Alternative polyadenylation (APA) is a regulatory mechanism that forms multiple 3' end on mRNA.
APA isoforms from the same gene can encode different proteins and/or contain different 3' untranslated regions (UTRs). Deregulation of APA has been associated with a number of human diseases. Since longer UTRs have more binding sites for microRNAs and/or RNA-binding proteins in comparison to shorter UTRs, APA require different stability, translation efficiency, and/or intracellular localization. 
Mammalian PASs have a number of key cis elements.
* A(A/U)AAA hexamer
* U/GU-rich downstream element (DSE)
* U-rich upstream auxiliary elements (USEs)
* Upstream sequences conforming to the consensus UGUA
PAS sequences are variable, and many PASs lack one or more cis elements. PAS recognition is accomplished by protein-RNA interactions.
CPSF synergistically binds to the AAUAAA hexamer and CstF synergistically binds to the downstream element (DSE). The CFI complex binds to the UGUA motifs. CPSF, CstF, and CFI bind directly to RNA. They also recruit other proteins such as CFII, symplekin, and the poly(A) polymerase (PAP) to assemble the mRNA 3' processing complex, also known as the cleavage and polyadenylation complex. The assembly of these factors are facilitated by the C-terminal domain (CTD) of the RNA polymerase II (RNAP II) large subunit. The CTD provides a landing pad for mRNA processing factors.