azira. It has high identity to survivors. In Azira, it is clear that gene #66 loses coding potential 1/2 way through the ORF, most likely due to losing a stop site. Gene #67 has coding potential across the entire ORF and this gene in most PHAM members is annotated with the longer ORF. Calling the LORF results in a 121bp overlap to gene #66 and this is what has been annotated for Survivors. All other phages that have this gene, do NOT have long overlaps to the previous gene as they all have smaller genes that precede it.

Its obvious that Azira gp67 should be annotated to include the full ORF, especially since gp66 has no CP right at the point that gp67 starts, just as Survivors, but this highly violates the gene overlap rules.

Anyone have any thoughts on this. I enclosed the Genmark map and you can see the situation, Azira gp67 is the gene starting at 44,000.

As an added intrigue to this situation, there is a start site at 44161 for gp67 with a -4bp overlap to the end of gp66. Calling this results in a 93bp ORF and 31aa protein. Also violations of the general rule that ORFS are usually >120bp….
RS Pollenz
| posted 12 Feb, 2023 23:19
For now, I would call the big overlap, which I assume is the way that Survivors was called.
Let's continue to consider the Guiding Principles as guidelines.
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