Link to this post | posted 04 May, 2021 19:55

tsosieRL

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. 869Kb

Link to this post | posted 04 May, 2021 19:59

debbie

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. Thanks, debbie

Link to this post | posted 04 May, 2021 20:47
tsosieRL	Hi, Thank you for your help. Upstream: NKF downstream: holin Gap between 36 and 37 is -211. (see attached) 494Kb

Link to this post | posted 04 May, 2021 20:48
tsosieRL	Attached is the dnam5 file for your reference. Thanks again. 30Kb

Link to this post | posted 05 May, 2021 01:02
debbie	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? debbie

Link to this post | posted 06 May, 2021 19:50
tsosieRL	Thank you Debbie, We agree with your response because we did not see a clear function for this gene. Ranalda and SKC team