rpb1 P36594 CTD S2 phosphorylated
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#121 rpb1 P36594 CTD S2 phosphorylated
I'm trying to annotate a binding interaction wihich occures when the C terminal domain S2 is phosphorylated....
Do you have a way to do this (it's tricky I guess becase we don't know the phosphorylation status of the other phospho residues nexesarily)
PMID:28367989
Please take a look at http://purl.obolibrary.org/obo/PR_000048846 for how we handled it for the human ortholog. In your case it would just be position 2 that is specified. If this is suitable I'll go ahead and make the appropriate pombe version.
Awesome, that's perfect.
v
The only other question I have is whether or not you want terms for phosphorylations at other positions (like S5 or S7), and a term for the unphosphorylated form as well. If you are interested in catch-all terms, I could make a "S2P or S5P" version for the binding-competent form, and a "S7P or non-phosphorylated" version for the form that isn't bound.
I guess it would be useful to add all as there a few papers on CTD domain, Im sure we can use them,
I can tell everyone that they exist.
I have created the following terms. The first is the pombe pol II protein itself, and the rest are the individual modified (or not) forms. The numbering of the modified forms will be odd because there are existing terms for human orthologs, and we try to keep the numbering the same to avoid confusion. I didn't create the catch-all terms because I believe you would simply annotate to the individual ones anyway. If you do want the catch-alls, I can create them as well.
PR:000044736 = gene-level term
PR:000044737 = S5P
PR:000044738 = S2P
PR:000044739 = S7P
PR:000044740 = not phosphorylated
[Term]
id: PR:000044736
name: DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe)
def: "A DNA-directed RNA polymerase II subunit RPB1 that is encoded in the genome of Schizosaccharomyces pombe." [PRO:DAN]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-rpb1" EXACT PRO-short-label [PRO:DNx]
synonym: "DNA-directed RNA polymerase III largest subunit (Schizosaccharomyces pombe)" EXACT []
synonym: "RNA polymerase II subunit 1 (Schizosaccharomyces pombe)" EXACT []
synonym: "RNA polymerase II subunit B1 (Schizosaccharomyces pombe)" EXACT []
synonym: "SPBC28F2.12" RELATED []
intersection_of: PR:000012987 ! DNA-directed RNA polymerase II subunit RPB1
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe 972h-
intersection_of: has_gene_template PomBase:SPBC28F2.12 ! rpb1 (Schizosaccharomyces pombe)
[Term]
id: PR:000044737
name: DNA-directed RNA polymerase II subunit rpb1 phosphorylated 3 (Schizosaccharomyces pombe)
def: "A DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe) that has been post-translationally modified to include phosphoserine at position 5 of one or more C-terminal heptad repeats (YSPTSPS)." [PRO:DAN, PomBase:VW, PMID:28367989]
comment: Category=organism-modification. Requested by=PomBase. Note: This form is competent for Seb1 interaction.
synonym: "Spom-rpb1/Phos:3" EXACT PRO-short-label [PRO:DAN]
synonym: "S5P-Pol II (Schizosaccharomyces pombe)" EXACT [PRO:DAN, PMID:28367989]
is_a: PR:000044736 ! DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
[Term]
id: PR:000044738
name: DNA-directed RNA polymerase II subunit rpb1 phosphorylated 5 (Schizosaccharomyces pombe)
def: "A DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe) that has been post-translationally modified to include phosphoserine at position 2 of one or more C-terminal heptad repeats (YSPTSPS)." [PRO:DAN, PomBase:VW, PMID:28367989]
comment: Category=organism-modification. Requested by=PomBase. Note: This form is competent for Seb1 interaction.
synonym: "Spom-rpb1/Phos:5" EXACT PRO-short-label [PRO:DAN]
synonym: "S2P-Pol II (Schizosaccharomyces pombe)" EXACT [PRO:DAN, PMID:28367989]
is_a: PR:000044736 ! DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
[Term]
id: PR:000044739
name: DNA-directed RNA polymerase II subunit rpb1 phosphorylated 6 (Schizosaccharomyces pombe)
def: "A DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe) that has been post-translationally modified to include phosphoserine at position 7 of one or more C-terminal heptad repeats (YSPTSPS)." [PRO:DAN, PomBase:VW, PMID:28367989]
comment: Category=organism-modification. Requested by=PomBase. Note: This form is not competent for Seb1 interaction.
synonym: "Spom-rpb1/Phos:6" EXACT PRO-short-label [PRO:DAN]
synonym: "S7P-Pol II (Schizosaccharomyces pombe)" EXACT [PRO:DAN, PMID:28367989]
is_a: PR:000044736 ! DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
[Term]
id: PR:000044740
name: DNA-directed RNA polymerase II subunit rpb1 CTD-unphosphorylated form (Schizosaccharomyces pombe)
def: "A DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe) that lacks phosphorylation of any C-terminal heptad repeat (YSPTSPS)." [PRO:DAN, PomBase:VW, PMID:28367989]
comment: Category=organism-modification. Requested by=PomBase. Note: This form is not competent for Seb1 interaction.
synonym: "Spom-rpb1/UnPhos:CTD" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000044736 ! DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
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