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Updated: Feb 12, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
Kevin C H Ha1,2, Benjamin J Blencowe3,4, Quaid Morris5,6,7,8
1Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5A 1A8, Canada.
Abstract:
Alternative polyadenylation (APA) affects most mammalian genes. The genome-wide investigation of APA has been hampered by an inability to reliably profile it using conventional RNA-seq. We describe 'Quantification of APA' (QAPA), a method that infers APA from conventional RNA-seq data. QAPA is faster and more sensitive than other methods. Application of QAPA reveals discrete, temporally coordinated APA programs during neurogenesis and that there is little overlap between genes regulated by alternative splicing and those by APA. Modeling of these data uncovers an APA sequence code. QAPA thus enables the discovery and characterization of programs of regulated APA using conventional RNA-seq.
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