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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: RNA stem-loop binding etc #8198

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

I would like to annotate proteins that bind RNA stem-loops in various snRNAs. I notice we already have several RNA binding terms for specific snRNAs but this doesn't really capture the stem-loop binding aspect (it could bind some other part of the snRNA). I don't really want to add a specific stem-loop binding term for each snRNA as this can be captured in col8/16 so could we add snRNA stem-loop binding?. We already have the specific term histone pre-mRNA stem-loop binding GO:0071207 so these could share a more general new parent RNA stem-loop binding. (The paper I am curating is PMID: 20455544).

Following the pattern with DNA hairpin binding, we may also want a general grouping parent 'RNA secondary structure binding' but it may be hard to figure out what children of RNA binding are specific to secondary v primary structure.

Thanks, Susan

Reported by: stweedie

Original Ticket: geneontology/ontology-requests/7984

gocentral commented 13 years ago

Original comment by: rebeccafoulger

gocentral commented 13 years ago

Hi Susan,

I've added in: RNA stem-loop binding ; GO:0035613 synonym: RNA hairpin binding synonym: RNA hairpin loop binding Interacting selectively and non-covalently with a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop. PMID:16568238 PMID:20455544 GOC:sart

snRNA stem-loop binding ; GO:0035614 synonym: small nuclear RNA stem-loop binding synonym: snRNA hairpin binding synonym: snRNA hairpin loop binding Interacting selectively and non-covalently with a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop. PMID:16568238 PMID:20455544 GOC:sart

If more structure-specific terms are needed, I'll add in a grouping parent. Most children of RNA binding at the mo are type- or sequence-specific.

Thanks, Becky

Original comment by: rebeccafoulger

gocentral commented 13 years ago

Original comment by: rebeccafoulger