#9526 localization of ion channels

BHF-UCL
closed-rejected
nobody
5
2012-06-08
2012-06-07
Ruth
No

Hi

I am annotating some ANK proteins and I think they would benefit from having ion channel localization as a GO term. PMID:15178757 identifies that ANK2 in mouse and human affect the localization of Na/Ca exchanger, Na/K ATPase, and inositol trisphosphate (InsP(3)) receptor to transverse-tubule/sarcoplasmic reticulum sites in cardiomyocytes. Whereas downregulation of ANK3 prevents correct plasma membrane localisation of Sodium channels PMID:18180363, PMID:17620337.

So possible terms:
GO:0072659 protein localization in plasma membrane
>is_a child ion channel localization in plasma membrane

GO:0070972 protein localization in endoplasmic reticulum
>is_a child protein localization in sarcoplasmic reticulum
>>is_a child ion channel localization in sarcoplasmic reticulum
>>is_a child receptor localization in sarcoplasmic reticulum

What do you think?

Ruth

Discussion

  • Ruth
    Ruth
    2012-06-08

    In addition, annotation of mouse Ank2 PMID:16292983
    New terms:
    ion channel localization in T-tubule
    receptor localization in T-tubule
    or should I just use GO:0033365 protein localization to organelle and Column 16 for this?

     
  • Hi Ruth,

    I'd personally agree with adding your suggested terms
    (certainly GO:NEW protein localization in sarcoplasmic reticulum).
    I'll wait to hear if there are comments on the ion channel and receptor children terms, otherwise I'll put them in.

    Thanks
    Paola

     
  • Sorry, only just saw your comment below. I'd opt for using GO:0033365 protein localization to organelle and Column 16.

     
  • Valerie Wood
    Valerie Wood
    2012-06-08

    Hi Ruth,

    Do you know the specific gene products whaich are localized? if so i would just use these as the localization targets in column 16.

    With you suggestion, it opens another axis of classification under the localization node where you could (potentially) have any protin family, of fuction
    (transcription factor localization to chromatin, transcription factor localization to nucleus, ubiquitin ligase localization to chromatin etc. to infinity)

    just thoughts...but presumably you know the specific proteins and this would be more informative long term?
    VAl

     
  • Ruth
    Ruth
    2012-06-08

    thanks for everyone's suggestions, will take advantage of column16 then
    Ruth

     
    • status: open --> closed-rejected