quick: Tf2-10 (SPBC1E8.04) in pombe/human ortholog table

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

I think you store /colour=4 as annotation_status=transposon

Original comment by: ValWood

[pombase-admin]

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

[pombase-admin]

Fixed! Sorry it took so long to work out.

I'm doing a new load now.

Original comment by: kimrutherford

[pombase-admin]

• status: open --> closed-fixed

Original comment by: kimrutherford