Group II introns are a large class of self-catalytic ribozymes and mobile genetic elements found within the genes of all three domains of life.

[4] For example, group II introns can be modified to make site-specific genome insertions and deliver cargo DNA such as reporter genes or lox sites [5] The secondary structure of group II introns is characterized by six typical stem-loop structures, also called domains I to VI (DI to DVI, or D1 to D6).

The proximal helix structures of the six domains are connected by a few nucleotides in the central region (linker or joiner sequences).

Due to its enormous size, the domain I was divided further into subdomains a, b, c, and d. Sequence differences of group II introns that led to a further division into subgroups IIA, IIB and IIC were identified, along with varying distance of the bulged adenosine in domain VI (the prospective branch point forming the lariat) from the 3' splice site, and the inclusion or omission of structural elements such as a coordination loop in domain I, which is present in IIB and IIC introns but not IIA.

The branch site, both exons, the catalytically essential regions of DV and J2/3, and ε−ε' are in close proximity before the first step of splicing occurs.

In these permuted forms of the ribozyme, the elements of the conserved group II intron structure are present, but occur in a different order.

Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps, with both also using magnesium ions to stabilize the leaving group in each step, which has led some to theorize a phylogenetic link between group II introns and the nuclear spliceosome.

Further evidence for this link includes structural similarity between the U2/U6 junction of spliceosomal RNA and domain V of group II introns, which contains the catalytic AGC triad and much of the heart of the active site, as well as parity between conserved 5' and 3' end sequences.