Closed pombase-admin closed 9 years ago
Tf2-13 (SPCC1494.11c)
I had a look and they all seem to be similarly annotated (no have SO IDs yet)
Original comment by: ValWood
I leave the transposon out of the pombe/cerevisiae ortholog table. and they appear to be left out of the human ortholog table too, except for this one? Tf2-10 (SPBC1E8.04)
Hi. Where are you seeing this? It's not in ortholog table from the latest load: http://curation.pombase.org/dumps/pombase-build-2013-10-24-v8-l1/pombase-build-2013-10-24-v8-l1.human-orthologs.txt
Original comment by: kimrutherford
SPBC1E8.04 NONE
Ah, I didn't realise you were talking about that one - it's got no ortholog. I thought you were talking about orthologs. I was confused.
Can you give me an example of one that doesn't appear in the ortholog table?
I had a look at the code and it looks like it will export anything that is has an mRNA in Chado. Those features come from CDSs that aren't pseudogenes.
Original comment by: kimrutherford
I'm wondering why it is in the table at all. Other transposons aren't (they would all be NONE), but why this one? it's inconsistent.
I would say the ortholog table should only contain CDS (at present). We might have an ncRNA ortholog table in the future....., but we don't want to include transposons.
Original comment by: ValWood
I would say the ortholog table should only contain CDS
I'm still confused. Your example (SPBC1E8.04) is a CDS annotation, so it should be in the table?
Do you have an example of one that isn't in the table?
Original comment by: kimrutherford
Oh maybe they are all in the table....I thought that only 3 were, I don't know why.
So all that needs to happen for this ticket is that CDS with a 'transposon' annotation status should be excluded from the table
val
Original comment by: ValWood
So all that needs to happen for this ticket is that CDS with a 'transposon' annotation status should be excluded from the table
OK, but what do you mean by "annotation status"?
This is the full annotation from your example gene:
/colour=4
/controlled_curation="term=Tf2-type transposon;
date=19700101"
/controlled_curation="term=warning, frameshifted;
cv=warning; date=19700101"
/obsolete_name="Tf-pseudoII"
/obsolete_name="Tf2-10-pseudo"
/obsolete_name="SPBC1E8.04c"
/systematic_id="SPBC1E8.04"
/product="retrotransposable element/transposon Tf2-type"
/primary_name="Tf2-10"
Original comment by: kimrutherford
I think you store /colour=4 as annotation_status=transposon
Original comment by: ValWood
Ah, Thanks! I'd forgotten about that. Yep that's the case, I just checked in Chado. I'll change the exporter to ignore genes with the transposon status.
Original comment by: kimrutherford
Fixed! Sorry it took so long to work out.
I'm doing a new load now.
Original comment by: kimrutherford
Original comment by: kimrutherford
I leave the transposon out of the pombe/cerevisiae ortholog table. and they appear to be left out of the human ortholog table too, except for this one?
Tf2-10 (SPBC1E8.04)
(I'm not sure how the others are ommitted, as these are annotated as CDS (maybe this one doesn't have something which the others have?)
Original comment by: ValWood