splice site

• スプライス部位

WordNet

1. serve in a specific professional capacity; "the priest sat for confession"; "she sat on the jury"
2. be around, often idly or without specific purpose; "The object sat in the corner"; "We sat around chatting for another hour" (同)sit around
3. be seated (同)sit_down
4. be in session; "When does the court of law sit?"
5. be located or situated somewhere; "The White House sits on Pennsylvania Avenue"
6. join together so as to form new genetic combinations; "splice genes"
7. a junction where two things (as paper or film or magnetic tape) have been joined together; "the break was due to an imperfect splice" (同)splicing
8. join by interweaving strands; "Splice the wires"
9. join the ends of; "splice film"
10. the piece of land on which something is located (or is to be located); "a good site for the school" (同)land site
11. physical position in relation to the surroundings; "the sites are determined by highly specific sequences of nucleotides" (同)situation

PrepTutorEJDIC

1. (…に)『座る』,座っている《+『at』(『on, in』)+『名』》・着席する《+『down』》・(…に)〈鳥などが〉『止まる』,休む《+『on』+『名』》・〈めんどりが〉卵を抱く,巣に就く / 《場所の副詞[句]を伴って》(ある場所に)『位置する』・ (画家・写真家のために)ポーズをとる・しっとしている,動かないでいる・(議員・委員などの)職に就いている《+『on』+『名』》・〈議会・法廷などが〉開会(開廷)される・(…に)負担となる,重荷となる《+『on』(『upon』)+『名』》・〈衣服などが〉(…に)合う,似合う《+『on』+『名』》・〈人〉‘を'座らせる,着席させる《+『down』+『名,』+『名』+『down』》・〈馬〉‘に'乗る・《英》〈試験〉‘を'受ける
2. 〈綱などの端と端と〉‘を'組み(より)継ぎする;〈材木など)‘を'重ね継ぐ,〈フィルム・テープ〉‘を'つなぐ / 《受動態で》《話》〈二人〉‘を'結婚させる / (綱の)より継ぎ;(材木の)重ね継ぎ;(フィルム・テープの)接合 / より(重ね)継ぎ目
3. (町・建物などの)『場所』;敷地,用地 / 遺跡;(事件などの)現場 / 〈建物など〉‘を'位置させる(locate)
4. =ti

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/12/16 07:32:03」(JST)

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Simple illustration of exons and introns in pre-mRNA and the formation of mature mRNA by splicing.

In molecular biology and genetics, splicing is a modification of the nascent pre-messenger RNA (pre-mRNA) transcript in which introns are removed and exons are joined. For nuclear-encoded genes, splicing takes place within the nucleus after or concurrently with transcription. Splicing is needed for the typical eukaryotic messenger RNA (mRNA) before it can be used to produce a correct protein through translation. For many eukaryotic introns, splicing is done in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs), but there are also self-splicing introns.

Splicing pathways

Several methods of RNA splicing occur in nature; the type of splicing depends on the structure of the spliced intron and the catalysts required for splicing to occur.

Spliceosomal

Introns

The word intron is derived from the term intragenic region, that is, a region inside 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. 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).

Spliceosomal introns often reside within the sequence of eukaryotic protein-coding genes. Within the intron, 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 pyrimidines (C and U), or polypyrimidine tract. Upstream from the polypyrimidine tract is the branchpoint, which includes an adenine nucleotide. The consensus sequence for an intron (in IUPAC nucleic acid notation) is: A-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). 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. 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 usually only affects a single amino acid, can manifest as a deletion in the final protein.

Formation and activity

Splicing is catalyzed by the spliceosome, a large RNA-protein complex composed of five small nuclear ribonucleoproteins (snRNPs, pronounced 'snurps'). Assembly and activity of the spliceosome occurs during transcription of the pre-mRNA. The RNA components of snRNPs interact with the intron and are involved in catalysis. Two types of spliceosomes have been identified (major and minor) which contain different snRNPs.

• The major spliceosome splices introns containing GU at the 5' splice site and AG at the 3' splice site. It is composed of the U1, U2, U4, U5, and U6 snRNPs and is active in the nucleus. In addition, a number of proteins including U2 small nuclear RNA auxiliary factor 1 (U2AF35), U2AF2 (U2AF65) and SF1 are required for the assembly of the spliceosome. The spliceosome forms different complexes during the splicing process:

• Complex E
  • The U1 snRNP binds to the GU sequence at the 5' splice site of an intron;
  • Splicing factor 1 binds to the intron branch point sequence;
  • U2AF1 binds at the 3' splice site of the intron;
  • U2AF2 binds to the polypyrimidine tract;

• Complex A (pre-spliceosome)
  • The U2 snRNP displaces SF1 and binds to the branch point sequence and ATP is hydrolyzed;

• Complex B (pre-catalytic spliceosome)
  • The U5/U4/U6 snRNP trimer binds, and the U5 snRNP binds exons at the 5' site, with U6 binding to U2;

• Complex B*
  • The U1 snRNP is released, U5 shifts from exon to intron, and the U6 binds at the 5' splice site;

• Complex C (catalytic spliceosome)
  • U4 is released, U6/U2 catalyzes transesterification, making the 5'-end of the intron ligate to the A on intron and form a lariat, U5 binds exon at 3' splice site, and the 5' site is cleaved, resulting in the formation of the lariat;

• Complex C* (post-spliceosomal complex)
  • U2/U5/U6 remain bound to the lariat, and the 3' site is cleaved and exons are ligated using ATP hydrolysis. The spliced RNA is released, the lariat is released and degraded, and the snRNPs are recycled.

This type of splicing is termed canonical splicing or termed the lariat pathway, which accounts for more than 99% of splicing. By contrast, when the intronic flanking sequences do not follow the GU-AG rule, noncanonical splicing is said to occur (see "minor spliceosome" below).

• The minor spliceosome is very similar to the major spliceosome, but instead it splices out rare introns with different splice site sequences. While the minor and major spliceosomes contain the same U5 snRNP, the minor spliceosome has different but functionally analogous snRNPs for U1, U2, U4, and U6, which are respectively called U11, U12, U4atac, and U6atac. Unlike the major spliceosome, it is found outside the nucleus, but very close to the nuclear membrane.

• Trans-splicing is a form of splicing that joins two exons that are not within the same RNA transcript.

Self-splicing

Self-splicing occurs for rare introns that form a ribozyme, performing the functions of the spliceosome by RNA alone. There are three kinds of self-splicing introns, Group I, Group II and Group III. Group I and II introns perform splicing similar to the spliceosome without requiring any protein. This similarity suggests that Group I and II introns may be evolutionarily related to the spliceosome. Self-splicing may also be very ancient, and may have existed in an RNA world present before protein.

Two transesterifications characterize the mechanism in which group I introns are spliced:

1. 3'OH of a free guanine nucleoside (or one located in the intron) or a nucleotide cofactor (GMP, GDP, GTP) attacks phosphate at the 5' splice site.
2. 3'OH of the 5' exon becomes a nucleophile and the second transesterification results in the joining of the two exons.

The mechanism in which group II introns are spliced (two transesterification reaction like group I introns) is as follows:

1. The 2'OH of a specific adenosine in the intron attacks the 5' splice site, thereby forming the lariat
2. The 3'OH of the 5' exon triggers the second transesterification at the 3' splice site, thereby joining the exons together.

tRNA splicing

tRNA (also tRNA-like) splicing is another rare form of splicing that usually occurs in tRNA. The splicing reaction involves a different biochemistry than the spliceosomal and self-splicing pathways.

In the yeast Saccharomyces cerevisiae, a yeast tRNA splicing endonuclease heterotetramer, composed of TSEN54, TSEN2, TSEN34, and TSEN15, cleaves pre-tRNA at two sites in the acceptor loop to form a 5'-half tRNA, terminating at a 2',3'-cyclic phosphodiester group, and a 3'-half tRNA, terminating at a 5'-hydroxyl group, along with a discarded intron. Yeast tRNA kinase then phosphorylates the 5'-hydroxyl group using adenosine triphosphate. Yeast tRNA cyclic phosphodiesterase cleaves the cyclic phosphodiester group to form a 2'-phosphorylated 3' end. Yeast tRNA ligase adds an adenosine monophosphate group to the 5' end of the 3'-half and joins the two halves together. NAD-dependent 2'-phosphotransferase then removes the 2'-phosphate group.

Evolution

Splicing occurs in all the kingdoms or domains of life, however, the extent and types of splicing can be very different between the major divisions. Eukaryotes splice many protein-coding messenger RNAs and some non-coding RNAs. Prokaryotes, on the other hand, splice rarely and mostly non-coding RNAs. Another important difference between these two groups of organisms is that prokaryotes completely lack the spliceosomal pathway.

Because spliceosomal introns are not conserved in all species, there is debate concerning when spliceosomal splicing evolved. Two models have been proposed: the intron late and intron early models (see intron evolution).

Splicing diversity

	Eukaryotes	Prokaryotes
Spliceosomal	+	−
Self-splicing	+	+
tRNA	+	+

Biochemical mechanism

Diagram illustrating the two-step biochemistry of splicing

Spliceosomal splicing and self-splicing involve a two-step biochemical process. Both steps involve transesterification reactions that occur between RNA nucleotides. tRNA splicing, however, is an exception and does not occur by transesterification.

Spliceosomal and self-splicing transesterification reactions occur via two sequential transesterification reactions. First, the 2'OH of a specific branchpoint nucleotide within the intron, defined during spliceosome assembly, performs a nucleophilic attack on the first nucleotide of the intron at the 5' splice site, forming the lariat intermediate. Second, the 3'OH of the released 5' exon then performs a nucleophilic attack at the last nucleotide of the intron at the 3' splice site, thus joining the exons and releasing the intron lariat.

Alternative splicing

Main article: Alternative splicing

In many cases, the splicing process can create a range of unique proteins by varying the exon composition of the same mRNA. This phenomenon is then called alternative splicing. Alternative splicing can occur in many ways. Exons can be extended or skipped, or introns can be retained. It is estimated that 95% of transcripts from multiexon genes undergo alternative splicing, some instances of which occur in a tissue-specific manner and/or under specific cellular conditions. Development of high throughput mRNA sequencing technology can help quantify the expression levels of alternatively spliced isoforms. Differential expression levels across tissues and cell lineages allowed computational approaches to be developed to predict the functions of these isoforms. Given this complexity, alternative splicing of pre-mRNA transcripts is regulated by a system of trans-acting proteins (activators and repressors) that bind to cis-acting sites or "elements" (enhancers and silencers) on the pre-mRNA transcript itself. These proteins and their respective binding elements promote or reduce the usage of a particular splice site. However, adding to the complexity of alternative splicing, it is noted that the effects of regulatory factors are many times position-dependent. For example, a splicing factor that serves as a splicing activator when bound to an intronic enhancer element may serve as a repressor when bound to its splicing element in the context of an exon, and vice versa. In addition to the position-dependent effects of enhancer and silencer elements, the location of the branchpoint (i.e., distance upstream of the nearest 3’ acceptor site) also affects splicing. The secondary structure of the pre-mRNA transcript also plays a role in regulating splicing, such as by bringing together splicing elements or by masking a sequence that would otherwise serve as a binding element for a splicing factor.

Experimental manipulation of splicing

Splicing events can be experimentally altered by binding steric-blocking antisense oligos such as Morpholinos or Peptide nucleic acids to snRNP binding sites, to the branchpoint nucleotide that closes the lariat, or to splice-regulatory element binding sites.

Splicing errors

It has been suggested that one third of all disease-causing mutations impact on splicing. Common errors include:

• Mutation of a splice site resulting in loss of function of that site. Results in exposure of a premature stop codon, loss of an exon, or inclusion of an intron.
• Mutation of a splice site reducing specificity. May result in variation in the splice location, causing insertion or deletion of amino acids, or most likely, a disruption of the reading frame.
• Displacement of a splice site, leading to inclusion or exclusion of more RNA than expected, resulting in longer or shorter exons.

Although many splicing errors are safeguarded by a cellular quality control mechanism termed nonsense-mediated mRNA decay (NMD), a number of splicing-related diseases also exist, as suggested above.

Protein splicing

Main article: Protein splicing

In addition to RNA, proteins can undergo splicing. Although the biomolecular mechanisms are different, the principle is the same: parts of the protein, called inteins instead of introns, are removed. The remaining parts, called exteins instead of exons, are fused together. Protein splicing has been observed in a wide range of organisms, including bacteria, archaea, plants, yeast and humans.

See also

• cDNA
• Exon
• Intron
• Primary transcript
• Spliceosome
• Minor spliceosome
• Exon Junction Complex
• SWAP protein domain, a splicing regulator

References

External links

• Virtual Cell Animation Collection: mRNA Splicing
• RNA Splicing at the US National Library of Medicine Medical Subject Headings (MeSH)

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English Journal

• A 3' splice site mutation of IDS gene in a Chinese family with mucopolysaccharidosis type II.

• Jin P, Hao JW, Chen K, Dong CS, Yang YB, Mo ZH.SourceDivision of Endocrinology, 3nd Xiangya Hospital, Central South University, 410007 Changsha, Hunan, China.
• Gene.Gene.2013 Oct 10;528(2):236-40. doi: 10.1016/j.gene.2013.06.084. Epub 2013 Jul 16.
• The purpose of this study was to identify the underlying genetic cause in a four generation Chinese family diagnosed with mucopolysaccharidosis type II. Peripheral blood samples were collected from family members and the iduronate-2-sulfatase (IDS) gene was analyzed by DNA sequencing. The impact of
• PMID 23867855

• Mutation spectrum of phenylketonuria in Syrian population: Genotype-phenotype correlation.

• Murad H, Dabboul A, Moassas F, Alasmar D, Al-Achkar W.SourceMolecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission, Damascus, Syria. Electronic address: ascientific@aec.org.sy.
• Gene.Gene.2013 Oct 10;528(2):241-7. doi: 10.1016/j.gene.2013.07.001. Epub 2013 Jul 12.
• Characterization of the molecular basis of phenylketonuria (PKU) in Syria has been accomplished through the analysis of 78 unrelated chromosomes from 39 Syrian patients with PKU. Phenylalanine hydroxylase (PAH) gene mutations have been analyzed by using molecular detection methods based on the restr
• PMID 23856132

• Internal ribosome entry site-mediated translational regulation of ATF4 splice variant in mammalian unfolded protein response.

• Chan CP, Kok KH, Tang HM, Wong CM, Jin DY.SourceDepartment of Biochemistry and State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong.
• Biochimica et biophysica acta.Biochim Biophys Acta.2013 Oct;1833(10):2165-75. doi: 10.1016/j.bbamcr.2013.05.002. Epub 2013 May 9.
• Activating transcription factor 4 (ATF4) is a master regulator of genes involved in unfolded protein response (UPR) and its translation is regulated through reinitiation at upstream open reading frames. Here, we demonstrate internal ribosome entry site (IRES)-mediated translation of an alternatively
• PMID 23665047

Japanese Journal

• Post-transcriptional Regulation in Mitochondria of Rice and Wheat at Low Temperatures

• KURIHARA-YONEMOTO Shiho
• Japan Agricultural Research Quarterly: JARQ 48(1), 17-28, 2014
• … However no correlation is observed between post-transcriptional events and the organization of introns: the primary sequence of introns, splicing manner (cis or trans), intron length, and splice-site sequence. …
• NAID 130003396720

• A New Enpp1 allele, Enpp1ttw-Ham, Identified in an ICR Closed Colony

• TAKABAYASHI Shuji,SETO Shintaro,KATOH Hideki
• Experimental Animals 63(2), 193-204, 2014
• … We sequenced all exons and exon/intron boundaries of Enpp1 in the normal and mutant mice, and identified a G-to-T substitution (c.259+1G>T) in the 5′ splice donor site of intron 2 in the Enpp1 gene of the mutant mice. …
• NAID 130003391624

• 側方入出射を利用したマルチコア光ファイバ接続の軸回転調整 (光ファイバ応用技術)

• 田中 正俊,八若 正義,藤巻 洋介 [他]
• 電子情報通信学会技術研究報告 = IEICE technical report : 信学技報 113(306), 37-42, 2013-11-21
• NAID 40019909600

Related Pictures

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★リンクテーブル★

リンク元	「スプライス部位」
拡張検索	「3' splice site」「5' splice site」「RNA splice site」「splice-site mutation」
関連記事	「sit」「site」「splice」

「スプライス部位」

　　[★]

英

splice site

関

スプライシング

「3' splice site」

　　[★]

3'スプライス部位

関

5' splice site、RNA splice site、splice acceptor site、splice donor site

「5' splice site」

　　[★]

5'スプライス部位

関

3' splice site、RNA splice site、splice acceptor site、splice donor site

「RNA splice site」

　　[★]

• RNAスプライス部位

関

3' splice site、5' splice site、splice acceptor site、splice donor site

「splice-site mutation」

　　[★]

• スプライス部位変異

「sit」

　　[★]

• vi.

• (過去-過去分詞sat)座る、位置する

関

lie、locate、location、loci、locus、map、position、rank、seat、situated、situation、stand、topo

　 　 　 　 　 　

「site」

　　[★]

• n.

• 部位、場所、サイト

関

location、loci、locus、place、topo

　 　 　

「splice」

　　[★]

• スプライスする、(RNA)プライシングの

関

splicing