Editing RNA splicing (section)

====Introns====
The word ''intron'' is derived from the terms ''intragenic region'',<ref>{{cite journal | vauthors = Gilbert W | title = Why genes in pieces? | journal = Nature | volume = 271 | issue = 5645 | pages = 501 | date = February 1978 | pmid = 622185 | doi = 10.1038/271501a0 | s2cid = 4216649 | doi-access = free | bibcode = 1978Natur.271..501G }}</ref> and ''intracistron'',<ref>{{cite journal | vauthors = Tonegawa S, Maxam AM, Tizard R, Bernard O, Gilbert W | title = Sequence of a mouse germ-line gene for a variable region of an immunoglobulin light chain | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 75 | issue = 3 | pages = 1485–1489 | date = March 1978 | pmid = 418414 | pmc = 411497 | doi = 10.1073/pnas.75.3.1485 | doi-access = free | bibcode = 1978PNAS...75.1485T }}</ref> that is, a segment of DNA that is located between two exons of a [[gene]]. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in the unprocessed RNA transcript. As part of the RNA processing pathway, introns are removed by RNA splicing either shortly after or concurrent with [[transcription (genetics)|transcription]].<ref>{{cite journal | vauthors = Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R | display-authors = 6 | title = Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs | journal = Genome Research | volume = 22 | issue = 9 | pages = 1616–1625 | date = September 2012 | pmid = 22955974 | pmc = 3431479 | doi = 10.1101/gr.134445.111 }}</ref> Introns are found in the genes of most organisms and many viruses. They can be located in a wide range of genes, including those that generate [[proteins]], [[ribosomal RNA]] (rRNA), and [[transfer RNA]] (tRNA).<ref>{{cite journal | vauthors = Roy SW, Gilbert W | title = The evolution of spliceosomal introns: patterns, puzzles and progress | journal = Nature Reviews. Genetics | volume = 7 | issue = 3 | pages = 211–221 | date = March 2006 | pmid = 16485020 | doi = 10.1038/nrg1807 | s2cid = 33672491 }}</ref>

Within introns, a donor site (5' end of the intron), a branch site (near the 3' end of the intron) and an acceptor site (3' end of the intron) are required for splicing.  The splice donor site includes an almost invariant sequence GU at the 5' end of the intron, within a larger, less highly conserved region. The splice acceptor site at the 3' end of the intron terminates the intron with an almost invariant AG sequence.  Upstream (5'-ward) from the AG there is a region high in [[pyrimidine]]s (C and U), or [[polypyrimidine tract]].  Further upstream from the polypyrimidine tract is the branchpoint, which includes an adenine nucleotide involved in lariat formation.<ref>{{cite journal | vauthors = Clancy S | title = RNA Splicing: Introns, Exons and Spliceosome | journal = Nature Education | year = 2008 | volume = 1 | issue = 1 | pages = 31 | url = http://www.nature.com/scitable/topicpage/rna-splicing-introns-exons-and-spliceosome-12375 | access-date = 31 March 2011 | archive-url = https://web.archive.org/web/20110315060903/http://www.nature.com/scitable/topicpage/RNA-Splicing-Introns-Exons-and-Spliceosome-12375 | archive-date = 15 March 2011 | url-status = live }}</ref><ref name=Black>{{cite journal | vauthors = Black DL | title = Mechanisms of alternative pre-messenger RNA splicing | journal = Annual Review of Biochemistry | volume = 72 | issue = 1 | pages = 291–336 | date = June 2003 | pmid = 12626338 | doi = 10.1146/annurev.biochem.72.121801.161720 | s2cid = 23576288 | url = https://escholarship.org/uc/item/2hg605wm }}</ref> The [[consensus sequence]] for an intron (in IUPAC [[nucleic acid notation]]) is: G-G-[cut]-G-U-R-A-G-U (donor site) ... intron sequence ... Y-U-R-A-C (branch sequence 20-50 nucleotides upstream of acceptor site) ... Y-rich-N-C-A-G-[cut]-G (acceptor site).<ref name=WoS>{{cite book |year=2013 |chapter=[[Molecular Biology of the Cell (book)|Molecular Biology of the Cell]] |title=2012 Journal Citation Reports |publisher=[[Thomson Reuters]] |edition=Science |series=[[Web of Science]] |title-link=Journal Citation Reports }}</ref> However, it is noted that the specific sequence of intronic splicing elements and the number of nucleotides between the branchpoint and the nearest 3' acceptor site affect splice site selection.<ref name=Taggart>{{cite journal | vauthors = Taggart AJ, DeSimone AM, Shih JS, Filloux ME, Fairbrother WG | title = Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo | journal = Nature Structural & Molecular Biology | volume = 19 | issue = 7 | pages = 719–721 | date = June 2012 | pmid = 22705790 | pmc = 3465671 | doi = 10.1038/nsmb.2327 }}</ref><ref>{{cite journal | vauthors = Corvelo A, Hallegger M, Smith CW, Eyras E | title = Genome-wide association between branch point properties and alternative splicing | journal = PLOS Computational Biology | volume = 6 | issue = 11 | pages = e1001016 | date = November 2010 | pmid = 21124863 | pmc = 2991248 | doi = 10.1371/journal.pcbi.1001016 | veditors = Meyer IM | bibcode = 2010PLSCB...6E1016C | doi-access = free }}</ref> Also, point mutations in the underlying DNA or errors during transcription can activate a ''cryptic splice site'' in part of the transcript that usually is not spliced. This results in a [[mature messenger RNA]] with a missing section of an exon. In this way, a [[point mutation]], which might otherwise affect only a single amino acid, can manifest as a [[Indel|deletion]] or truncation in the final protein.{{cn|date=July 2024}}
[[File:Intron miguelferig.jpg|thumb|450px|center|'''Intron Exon Boundary''' '''in [[pre-mRNA]]''' '''1''' - 3' Splice site '''2''' - Poly pyrimidine Tract '''3''' - Branch site '''4''' - 5' splice site]]