Draft:Acceptor splice region: Difference between revisions
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An '''acceptor splice region''' or '''acceptor splice site,''' also known as '''3' splice site''', is the [[Directionality (molecular biology)|downstream]] part of an [[intron]], found at its 3' end.<ref name=":1">{{Cite web |title=RNA Splicing {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/topicpage/rna-splicing-introns-exons-and-spliceosome-12375/ |access-date=2024-09-11 |website=www.nature.com |language=en}}</ref><ref name=":0">{{Cite journal |last1=Baten |first1=AKMA |last2=Chang |first2=BCH |last3=Halgamuge |first3=SK |last4=Li |first4=Jason |date=2006-12-18 |title=Splice site identification using probabilistic parameters and SVM classification |journal=BMC Bioinformatics |volume=7 |issue=5 |pages=S15 |doi=10.1186/1471-2105-7-S5-S15 |doi-access=free |pmid=17254299 |pmc=1764471 |issn=1471-2105 }}</ref> The spliced site usually conserves the consensus dinucleotide AG.<ref name=":0" /> This region, along with the [[donor site]] (5' end of the intron)<ref name=":2">{{Cite journal |last1=Caminsky |first1=Natasha |last2=Mucaki |first2=Eliseos J. |last3=Rogan |first3=Peter K. |date=2014-11-18 |title=Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis |journal=F1000Research |volume=3 |pages=282 |doi=10.12688/f1000research.5654.1 |doi-access=free |issn=2046-1402 |pmc=4329672 |pmid=25717368}}</ref> and [[branch site]] (near the 3' end of the intron), is essential for the accurate RNA splicing, |
An '''acceptor splice region''' or '''acceptor splice site,''' also known as '''3' splice site''', is the [[Directionality (molecular biology)|downstream]] part of an [[intron]], found at its 3' end.<ref name=":1">{{Cite web |title=RNA Splicing {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/topicpage/rna-splicing-introns-exons-and-spliceosome-12375/ |access-date=2024-09-11 |website=www.nature.com |language=en}}</ref><ref name=":0">{{Cite journal |last1=Baten |first1=AKMA |last2=Chang |first2=BCH |last3=Halgamuge |first3=SK |last4=Li |first4=Jason |date=2006-12-18 |title=Splice site identification using probabilistic parameters and SVM classification |journal=BMC Bioinformatics |volume=7 |issue=5 |pages=S15 |doi=10.1186/1471-2105-7-S5-S15 |doi-access=free |pmid=17254299 |pmc=1764471 |issn=1471-2105 }}</ref> The spliced site usually conserves the consensus dinucleotide AG.<ref name=":0" /> This region, along with the [[donor site]] (5' end of the intron)<ref name=":2">{{Cite journal |last1=Caminsky |first1=Natasha |last2=Mucaki |first2=Eliseos J. |last3=Rogan |first3=Peter K. |date=2014-11-18 |title=Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis |journal=F1000Research |volume=3 |pages=282 |doi=10.12688/f1000research.5654.1 |doi-access=free |issn=2046-1402 |pmc=4329672 |pmid=25717368}}</ref> and [[branch site]] (near the 3' end of the intron), is essential for the accurate RNA splicing, allowing accurate removal of its corresponding intron from the RNA transcript. An acceptor splice region spans, on average, 28 bases.<ref name=":2" /><ref name=":1" /> |
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== Mechanism of action == |
== Mechanism of action == |
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=== Canonical acceptor splice sites === |
=== Canonical acceptor splice sites === |
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A canonical acceptor splice site conserves the consensus dinucleotide sequence GT-AG with the donor site, with GT being the donor secence and AC the acceptor sequence.<ref>{{Cite journal |last=Xiong |first=Feng |last2=Gao |first2=Jianjun |last3=Li |first3=Jun |last4=Liu |first4=Yun |last5=Feng |first5=Guoyin |last6=Fang |first6=Wenli |last7=Chang |first7=Hongfen |last8=Xie |first8=Jiang |last9=Zheng |first9=Haitao |last10=Li |first10=Tingyu |last11=He |first11=Lin |date=12 November 2008 |title=Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda |url=https://www.nature.com/articles/ejhg2008219 |journal=[[European Journal of Human Genetics]] |language=en |volume=17 |issue=4 |pages=510–516 |doi=10.1038/ejhg.2008.219 |issn=1476-5438 |via=Nature}}</ref> This type of acceptor splice site is the most common. In an analysis of 43 337 splice junction pairs from mammalian [[GenBank]] annotated genes, 98.71% contained the consensus splice dinucleotide AG on the acceptor site.<ref>{{Cite journal |last=Burset |first=M. |last2=Seledtsov |first2=I. A. |last3=Solovyev |first3=V. V. |date=2000-11-01 |title=Analysis of canonical and non-canonical splice sites in mammalian genomes |url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC113136/ |journal=Nucleic Acids Research |volume=28 |issue=21 |pages=4364–4375 |issn=0305-1048 |pmid=11058137}}</ref> |
A canonical acceptor splice site conserves the consensus dinucleotide sequence GT-AG<ref>{{Cite journal |last=Ng |first=Bernard |last2=Yang |first2=Fan |last3=Huston |first3=David P. |last4=Yan |first4=Yan |last5=Yang |first5=Yu |last6=Xiong |first6=Zeyu |last7=Peterson |first7=Leif E. |last8=Wang |first8=Hong |last9=Yang |first9=Xiao-Feng |date=December 2004 |title=Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes |url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902068/ |journal=The Journal of allergy and clinical immunology |volume=114 |issue=6 |pages=1463–1470 |doi=10.1016/j.jaci.2004.09.006 |issn=0091-6749 |pmc=3902068 |pmid=15577853 |via=PubMed Central}}</ref> with the donor site, with GT being the donor secence and AC the acceptor sequence.<ref>{{Cite journal |last=Xiong |first=Feng |last2=Gao |first2=Jianjun |last3=Li |first3=Jun |last4=Liu |first4=Yun |last5=Feng |first5=Guoyin |last6=Fang |first6=Wenli |last7=Chang |first7=Hongfen |last8=Xie |first8=Jiang |last9=Zheng |first9=Haitao |last10=Li |first10=Tingyu |last11=He |first11=Lin |date=12 November 2008 |title=Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda |url=https://www.nature.com/articles/ejhg2008219 |journal=[[European Journal of Human Genetics]] |language=en |volume=17 |issue=4 |pages=510–516 |doi=10.1038/ejhg.2008.219 |issn=1476-5438 |via=Nature}}</ref> This type of acceptor splice site is the most common. In an analysis of 43 337 splice junction pairs from mammalian [[GenBank]] annotated genes, 98.71% contained the consensus splice dinucleotide AG on the acceptor site.<ref name=":3">{{Cite journal |last=Burset |first=M. |last2=Seledtsov |first2=I. A. |last3=Solovyev |first3=V. V. |date=2000-11-01 |title=Analysis of canonical and non-canonical splice sites in mammalian genomes |url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC113136/ |journal=Nucleic Acids Research |volume=28 |issue=21 |pages=4364–4375 |issn=0305-1048 |pmid=11058137}}</ref> This sequence is spliced by the U2-type spliceosome<ref>{{Cite journal |last=Henriet |first=Simon |last2=Colom Sanmartí |first2=Berta |last3=Sumic |first3=Sara |last4=Chourrout |first4=Daniel |date=2019-10-07 |title=Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis |url=https://www.sciencedirect.com/science/article/pii/S0960982219310188 |journal=Current Biology |volume=29 |issue=19 |pages=3193–3199.e4 |doi=10.1016/j.cub.2019.07.092 |issn=0960-9822}}</ref> and is usually preceeded by a [[polypyrimidine tract]]<ref>{{Citation |last=Penn |first=J. K. M. |title=Alternative Splicing: Regulation of Drosophila melanogaster Sex Determination |date=2013-01-01 |work=Encyclopedia of Biological Chemistry (Second Edition) |pages=81–86 |editor-last=Lennarz |editor-first=William J. |url=https://www.sciencedirect.com/science/article/abs/pii/B9780123786302003169 |access-date=2024-09-21 |place=Waltham |publisher=Academic Press |isbn=978-0-12-378631-9 |last2=Graham |first2=P. |last3=Schedl |first3=P. |last4=Salz |first4=H. K. |editor2-last=Lane |editor2-first=M. Daniel}}</ref>. |
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=== Non-canonical acceptor splice sites === |
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Any acceptor splice site that does not adhere to the consensus dinucleotide sequence GT-AG is considered to be a non-canonical acceptor splice site. These are classified in seven possible types.<ref name=":3" /> |
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==== GC-AG acceptor splice sites ==== |
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== Mutations == |
== Mutations == |
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Last edited by HC226 (talk | contribs) 2 months ago. (Update) |
An acceptor splice region or acceptor splice site, also known as 3' splice site, is the downstream part of an intron, found at its 3' end.[1][2] The spliced site usually conserves the consensus dinucleotide AG.[2] This region, along with the donor site (5' end of the intron)[3] and branch site (near the 3' end of the intron), is essential for the accurate RNA splicing, allowing accurate removal of its corresponding intron from the RNA transcript. An acceptor splice region spans, on average, 28 bases.[3][1]
Mechanism of action
[edit]Types
[edit]There are several types of acceptor splice regions, classified by their nucleotide sequence and other factors.
Canonical acceptor splice sites
[edit]A canonical acceptor splice site conserves the consensus dinucleotide sequence GT-AG[4] with the donor site, with GT being the donor secence and AC the acceptor sequence.[5] This type of acceptor splice site is the most common. In an analysis of 43 337 splice junction pairs from mammalian GenBank annotated genes, 98.71% contained the consensus splice dinucleotide AG on the acceptor site.[6] This sequence is spliced by the U2-type spliceosome[7] and is usually preceeded by a polypyrimidine tract[8].
Non-canonical acceptor splice sites
[edit]Any acceptor splice site that does not adhere to the consensus dinucleotide sequence GT-AG is considered to be a non-canonical acceptor splice site. These are classified in seven possible types.[6]
GC-AG acceptor splice sites
[edit]Mutations
[edit]References
[edit]- ^ a b "RNA Splicing | Learn Science at Scitable". www.nature.com. Retrieved 2024-09-11.
- ^ a b Baten, AKMA; Chang, BCH; Halgamuge, SK; Li, Jason (2006-12-18). "Splice site identification using probabilistic parameters and SVM classification". BMC Bioinformatics. 7 (5): S15. doi:10.1186/1471-2105-7-S5-S15. ISSN 1471-2105. PMC 1764471. PMID 17254299.
- ^ a b Caminsky, Natasha; Mucaki, Eliseos J.; Rogan, Peter K. (2014-11-18). "Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis". F1000Research. 3: 282. doi:10.12688/f1000research.5654.1. ISSN 2046-1402. PMC 4329672. PMID 25717368.
- ^ Ng, Bernard; Yang, Fan; Huston, David P.; Yan, Yan; Yang, Yu; Xiong, Zeyu; Peterson, Leif E.; Wang, Hong; Yang, Xiao-Feng (December 2004). "Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes". The Journal of allergy and clinical immunology. 114 (6): 1463–1470. doi:10.1016/j.jaci.2004.09.006. ISSN 0091-6749. PMC 3902068. PMID 15577853 – via PubMed Central.
- ^ Xiong, Feng; Gao, Jianjun; Li, Jun; Liu, Yun; Feng, Guoyin; Fang, Wenli; Chang, Hongfen; Xie, Jiang; Zheng, Haitao; Li, Tingyu; He, Lin (12 November 2008). "Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda". European Journal of Human Genetics. 17 (4): 510–516. doi:10.1038/ejhg.2008.219. ISSN 1476-5438 – via Nature.
- ^ a b Burset, M.; Seledtsov, I. A.; Solovyev, V. V. (2000-11-01). "Analysis of canonical and non-canonical splice sites in mammalian genomes". Nucleic Acids Research. 28 (21): 4364–4375. ISSN 0305-1048. PMID 11058137.
- ^ Henriet, Simon; Colom Sanmartí, Berta; Sumic, Sara; Chourrout, Daniel (2019-10-07). "Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis". Current Biology. 29 (19): 3193–3199.e4. doi:10.1016/j.cub.2019.07.092. ISSN 0960-9822.
- ^ Penn, J. K. M.; Graham, P.; Schedl, P.; Salz, H. K. (2013-01-01), Lennarz, William J.; Lane, M. Daniel (eds.), "Alternative Splicing: Regulation of Drosophila melanogaster Sex Determination", Encyclopedia of Biological Chemistry (Second Edition), Waltham: Academic Press, pp. 81–86, ISBN 978-0-12-378631-9, retrieved 2024-09-21