Isoforms on genotype pages? /isoforms and allele nonenclature

[kimrutherford]

How do isoforms relate to genotypes?

This genotype looks like it's isoform specific because the three isoforms of prp10 have different sequences: https://www.pombase.org/genotype/prp10-1-A1089V,S1097F-amino_acid_mutation-expression-not_assayed

[ValWood]

I could not find any evidence that prp10 has multiple isoforms, and that two forms were not just splicing intermediates. So prp10 now has only one isoform.

So, back to the original question. Genotypes will be isoform specific. I guess we will need to say in Canto when we create a genotype which isoform the genotype relates to? I am not even sure if we have examples yet. For the wtfs there are deletions, I am not sure if the deletions apply to the entire locus but I assume so...

[ValWood]

We have a way to do this . I believe we just append the .1 to the allele name if is necessary to describe an isoform specific alleles. I thought I had used it but I can't find an example. I will take this to the curation tracker, we need to find an example and test it, because I have no idea how/ if this renders etc.

[kimrutherford]

We have a way to do this . I believe we just append the .1 to the allele name if is necessary to describe an isoform specific alleles.

We'll need to take care with that as there are a few alleles that end in ".1" or ".2" that aren't from multi-transcript genes: https://www.pombase.org/gene_alleles/SPBC12D12.01 https://www.pombase.org/genotype/srp7.1-disruption-disruption-expression-null

[ValWood]

Are there any others? I guess we could change them (although we said we wouldn't, I think this would make a good case)

[kimrutherford]

Are there any others?

No, just those three.

I will take this to the curation tracker, we need to find an example and test it, because I have no idea how/ if this renders etc.

As far as I know there is no special handling for .1, .2 etc. on allele names except in Manu's code for checking residues. Maybe that's all that's needed.

Let's have a chat about this on Zoom sometime.

[ValWood]

Yep it isn't super urgent.

[ValWood]

We do have an example trm1.1

https://github.com/pombase/canto/issues/2790#issuecomment-1776945280

[ValWood]

I think the issue here is to fix any alleles that are named x.1, so that they are not consumed with transcript IDs.

@kimrutherford First, how many are there?

[kimrutherford]

We have just sad1.1 and srp7.1

There's also one ending in ".2": sad1.2

[ValWood]

hmm, I thought there was a cut12 one too...

[kimrutherford]

hmm, I thought there was a cut12 one too...

Here are all the alleles of cut12: https://www.pombase.org/gene_alleles/SPBC649.05