Methods for Characterization of Alternative RNA Splicing

Methods Mol Biol. 2016:1402:229-241. doi: 10.1007/978-1-4939-3378-5_18.


Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.

Keywords: Alternative splicing; Minigene; RNA; RT-PCR; Splicing factors; Splicing regulation; Variable exon.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Animals
  • Exons
  • HEK293 Cells
  • Humans
  • RNA / genetics*
  • RNA Probes / genetics
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Transfection


  • RNA Probes
  • RNA