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F1 gene needs second opinon

| posted 04 May, 2021 19:55
We're working on an F1 cluster phage, JalFarm20. And we would like a second opinion if this region is in fact a gene.

Conclusion: Is the ORF a gene? NO?
Rationale for the decision:
1. GeneMark did not call this as a gene
2. Coding potential is mostly atypical
3. Starterator was not informative; only draft genomes in Pham #6182
4. In DNAMaster: Forward genes 35 and 37; this gene, 36, is a reverse gene that overlaps: 29,822-29,586 (reverse)
5. No synteny evident

We've added an attachment with screenshots.

Thank you for your help.
| posted 04 May, 2021 19:59
Hi folks,
I need more info. What is the relationship with the upstream and downstream gene in this genome? Cluster F genomes are chucked full of tiny genes that have the 4 bp overlap with each other. If this gene has that I would call it. Also blastn the sequence to see if this is more highly conserved. If it is, does that influence your call?
Looking forward to what you are thinking? Send the .dnam5 file is you want me to look further.
| posted 04 May, 2021 20:47
Thank you for your help.

Upstream: NKF
downstream: holin
Gap between 36 and 37 is -211. (see attached)
| posted 04 May, 2021 20:48
Attached is the dnam5 file for your reference.
Thanks again.
| posted 05 May, 2021 01:02
I would delete this gene because we don't believe that 2 genes exist in the same space of a genome. Genes can overlap a bit, but this is completely covered by the forward genes 35 and 37. they are better choices because it is unlikely that a gene would be in the opposite direction 'for no good reason'.
What do you think?
| posted 06 May, 2021 19:50
Thank you Debbie,
We agree with your response because we did not see a clear function for this gene.
Ranalda and SKC team
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