Streamlining differential exon and 3' UTR usage with diffUTR

BMC Bioinformatics. 2021 Apr 13;22(1):189. doi: 10.1186/s12859-021-04114-7.


Background: Despite the importance of alternative poly-adenylation and 3' UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data.

Results: We present the diffUTR Bioconductor package which streamlines and improves upon differential exon usage (DEU) analyses, and leverages existing DEU tools and alternative poly-adenylation site databases to enable differential 3' UTR usage analysis. We demonstrate the diffUTR features and show that it is more flexible and more accurate than state-of-the-art alternatives, both in simulations and in real data.

Conclusions: diffUTR enables differential 3' UTR analysis and more generally facilitates DEU and the exploration of their results.

Keywords: Alternative poly-adenylation; Alternative splicing; Differential exon usage; Gene expression; RNAseq; Transcriptomic; UTR; Untranslated region.

MeSH terms

  • 3' Untranslated Regions
  • Alternative Splicing
  • Computational Biology*
  • Exons / genetics
  • Poly A*
  • Transcriptome


  • 3' Untranslated Regions
  • Poly A