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#11570 NTR: pre-miRNA transmembrane transporter activity
closed-accepted
5
2015-03-18
2015-03-16
No
Could you please add "pre-miRNA transmembrane transporter activity"
As a child of GO:0051033 RNA transmembrane transporter activity.
This is to annotate Exportin-5 and Ran, which export pre-miRNAs from the nucleus to the cytoplasm. (see http://europepmc.org/abstract/MED/14681208).
Please add db_xrefs GOC:BHF_miRNA and GOC:rph.
Thanks,
Rachael.
Hi Rachael/Tanya
This isn't the correct parent for this term because its nucleocytoplasmic transport which isn't transmembrane. ...there should be documentation/guidelines about this somewhere...
you probably want :
GO:0005487 nucleocytoplasmic transporter activity
we also have
GO:0005049
Name nuclear export signal receptor activity
GO:0008262
Name importin-alpha export receptor activity
which should be related to
GO:0005487 nucleocytoplasmic transporter activity
but these 2 activities aren't specific for proteins (the export one also exports RNAs) so some revisions might be required.
I'm not sure if the mechanisms are any different for RNA and protein (or if any karyopherins are specific for either RNA or protein) but the importin terms are defined in terms of the 'recognition sequence'...It is possible this system works for RNAs similarly to proteins which do not have an NLS (these appear to be co-transported with an NLS bearing substrate.....).
Anyway the existing terms are a little confusing....
Sorry........
Val
Hi Val,
I¹m not sure I get the distinction. Transmembrane transporter activity
"Enables the transfer of a substance from one side of a membrane to the
other.² There is a tRNA transmembrane transporter activity (GO:0051034),
which is a child of RNA transmembrane transporter activity and Exportin-T
(O43592) that exports tRNA seems to have the same mechanism as Exportin-5
(Q9HAV4), I.e. Docks at the nuclear pore complex via binding to
nucleoporins.
Rachael.
On 16/03/2015 13:44, "rach_huntley" huntley@users.sf.net wrote:
Related
Ontology requests:
#11570Hi Rachael,
I was trying to find some old SF annotation tracker ticket which explain this more clearly but I can't trace any of them.
Ii found a couple via googling that I could not locate with a SF search
https://sourceforge.net/p/geneontology/annotation-issues/900/
https://sourceforge.net/p/geneontology/ontology-requests/8775/
These provide background and links to other tickets
Val
OK, thanks Val, that makes it clear.
Then the new term I guess should be ³pre-miRNA transporter activity² to be
a child of GO:0005487 nucleocytoplasmic transporter activity?
(This term currently has no child terms, so potentially a lot more could
be made).
Thanks,
Rachael.
On 18/03/2015 10:10, "Valerie Wood" val_wood@users.sf.net wrote:
Related
Ontology requests:
#11570Added.
[Term]
+id: GO:0090631
+name: pre-miRNA transporter activity
+namespace: molecular_function
+def: "Enables the directed movement of pre-miRNAs between the nucleus and the cytoplasm of a cell." [GOC:BHF_miRNA, GOC:rph, PMID:14681208]
+is_a: GO:0005487 ! nucleocytoplasmic transporter activity