Constitutive splicing is favored in strong splice sites, which have the conserved consensus sequences at 5 0 (CAG|GUAAGU) and 3 0 (NYAG|G) splice sites. Exons are usually shorter sequences, ranging from 50 to 250 bp, whereas introns can have broader length variation, from <100 bp to more than 1,000 bp, and around 20% of human introns are larger than 5 kb (Lander et al., 2001). In addition to constitutive exon splicing, the presence of alternative splice sites leads to variable ways to mature an mRNA ( Figure 2). Exons and introns might host alternative splice sites, which are similar to, but usually not as strong as, consensus splice sites (Fu & Ares, 2014;Kornblihtt et al., 2013). If a 5 0 or 3 0 alternative site lies within an exon, part of this exon might be read as an intron. Also, alternative splicing can lead to exon skipping, in which a constitutive 3 0 splice site fails to be recognized and assembly of spliceosome proceeds to the next available 3 0 splice site, which can result in exclusion of an exon. Alternatively, 5 0 splice sites might not be read as well, resulting in intron retention. In some transcripts, a mutual exclusion of exons might take place generating different messages . Cryptic splice sites are similar to consensus sites, but they are usually recognized only after a mutation in the gene, or of a spliceosome component, leading to alterations in the final message. In breast cancer, mutations in splicing factor 3B subunit 1 (SF3B1), for example, induce the use of cryptic 3 0 splice sites (DeBoever et al., 2015). Single nucleotide variants (SNVs) of 1,812 tumor samples were analyzed by whole-exome sequencing and revealed exon skipping and intron retention were among the most frequently observed alternative splicing events (Jung et al., 2015; Box 1).Alternative splicing mechanisms are dependent on recognition of splice site sequences in the pre-mRNA, which in turn depends on both the strength of sequences as well as the presence of proteins and signals that guide the spliceosome to these regions. Alternative exons in humans and mice are surrounded by more conserved regulatory sequences than constitutive exons, indicating the former ones are under strict regulation. Consistently, 30-50% of ISEs are located nearby alternative exons (Yeo, Van Nostrand, & Liang, 2007). Interestingly, ISEs and ESSs show a positional overlap in different pre-mRNA substrates, indicating the regulation depends on their positioning with respect to the 5 0 upstream exon and the bound proteins (Y. Wang et al., 2012). The ISSs can interfere with exon inclusion in different pre-mRNAs, and regulate 5 0 splice site choice, therefore, exerting alternative splicing regulation (Y. Wang et al., 2013). In this sense, mutations in exonic and intronic sequences are critical and might affect the balance of regulatory sequences and also their activity, since most effects in splicing are location-dependent. Intronic mutations are commonly associated with nonsense-mediated decay responses, caused by an increased rate of premature stop ...