SEA-PHAGES | Two overlapping DNA Primases in JPandJE

Two overlapping DNA Primases in JPandJE

Link to this post \| posted 23 Mar, 2022 18:55
powelleann	While checking gaps in our JPandJE draft genome we noticed two potentially overlapping DNA Primase ORFs, both in the reverse direction. The first was called by Glimmer the second was not, but there is coding potential present in the Genemark graph. The first extends from 31440 to 30808 and is 633bp long (Pham 15206). The second extends from 31681 to 31292 and is about 390 bp long (Pham 100144). There are 1:1 phagesdb BLAST matches for both of these sequences. They were also both annotated as DNA primase in Immanuel3 (genes 57 and 5. The overlap if both are included is 149 bp. We are not sure whether to include the second DNA primase molecule.Please let me know. Thank you in advance. Ann Powell

Link to this post | posted 23 Mar, 2022 18:55

While checking gaps in our JPandJE draft genome we noticed two potentially overlapping DNA Primase ORFs, both in the reverse direction. The first was called by Glimmer the second was not, but there is coding potential present in the Genemark graph. The first extends from 31440 to 30808 and is 633bp long (Pham 15206). The second extends from 31681 to 31292 and is about 390 bp long (Pham 100144). There are 1:1 phagesdb BLAST matches for both of these sequences. They were also both annotated as DNA primase in Immanuel3 (genes 57 and 5 smile

. The overlap if both are included is 149 bp.

We are not sure whether to include the second DNA primase molecule.Please let me know.

Thank you in advance.

Ann Powell

Link to this post \| posted 23 Mar, 2022 19:33
cdshaffer	Yes indeed you should add the second primase. This is one of those situations where I say "there are exceptions to every rule". In this case the overlap rule. For more details see: https://seaphages.org/forums/topic/4545/

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Two overlapping DNA Primases in JPandJE