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Splicing is a critical step in eukaryotic gene expression, which removes introns from pre-messenger RNA (pre-mRNA) and combines exons to form mature mRNA. The work on this thesis focuses particularly on recursive splicing, a type of alternative splicing that removes an intron in multiple steps. In vertebrates, recursive splicing has been observed in long introns of genes expressed in the brain. Disrupted splicing of long genes has been associated with genetic and neurological diseases, but the roles of recursive splicing in vertebrate genes remain unknown. The thesis has three parts. First, I describe the optimisation of CRISPR/Cas9 genome editing for the deletion of the cryptic splice sites within intronic sequences. Second, I validate a neuronal differentiation protocol starting from mouse embryonic stem cells. This cell model was created to study the effects of modifying recursive splice sites on gene expression during neuronal development. I show that perturbation of recursive splicing does not lead to major changes in mRNA abundance, but instead leads to changes in mRNA isoform expression from the Ank3 gene in differentiated neurons. I complement the cellular work with studies in a zebrafish model organism. Lastly, I focus on the recognition of cryptic splice sites by the spliceosome using a new transcriptomic method to monitor the position of the spliceosome on pre-mRNAs. Together, the research presented in this thesis provides insights into the recognition and function of cryptic splice sites during neuronal development.