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Matrix: UniProtKB-KW:KW-0819 tRNA processing /vesicle-mediated transport (-> SGD & POMBASE primary annotations) #2452

Closed ValWood closed 5 years ago

ValWood commented 5 years ago

RTT10 | WD40 domain-containing protein involved in endosomal recycling |   | tRNA processing |   | UniProt | Saccharomyces cerevisiae S288C | IEA | UniProtKB-KW:KW-0819 | wd repeat protein pthr14344 | gene |   | GO_REF:0000037 | 20190601

RTT10 appears to be http://amigo.geneontology.org/amigo/reference/PMID:21880895

is "tRNA processing " legacy?

sylvainpoux commented 5 years ago

Hi Val, I would leave the KW tRNA processing: RTT10 is "Required together with TRM7 for the methylation of the 2'-O-ribose of nucleotides at position 34 of the tRNA anticodon loop of tRNA(Phe) and tRNA(Leu(UAA))." Source: PMID:22912484

ValWood commented 5 years ago

Ok that's a strange one. I will create an exception for now but I also asked a tRNA modification expert.

v

ValWood commented 5 years ago

Yes, my source says "tRNA modification for sure"

Doesn't know about the endosomal transport role.

I will keep this as an exception , but keep an eye out for confirming information for the endosome recycling role.

In the meantime I'm going to hedge my bets and convert the pombe annotation from "endosomal recycling" to the more definite "tRNA metabolism" annotation

@srengel you might want to include the tRNA metabolism in the SGD GO annotations?

ValWood commented 5 years ago

I'm using

ISO to SGD GO:0002130 wobble position ribose methylation (based on teh UniProt and SGD descriptions)

ValWood commented 5 years ago

I also updated Trm7 to if you could make those more specific /GO="aspect=F; term=tRNA 2'-O-methyltransferase activity; GOid=GO:0106050; evidence=ISS; db_xref=GO_REF:0000024; with=SGD:S000000265; date=20190624" /GO="aspect=P; term=wobble position ribose methylation; GOid=GO:0002130; evidence=ISS; db_xref=GO_REF:0000024; with=SGD:S000000265; date=20190624" (currently tRNA methyltransferase/,ethylation)

srengel commented 5 years ago

i've added the P GO:0002130 to RTT10, but i haven't yet found a paper that i can use for the F without a contributes_to...but i've only just started...

ValWood commented 5 years ago

I didn't get an F for RTT10, and I didn't see any. The person I spoke to said it was

" a helper protein for a tRNA methylase for sure"

srengel commented 5 years ago

oh thanks, oops i was reading TRM7 as RTT10 in the comment about making the annotations more specific. i'll take a look at TRM7...

srengel commented 5 years ago

ok added F 106050 and P 2130 to TRM7.

ValWood commented 5 years ago

OK I think we are done here until more info on the endosomal role...

ValWood commented 5 years ago

exception added for RTT10 ( & orthologs) in the intersection with vesicle-mediated transport