Find out retained intron sequence from Ensembl

Question

[Priyanka]

Is there anyway of knowing which introns are retained in transcript with biotype retained intron in Ensembl database?

Answer 1

[Ben_Ensembl]

Hi Priyanka, This information is not stored anywhere in the Ensembl databases. The vast majority of retained introns are annotated are final exon of a transcript, but can also be found anywhere in the transcript. Annotation of intron retention is always made relative to introns in other transcripts, so the best way to visualise this is by looking at all of the transcripts for a single gene through the Gene Tab. E.g: https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000139618;r=13:32315086-32400268

[Priyanka]

Hi Ben,

Thanks for the suggestion. So if I am reading the gene tab correct then the small hollow block(marked with blue line) is the segment of intron in the retained intron transcript relative to other protein coding transcripts?

[Ben_Ensembl]

Hi Priyanka, That is correct- the boxes represent exons in each transcript (hollow boxes are non-coding while filled-in coloured boxes are coding exon sequence) and are aligned against the reference genome reading across the page, so you can see that there is an exon in ENST00000700199 (BRCA2-211) that corresponds with intronic sequence in the other transcripts.

[Priyanka]

Thanks a bunch Ben. This has been extremely helpful.