merge: 2 splicing F terms

[gocentral]

Hi,

It seems we could merge these 2 terms:

RNA splicing factor activity, transesterification mechanism ; GO:0031202

spliceosomal catalysis ; GO:0000385

They're essentially the same thing. Basically, a "splicing factor' is part of a complex that catalyzes these 2 transesterification reactions.

If this is done, I don't really care which term name we keep, I can see advantages of either, but the kept term should keep all the parents of the existing terms.

-Karen

Reported by: krchristie

Original Ticket: "geneontology/ontology-requests/4945":https://sourceforge.net/p/geneontology/ontology-requests/4945

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Based on annotations, I would use GO:0031202 as the primary ID, and we might as well use its name as primary.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=473890 Originator: YES

I just realized that I stuck a comment meant for this item into the other splicing related SF item item I submitted on the same day.

For the parentage, I think I may be coming around to Val's way of thinking that one might not want to see all the individual genes that could be annotated with this F term inherit "RNA binding" from that parentage, so perhaps it would be best if the merged term only had the catalysis parent. And then any individual genes that have 'RNA binding' activity can be annotated directly.

-Karen

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=436423 Originator: NO

If there are gps that have the transesterification catalytic activity but don't bind RNA, we shouldn't include the RNA binding parent. But if catalyzing a splicing transesterification reaction always entails binding RNA, then the parent makes sense, and there's no particular reason not to include it.

Val's concern about binding had to do with translation factors, and she knew or suspected that not all do bind RNA directly.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=473890 Originator: YES

I think this a comparable situation to the one Val brought up for translation factors because, as Harold pointed out, we're talking about the function of a complex. Catalysis of transesterifications in splicing is a similar situation in that in order to catalyze a transesterification, the spliceosome binds RNA, but each individual gene product does not. I would suspect that not all of the gene products characterized as being specifically involved in catalysis of either the first or second transesterifications bind RNA directly.

-Karen

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=436423 Originator: NO

all righty then, merged and kept only the catalytic activity parent.

best check the def ... I just kept what we had for GO:0031202

m

Original comment by: mah11

[gocentral]

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

Original comment by: mah11

[gocentral]

Logged In: YES user_id=473890 Originator: YES

Hmmm,

actually, I think the def could use some adjustment. Right now it seems like it might specifically mean the second step, while as the parent term of both the first and second transesterification reactions, it needs to be general enough to encompass both. Here are the current defs. I reopened the item so that the def change doesn't get missed.

GO:0031202 - RNA splicing factor activity, transesterification mechanism Def - An activity which binds RNA and functions to assist splicing of substrate RNA(s) by facilitating the formation and stabilization of a catalytic conformation in which the splice junctions of the RNA(s) to be spliced are positioned for a transesterification reaction that occurs between two sites within the RNA(s) to be spliced.

GO:0000384 - first spliceosomal transesterification activity Def - Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon.

GO:0000386 - second spliceosomal transesterification activity Def - Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure.

Maybe the def of GO:0031202 should be adjusted to something like this:

An activity which assists splicing of substrate RNA(s) by facilitating the formation and stabilization of a series of catalytic conformations in which key RNA sequences are positioned for a series of two transesterification reactions which result in removal of the intron sequence and joining of two exons.

thanks,

-Karen

Original comment by: krchristie

[gocentral]

• status: closed-accepted --> open-accepted

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Def updated; I used your suggestion.

Original comment by: mah11

[gocentral]

• status: open-accepted --> closed-accepted

Original comment by: mah11