Editing Intron (section)

== Classification ==
Splicing of all intron-containing RNA molecules is superficially similar, as described above. However, different types of introns were identified through the examination of intron structure by DNA sequence analysis, together with genetic and biochemical analysis of RNA splicing reactions. At least four distinct classes of introns have been identified:
*[[RNA splicing#Spliceosomal|Introns in nuclear protein-coding genes]] that are removed by [[spliceosome]]s (spliceosomal introns)
* Introns in nuclear and archaeal [[transfer RNA]] genes that are removed by proteins (tRNA introns)
* Self-splicing [[Group I catalytic intron|group I introns]] that are removed by [[Ribozyme|RNA catalysis]]
* Self-splicing [[group II intron]]s that are removed by RNA catalysis
[[Group III intron]]s are proposed to be a fifth family, but little is known about the biochemical apparatus that mediates their splicing. They appear to be related to group II introns, and possibly to spliceosomal introns.<ref>{{cite journal | vauthors = Copertino DW, Hallick RB | title = Group II and group III introns of twintrons: potential relationships with nuclear pre-mRNA introns | journal = Trends in Biochemical Sciences | volume = 18 | issue = 12 | pages = 467–471 | date = December 1993 | pmid = 8108859 | doi = 10.1016/0968-0004(93)90008-b }}</ref>

=== Spliceosomal introns ===
{{see also|RNA splicing#Spliceosomal|}}
Nuclear pre-mRNA introns (spliceosomal introns) are characterized by specific intron sequences located at the boundaries between introns and exons.<ref>{{cite journal | vauthors = Padgett RA, Grabowski PJ, Konarska MM, Seiler S, Sharp PA | title = Splicing of messenger RNA precursors | journal = Annual Review of Biochemistry | volume = 55 | pages = 1119–1150 | year = 1986 | pmid = 2943217 | doi = 10.1146/annurev.bi.55.070186.005351 }}</ref> These sequences are recognized by spliceosomal RNA molecules when the splicing reactions are initiated.<ref>{{cite journal | vauthors = Guthrie C, Patterson B | title = Spliceosomal snRNAs | journal = Annual Review of Genetics | volume = 22 | pages = 387–419 | year = 1988 | pmid = 2977088 | doi = 10.1146/annurev.ge.22.120188.002131 }}</ref> In addition, they contain a branch point, a particular nucleotide sequence near the 3' end of the intron that becomes covalently linked to the 5' end of the intron during the splicing process, generating a branched {{Clarify|post-text=(complicated jargon)|text=(''lariat'')|date=January 2024}} intron. Apart from these three short conserved elements, nuclear pre-mRNA intron sequences are highly variable. Nuclear pre-mRNA introns are often much longer than their surrounding exons.

=== tRNA introns ===
Transfer RNA introns that depend upon proteins for removal occur at a specific location within the anticodon loop of unspliced tRNA precursors, and are removed by a tRNA splicing endonuclease. The exons are then linked together by a second protein, the tRNA splicing ligase.<ref>{{cite journal | vauthors = Greer CL, Peebles CL, Gegenheimer P, Abelson J | title = Mechanism of action of a yeast RNA ligase in tRNA splicing | journal = Cell | volume = 32 | issue = 2 | pages = 537–546 | date = February 1983 | pmid = 6297798 | doi = 10.1016/0092-8674(83)90473-7 | s2cid = 44978152 }}</ref> Note that self-splicing introns are also sometimes found within tRNA genes.<ref>{{cite journal | vauthors = Reinhold-Hurek B, Shub DA | title = Self-splicing introns in tRNA genes of widely divergent bacteria | journal = Nature | volume = 357 | issue = 6374 | pages = 173–176 | date = May 1992 | pmid = 1579169 | doi = 10.1038/357173a0 | s2cid = 4370160 | bibcode = 1992Natur.357..173R }}</ref>

=== Group I and group II introns ===
{{see also|Group I catalytic intron|Group II intron}}
Group I and group II introns are found in genes encoding proteins ([[messenger RNA]]), [[transfer RNA]] and [[ribosomal RNA]] in a very wide range of living organisms.<ref>{{cite journal | vauthors = Cech TR | title = Self-splicing of group I introns | journal = Annual Review of Biochemistry | volume = 59 | pages = 543–568 | year = 1990 | pmid = 2197983 | doi = 10.1146/annurev.bi.59.070190.002551 }}</ref><ref>{{cite journal | vauthors = Michel F, Ferat JL | title = Structure and activities of group II introns | journal = Annual Review of Biochemistry | volume = 64 | pages = 435–461 | year = 1995 | pmid = 7574489 | doi = 10.1146/annurev.bi.64.070195.002251 }}</ref> Following transcription into RNA, group I and group II introns also make extensive internal interactions that allow them to fold into a specific, complex [[Nucleic acid tertiary structure|three-dimensional architecture]]. These complex architectures allow some group I and group II introns to be ''self-splicing'', that is, the intron-containing RNA molecule can rearrange its own covalent structure so as to precisely remove the intron and link the exons together in the correct order. In some cases, particular intron-binding proteins are involved in splicing, acting in such a way that they assist the intron in folding into the three-dimensional structure that is necessary for self-splicing activity. Group I and group II introns are distinguished by different sets of internal conserved sequences and folded structures, and by the fact that splicing of RNA molecules containing group II introns generates branched introns (like those of spliceosomal RNAs), while group I introns use a non-encoded guanosine nucleotide (typically GTP) to initiate splicing, adding it on to the 5'-end of the excised intron.