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#1123 UniProtKB-KW:KW-0415 karyogamy

UniProt
open
nobody
None
5
2014-01-24
2013-12-02
Valerie Wood
No

pombe P40383 is mapped by IEA to karyogamy.
This seems to be indirect?

Discussion

  • rach_huntley
    rach_huntley
    2013-12-13

    Sent to UniProt

     
  • Marc Feuermann
    Marc Feuermann
    2013-12-18

    Hi Val,

    Yes this is an indirect mapping by similarity to the S. cerevisae ortholog (P22147).
    See PubMed:15358132
    "Posttranscriptional regulation of the karyogamy gene by Kem1p/Xrn1p exoribonuclease and Rok1p RNA helicase of Saccharomyces cerevisiae."

    Mutational analysis has shown that Kem1p/Xrn1p participates in microtubule-related functions such as nuclear fusion (karyogamy) during mating,...

    Regards,
    Marc.

     
  • Valerie Wood
    Valerie Wood
    2013-12-18

    Hi Marc,

    Here, I mean not that the mapping is transitive, but that the effect on the process is "indirect" It isn't annotated to Karyogamy at SGD because this information came from a HTP screen http://www.ncbi.nlm.nih.gov/pubmed/2076815
    it is affecting a process which is not directly related to karogamy, but is upstream and affects many processes, is not specific to karyogamy. We would not make a GO annotation for this.

    Therefore the maping is not appropriate. Although I wonder why a defect in karyogamy phenotype is not reported at SGD.

    Val

     
    Last edit: Valerie Wood 2013-12-18
  • Marc Feuermann
    Marc Feuermann
    2013-12-18

    Yes Val I understood. Sorry my previous answer was a bit too quick. It is indirect since it regulates genes involved in karyogamy. So it is indirectly involved in karyogamy. I perfectly understand your point of view but I think that most of the functions shown by mutational studies might be indirect which means that there are many annotations which could be questioned. It's again a question of politics and how far we annotate.

     
  • Valerie Wood
    Valerie Wood
    2013-12-18

    Actually this one might not be indirect. It could be regulatory (in which case we would annotated to "regulation of karyogamy" and the mapping would be OK.

    If it was via splicing, or RNA processing we would not consider this as "regulation" because it would not be normally regulating the process, but the defect would compromise a number of "downstream" processes. This is different from true 'regulation'

    Here the effect of the nuclease may be part of the upstream control of karyogamy. Here it is harder to know. We can see what SGD says.

     
  • Marc Feuermann
    Marc Feuermann
    2013-12-18

    :-)

     
  • Stacia Engel
    Stacia Engel
    2014-01-24

    I am not finding any info that would indicate that XRN1 is actually involved in karyogamy or in the direct regulation of karyogamy. it really just regulates expression of genes like cyclins, and RNA helicases, etc.

    i think the mapping should be removed. it's too far out for GO annotation.

    i have, however, added a phenotype annotation: "nuclear fusion during mating: absent"