ntr: snRNA 3'-end processing

[gocentral]

Hi,

Reading this paper:

van Hoof A, Lennertz P, Parker R (2000) Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. EMBO J 19(6):1357-65 PMID:10716935

Since we already have lots of terms for 3'-end processing of various types of RNAs, I think we need one for 'snRNA 3'-end processing'.

I think there is also an organizational issue with the children of the existing term 'RNA 3'-end processing'. Currently, we have this:

- 'RNA 3'-end processing' -- 'mitochondrial RNA 3'-end processing' -- 'mRNA 3'-end processing' -- 'ncRNA 3'-end processing' -- 'RNA polyadenylation' -- 'rRNA 3'-end processing' -- 'snoRNA 3'-end processing' -- 'tRNA 3'-end processing'

but as currently defined, ncRNA is inclusive of rRNA, snoRNA, and tRNA, so we either need to define ncRNA's to be non-coding RNAs that are not other specific types of ncRNAs, or we need to change the structure to be something like this:

- 'RNA 3'-end processing' -- 'mitochondrial RNA 3'-end processing' -- 'mRNA 3'-end processing' -- 'ncRNA 3'-end processing' --- 'rRNA 3'-end processing' --- 'snRNA 3'-end processing' ; GO:new --- 'snoRNA 3'-end processing' --- 'tRNA 3'-end processing' -- 'RNA polyadenylation'

I think the structural change to the relationships is probably the way to go.

Parentage, the new term should be under both of these terms:

• 'RNA 3'-end processing' ; GO:0031123
• 'snRNA processing' ; GO:0016180

Standard def will be fine.

thanks,

-Karen

Reported by: krchristie

Original Ticket: "geneontology/ontology-requests/5040":https://sourceforge.net/p/geneontology/ontology-requests/5040

[gocentral]

Logged In: YES user_id=473890 Originator: YES

forgot to include my annotation comment: Annotation for Rex2 by IMP for new term.

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=473890 Originator: YES

Hmmm, wonder if it would be worth having individual terms for processing of U1, U2, U4, U5, and U6. These are all very conserved....

another annotation comment from the same paper: Rnh70, Rex2, Rex3, each by IGI with the other 2 for the new snRNA 3'-end processing term (specifically U5 and also RNA subunit of RNaseP; Rex2 by IMP is U4 specifically).

-K

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I have implemented the eminently sensible new structure, and added a slew of new terms: ncRNA processing GO:0034470 ncRNA 5'-end processing GO:0034471 snRNA 3'-end processing GO:0034472 U1 snRNA 3'-end processing GO:0034473 U2 snRNA 3'-end processing GO:0034474 U4 snRNA 3'-end processing GO:0034475 U5 snRNA 3'-end processing GO:0034476 U6 snRNA 3'-end processing GO:0034477 sibling terms moved to is_a ncRNA 3'-end processing GO:0043628: rRNA 3'-end processing GO:0031125 snoRNA 3'-end processing GO:0031126 tRNA 3'-end processing GO:0042780

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11