Review annotations to 'P-type divalent copper transporter activity'

[pgaudet]

Hello, I created the term 'GO:0140581 P-type monovalent copper transporter activity' for https://github.com/geneontology/go-ontology/issues/20699 and it looks like existing annotations to 'GO:0043682 P-type divalent copper transporter activity' are incorrect.

I created a spreadsheet to review the annotations: https://docs.google.com/spreadsheets/d/1EKIvjzUPQwgCTk3F4LJdjK06hEGNYIp_4a_BtO9T0XU/edit#gid=0

There are 4 MGI and 1 CGD annotations to review.

Thanks, Pascale

[pgaudet]

Annotations are here: https://docs.google.com/spreadsheets/d/1EKIvjzUPQwgCTk3F4LJdjK06hEGNYIp_4a_BtO9T0XU/edit#gid=0

Please note that I just created the term a few minutes ago; the term will be available with some delay, depending on release cycles.

[hdrabkin]

Why are they wrong? Are you implying that they should be monovalent Cu? the genes annotated are named 'Cu++ transporting' ; I haven't looked at the refs yet because until I get the replacement term if needed, I won't actually do anything.

[pgaudet]

@hdrabkin this is what I wrote in the comment inthe spreadsheet: "Described in Uniprot as an Cu1 transporter; also change gene product in MGI ? "

[hdrabkin]

This make take a while if this means a nomen event.

[pgaudet]

is 'nomen' = nomenclature ? I dont see how that affects the GO annotations.

[hdrabkin]

The suggestion above was that the gene is mis-named , because the official gene name for the first one is   | Atp7a | ATPase, Cu++ transporting, alpha polypeptide implying divalent copper So, our nomen group needs to be advised if this is really not a divalent copper transporter.

[hdrabkin]

Same for Atp7b

[hdrabkin]

THe papers used for assays in these annotations are using CuCl2 (which is Cu++, NOT Cu+_ We will also check with HGNC, who we co-ordinate with

[hdrabkin]

From nomen: . HGNC have renamed their ATPases with the word copper replacing Cu++. I will be happy to update ours to agree. It should be public in about two weeks. This still does not explain the papers using CuCl2 for their assays. I wonder if actually it can do both.

[suzialeksander]

@hdrabkin did you ever resolve this? looks like the annotations still exist.

[deustp01]

@LiNiMGI Do you know the answer to this, or can you check in the appropriate place in MGI? (Or have I misunderstood and someone else inherited this problem from Harold?)

[LiNiMGI]

@deustp01 Thanks, i will take a look. Li

[LiNiMGI]

Assays used in both papers for these MGI annotations are using CuCl2. Also a review article PMID:32333855 says Atp7a is a Cu2 transporter, so it might actually can do both. I will keep the MGI annotation and close this ticket for now. Thanks, Li