Stem loop structures can sometimes be found in introns. mA residues located in these stem-loops weaken base-pairing interactions within the stem, thus altering the structure of the mRNA. This phenomenon is known as mA-Switch.  The mA mark has an important role in alternative splicing, since it increases the accessibility of hnRNPC to its binding site. The heterogeneous nuclear ribonucleoprotein C (hnRNPC) is a RNA-binding protein that complexes with both heterogeneous nuclear RNA (hnRNA) and pre-mRNA to participate in pre-mRNA processing. hnRNPC binds to a uridine-rich region in introns that can usually form stem-loops. The destabilization of the stem-loop exposes the hnRNPC binding site, which increases the accessibility of the protein to the region. Because hnRNPC must be bound to pre-mRNA in order to fulfill its function, increased accessibility means higher activity of hnRNPC. Therefore, mA residues located in stem-loops of introns enhance the activity of hnRNPC, which results in increased alternative splicing. Evidence supporting this claim identified that decreased mA levels in the transcriptome lead to significantly reduced hnRNPC binding.
mA also has additional roles in alternative splicing by acting as the binding site for YTHDC1 (YTHDC1 binds to mA residues located in alternative exons). YTHDC1 has a double role in alternative splicing. First of all, it recruits the serine and arginine-rich splicing factor 3 (SRSF3), which promotes exon inclusion. In addition, YTHDC1 blocks binding of SRSF10, a protein involved in exon-skipping.
Due to the role of mA in alternative splicing, pre-mRNAs have higher levels of mA than mature mRNAs. Moreover, mA is more abundant in mRNAs that undergo alternative splicing compared to genes that code a single isoform. This is because alternatively spliced mRNAs are enriched in METTL3 binding sites. Splicing is affected in Mettl3 knock-out mice, resulting in increased frequency of exon skipping and intron retention. However, mA is not a general unspecific splicing factor, it only participates in the alternative splicing of certain mRNAs and lncRNAs.