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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: "lncRNA 3' end processing & lncRNA processing & lncRNA surveillance #26988

Closed ValWood closed 7 months ago

ValWood commented 7 months ago

Please provide as much information as you can:

standard def

TERC (a lncRNA)

required for https://github.com/geneontology/go-ontology/issues/26761 @RLovering

ValWood commented 7 months ago

It looks like we already have

polyadenylation-dependent snoRNA 3'-end processing (make exact synonym)

to describe co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway for snos,

pgaudet commented 7 months ago

Can you paste the new term stanza in the ticket? (generally) - makes it easier to keep track.

Thanks, Pascale

ValWood commented 7 months ago

[Term] id: GO:0180035 name: lncRNA processing namespace: biological_process def: "Any process involved in the conversion of one or more primary lncRNA transcripts into one or more mature lncRNA molecules." [PMID:31276588] is_a: GO:0006396 ! RNA processing property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26988" xsd:anyURI created_by: vw creation_date: 2024-02-14T14:46:35Z

[Term] id: GO:0180036 name: nuclear lncRNA surveillance namespace: biological_process def: "A process that identifies and degrades defective or aberrant lncRNAs within the nucleus." [GOC:vw] is_a: GO:0071027 ! nuclear RNA surveillance property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26988" xsd:anyURI created_by: vw creation_date: 2024-02-14T15:37:20Z

[Term] id: GO:0180034 name: co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway namespace: biological_process def: "Any process involved in transcription termination-coupled 3' processing of RNA polymerase II lncRNA transcripts by the 3' end cleavage and addition of a poly(A) tail." [PMID:31276588] synonym: "lncRNA 3' end processing" BROAD [] synonym: "lncRNA 3'-end processing" BROAD [] is_a: GO:0180012 ! co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway is_a: GO:0180035 ! lncRNA processing property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26988" xsd:anyURI

ValWood commented 7 months ago

I had to revert polyadenylation-dependent snoRNA 3'-end processing and move it out from under co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway

It seems that snoRNA processing is very different (there might be multiple pathways?) some pathways involve TRAMP/exosome which is not the case for co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway I'm trying to locate good reviews but we will need to deal with this separately.