UniProt mappings to cell cycle

[gocentral]

A number of fission yeast proteins have acquired a KW mapping to "cell cycle"

Although these do display cell cycle defects this phenotype is due to a splicing defect and is indirect. We would not now annotate these to cell cycle process (only to phenotype)

could the mappings be deleted?

Thanks

Val

SPBC19G7.10c topoisomerase II-associated deadenylation-dependent mRNA-decapping factor (predicted) SPAC644.12 cdc5 splicing factor Cdc5 SPBC211.02c cwf3 complexed with Cdc5 protein Cwf3 SPBC31F10.11c cwf4 complexed with Cdc5 protein Cwf4 SPCC16A11.05c dim1 U4/U6 x U5 tri-snRNP complex subunit Dim1 SPAPJ698.03c prp12 U2 snRNP-associated protein Sap130 SPBC6B1.10 prp17 splicing factor Prp17 SPBP22H7.07 prp5 WD repeat protein Prp5

Reported by: ValWood

Original Ticket: geneontology/annotation-issues/1191

[gocentral]

ditto these, are phenotypes as a result of RNA processing defects

SPAC19D5.03 cid1 SPAC12G12.13c cid14 SPAC17H9.01 cid16 SPCC338.04 cid2 SPBC26H8.10 dis3

and I couldn't find the basis for this one: erh1 (SPAC19G12.17)

thanks

Val

Original comment by: ValWood

[gocentral]

These are indirect SPBC27B12.08 Pof6 interacting protein Sip1, predicted AP-1 accessory protein SPCC830.07c DNAJ domain protein, involved in translation initiation Psi1 SPAC12G12.14c pfs2 WD repeat protein Pfs2

For these I don't see any evidence (from fission yeast or orthologs) art1 (SPBC19G7.08c) arrestin family protein Art1 (unknown) SPBC582.05c brc1 BRCT domain protein Brc1 (repair)

Original comment by: ValWood

[gocentral]

Sent to UniProt.

Original comment by: rachhuntley

[gocentral]

Hi Val, I've removed the KW from all these entries and entries corresponding to fungal orthologs. The modifications will be available publicly in 2 release time. Thanks, Marc.

Original comment by: marcfeuermann

[gocentral]

OK, were the mappings restricted to fungi? the same will be true for higher eukaryotes too. There will be a few more of these cell cycle ones, when I get chance to go through them ;) v

Original comment by: ValWood

[gocentral]

For the moment I've just cleaned the fungal entries in which the non appropriate KWs were mostly propagated. I've also looked in higher eukaryotes (mammals, plants,...) but the KW "Cell cycle" was not present, at least in these families. However, it is clear that there are probably such cases in non-fungal entries. We would need to check all the Swiss-Prot entries having this KW (almost 30 years of annotation) which would take much time we unfortunately do not have. But yes, do not hesitate to send us those you find. Regards, Marc.

Original comment by: marcfeuermann

[gocentral]

Here are a few more. Don't worry about the metazoan, any violations should become apparent from the annotation intersection consistency checks later. Val

Q9UTE6 Protein mak16 SPAC222.06.1 GO:0007049 cell cycle UniProt ribosome biogenesis

Q9P7S8 Protein rax1 (add name) SPAC23G3.05c.1 GO:0007049 cell cycle UniProt no evidence

Q96UP3 Telomere length regulator protein rif1 SPAC6F6.17.1 GO:0007049 cell cycle UniProt telomere maintenance

UniProtKB/SwissProt Q92344 Kinetochore protein fta5 SPAC1F8.06.1 GO:0007049 cell cycle UniProt (is actually a cell surface glycoprotein, we removed kinetochore)

SPAC1142.03c.1 GO:0007049 cell cycle UniProt UniProtKB/SwissProt Q92344 Kinetochore protein fta5 (is actually a cell surface glycoprotein, we removed kinetochore)

Q10337 BRCT-containing protein 1 SPBC582.05c.1 GO:0007049 cell cycle UniProt recombination and repair

UniProtKB/SwissProt Q10326 Meiotically up-regulated gene 8 protein SPAC32A11.01.1 GO:0007049 cell cycle UniProt (not enough information from increased expression to make a cell cycle annotation)

UniProtKB/SwissProt Q10294 cAMP-independent regulatory protein pac2 SPAC31G5.11.1 GO:0007049 cell cycle UniProt (conjugation)

UniProtKB/SwissProt Q10168 Nucleoporin nsp1 SPAC26A3.15c.1 GO:0007049 cell cycle UniProt (I am removing the PomBase IMP cell division annotation too)

Original comment by: ValWood