Alternative splicing in gencode annotations

Question

[Julian.dekker]

Hi there,

I don't quite understand how alternative splicing looks like in a gencode annotation. Is it each transcript? or just the transcripts of type "retained_intron" or "disrupted_domain"? or should I be looking at the positions for each annotated gene? or maybe I should look at the exon numbers? maybe something else?

I hope someone can help me understand this.

Julian

Answer 1

[Kristoffer Vitting-Seerup]

It is in the comparison of transcripts. When you compare two transcripts you can see which splicing was needed to produce this transcript. Another approach is to compare a transcript with the hypothetical pre-mRNA you get by combining all exons (excluding retained introns).