[Pombase-curation-tasks] [ pombase-Curation tasks-3274373 ] mating type region update

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Curation tasks item #3274373, was opened at 2011-04-04 16:18
Message generated for change (Comment added) made by val_wood
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Valerie Wood (val_wood)
Assigned to: Nobody/Anonymous (nobody)
Summary: mating type region update

Initial Comment:
Need to follow this up at some point. MAy need to check further with Juan...


Yes, what Xavi did is perfect.  He's put together mat2 and mat3 with adjacent regions (which should be present in all h90 strains).  In h90 cells, mat1 would switch between having a p cassette or a m cassette.  In 972 h- there is a deletion of mat2-p.  However, in some h+ strains there is a deletion of mat3-M, but more frequently there are mutations that prevent the switching from P to M, although mat2-P is still there.  Therefore, one would have to assemble a different region for each strain.  I think the configuration of the different h+ and h- strains is described in the very old pombe book.  Anyway, most of the time people don't even know which h+ or h- allele they have.

I think it would help to annotate mat1-m and mat3-m as such in the main contig (rather than calling them matmi_1 and _2 - or at least add a note), so that people know which one they are looking at.   Also, it would help to annotate the features of the mating type region that Xavi put in his contig and that are present in 972 (like the IR-L and IR-R regions, or the homology boxes).  Finally, would it be possible to add a note somewhere directing people to the mating type contig?

I hope this is useful - let me know if I can help with anything else

Juan


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>Comment By: Valerie Wood (val_wood)
Date: 2011-04-04 21:45

Message:
These were follow up question, no response need to follow up again,

I made
mat1-m the primary name for SPBC1711.01
and mat3-m the primary name for SPBC27G7.17
is that correct?

I will add the features Xavi annotated to the main genome seq. This will
take a bit of time, so I will do it in a couple of months when I do all
of
the pending sequence changes.

Do you think we should have links to the mating type contig from the
genes in the region in the main sequence? I don't think there is
currently
an easy way to do this with GeneDB. I can make sure that it happens
later.
I could add a link from the project page and the genedb front page.


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