Finding exons that are always included
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3 months ago
smurph50 ▴ 50

How would I approach the problem of finding hg38 exons that are not affected by alternative splicing/are always included across all cell types?

Is there an easier way than looking at percent spliced in from published alternative splicing datasets of many different tissues?

alternative-splicing exon • 490 views
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3 months ago

you can have a look at intropolis:

intropolis is a list of exon-exon junctions found across 21,504 human RNA-seq samples on the Sequence Read Archive (SRA)

https://github.com/nellore/intropolis

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3 months ago
cmdcolin ★ 3.7k

one search term you might look for are "constitutive exons". I believe this term is used in literature for similar concept. see https://www.ebi.ac.uk/ols/ontologies/ensemblglossary/terms?iri=http://ensembl.org/glossary/ENSGLOSSARY_0000074 "Exons that are not spliced out, therefore present in all transcripts of a given gene." (though some other definitions in papers use thresholds other than 100%, and indeed, use "percent spliced in" (PSI) as a metric)

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Thank you! Your answer led me to hexevent which has a list of constitutive exons.

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Please post the relevant information (links etc) as an answer since future visitors will find it useful.

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3 months ago

GTEX has all the exon expression across all isoforms in their catalog. there is almost always some weird isoform that skips an exon but is either lowly expressed or artefactual.

https://gtexportal.org/home/downloads/adult-gtex

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