mRNA processing (Rattus norvegicus)

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mRNA CappingU4/U6exon 1GUFormation of the Spliceosomal B complexProcessing of Intron-Containing Pre-mRNA(2)exon 2P-SF3b14b35Formation of pre-mRNPsU2RNA helicaseCPSFU6Additional SR proteinsAGexon 1Cleavage of mRNA at the 3'-endYYYYmRNA polyadenylationKinases Phosphorylating RS domains?intronPoly(A)pb IIYYYYUGU2 snRNP55 G capFormation of the Spliceosomal E complexSR-proteinsAG3SR-proteinsPrimary RNA transcriptSR-binding sitesCPSFexon 1exon 2Polr2ahnRNP regulatorsFormation of the Spliceosomal B complex553pre-mRNAA5mRNA cappingAGmRNA splicing (major pathway)Poly(A) polymerase alpha3SR-binding sitesCFImRNA 3'-end processingMethylation of mRNAexon 2YYYYYYYYCF IICAexon 2(2c)U5(2a)3U2 snRNPAAAAAAAexon 1U4:U5:U6 tri-snRNP complex5YYYY(3)5U2 snRNPsAdditional Factorsexon 1Rngtt (capping enzyme)AU1AFormation of the active Spliceosomal C complexright click on blue text for detailed informationRegulation ofAlternative Splicing3Formation of the Spliceosomal E complex5degradedPoly(A) polexon 2Formation of pre-mRNPsCleavage at the 3'-Splice-Site and Exon LigationSR-kinases653ANote: New participating members shown at each step3Internal methylation of mRNAsplicesome associated helicasesFormation of the Spliceosomal A complexSR protein phosphatasesP3U5Poly(A)-binding protein IIU2AFCstFheterogeneous nuclear ribonucleoproteinsAAUAAAU1 snRNPAInternal methylation of mRNA3AGAGsnRNP Sm core complexUGCF IIAdditional FactorsSR-proteinsRNAi pathway(1)SR-repressor proteinssplicing factor SF3BsnRNP Sm core complexAccessory ProteinsRNA helicase AmRNA splice site selection5Additional FactorsCstFSpt5U4U2AFU6 snRNPiPo5CF I(2b)SR protein kinasesFormation of the Spliceosomal A complexMisc.AGU5 snRNPPutative Alternative SplicingRegulatorsYYYYhnRNPsA3snRNP Sm core complexPi5Cap BindingFormation of the Spliceosomal C complexLariat Formation and 5'-Splice Site Cleavage3U4 snRNPexon 1U1 snRNP5splicing factor SF3ASR-phosphatasesSerine/Argenine Rich Proteins(SR)exon 2Rnmt (methyltransferase)SNRPGNcbp1HnrnpuU4 snRNADdx20Dhx9SnrpelCpsf4U5 snRNASFRS5Cdc40Sfrs16RngttHnrnpabSrpk1Clk3Clk1SNRPD3U1 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


Description

This process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' polyadenylation, and RNA splicing, which occur in the cell nucleus before the RNA is translated.

5' Capping: Capping of the pre-mRNA involves the addition of 7-methylguanosine (m7G) to the 5' end. The cap protects the 5' end of the primary RNA transcript from attack by ribonucleases that have specificity to the 3'5' phosphodiester bonds.

3' Processing: The pre-mRNA processing at the 3' end of the RNA molecule involves cleavage of its 3' end and then the addition of about 200 adenine residues to form a poly(A) tail. As the poly(A) tails is synthesised, it binds multiple copies of poly(A) binding protein, which protects the 3'end from ribonuclease digestion.

Splicing: RNA splicing is the process by which introns, regions of RNA that do not code for protein, are removed from the pre-mRNA and the remaining exons connected to re-form a single continuous molecule.

Description adapted from Wikipedia: http://en.wikipedia.org/wiki/Post-transcriptional_modification

Comments

GenMAPP notes 
Gene lists from obtained from InterPro 9-23-2003: Mm RNA-binding region RNP-1 (RNA recognition motif)
GenMAPP remarks 
Adapted from http://www.reactome.org.
HomologyConvert 
This pathway was inferred from Homo sapiens pathway WP411(r30272) with a 80% conversion rate.

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Ontology Terms

 

Bibliography

  1. Carmody SR, Wente SR; ''mRNA nuclear export at a glance.''; J Cell Sci, 2009 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
117004view11:17, 16 May 2021EweitzModified title
95766view14:20, 19 January 2018MkutmonHomology conversion update
78477view10:28, 7 January 2015MaintBotadded missing graphIds
71768view20:30, 17 October 2013MaintBotAutomated update of data sources
69333view18:50, 8 July 2013MaintBotUpdated to 2013 gpml schema
67500view11:10, 26 June 2013DdiglesOntology Term : 'spliceosome pathway' added !
47776view05:42, 6 April 2012Khanspersupdated xref
41645view02:33, 2 March 2011MaintBotRemoved redundant pathway information and comments
35232view19:07, 11 February 2010KhanspersUpdated xrefs
35231view18:57, 11 February 2010KhanspersModified description
34047view19:01, 9 December 2009MaintBotAutomatic update of empty xrefs
32458view17:25, 15 August 2009MaintBotFixed text labels
32141view13:58, 14 August 2009MaintBotFixed group labels
31474view21:20, 13 August 2009MaintBotFixed text labels
30968view00:48, 30 July 2009MaintBotConverted from Homo sapiens
21792view11:32, 14 November 2008MaintBot[[Pathway:Rattus norvegicus:mRNA processing Reactome]] moved to [[Pathway:WP529]]: Moved to stable identifier
8276view13:46, 7 January 2008MaintBot[[Pathway:Rat:mRNA processing Reactome]] moved to [[Pathway:Rattus norvegicus:mRNA processing Reactome]]: Renaming species
7758view16:16, 18 December 2007MaintBotfixed category names
7320view12:42, 4 November 2007MaintBotAdded categories to GPML
6611view22:20, 22 May 2007Nsalomonisgpml file for [[Rat:mRNA_processing_Reactome]]

External references

DataNodes

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NameTypeDatabase referenceComment
ATPMetabolite
Brunol4GeneProduct307540 (Entrez Gene)
CLK4GeneProduct287269 (Entrez Gene)
CSTF2GeneProduct683927 (Entrez Gene)
Cd2bp2GeneProduct293505 (Entrez Gene)
Cdc40GeneProduct361859 (Entrez Gene)
Clk1GeneProduct301434 (Entrez Gene) PMID: 15010457: Inhibitor John C. Bell, PhD

Professor, Depts. of Medicine and Biochemistry, Microbiology & Immunology University of Ottawa Career Scientist, Ottawa Regional Cancer Centre Associate Scientist, The Ottawa Hospital Research Institute Telephone: 613-737-7700 ext 6893 Fax: 613-247-3524 Email: [email protected] The control of pre-mRNA splicing by the Clk kinase family

We are studying a family of kinases which we believe provide an interface between intracellular signaling networks and the post-transcriptional mechanism of mRNA splicing. We are performing a structure:function analysis of the three Clk family members to identify domains in the three proteins which are involved in regulating splicing. Using homologous recombination we are generating null strains of mice which are lacking one, two or all three Clk genes. The Clk kinases all possess dual specificity kinase activity and yeast expression systems are being used to produce large amounts of the kinase to perform a detailed analysis of the sites of serine, threonine and tyrosine autophosphorylation within the kinase.
Clk2GeneProduct365842 (Entrez Gene)
Clk3GeneProduct171305 (Entrez Gene)
Clp1GeneProduct311166 (Entrez Gene)
Cpsf1GeneProduct366952 (Entrez Gene)
Cpsf2GeneProduct299256 (Entrez Gene)
Cpsf3GeneProduct298916 (Entrez Gene)
Cpsf4GeneProduct304277 (Entrez Gene)
Cpsf5GeneProduct291877 (Entrez Gene)
Cstf1GeneProduct311670 (Entrez Gene)
Cstf2tGeneProduct309338 (Entrez Gene)
Cstf3GeneProduct362178 (Entrez Gene)
Cugbp1GeneProduct362160 (Entrez Gene)
Cugbp2GeneProduct29428 (Entrez Gene)
Ddx1GeneProduct84474 (Entrez Gene)
Ddx20GeneProduct84473 (Entrez Gene)
Dhx15GeneProduct289693 (Entrez Gene)
Dhx16GeneProduct294232 (Entrez Gene)
Dhx38GeneProduct292007 (Entrez Gene)
Dhx8GeneProduct287727 (Entrez Gene)
Dhx9GeneProduct304859 (Entrez Gene)
Dicer1GeneProduct299284 (Entrez Gene)
Dnajc8GeneProduct313035 (Entrez Gene)
Eftud2GeneProduct287739 (Entrez Gene)
FUSIP1GeneProduct362630 (Entrez Gene) FUSI MOUSE PMID: 11684676
FusGeneProduct317385 (Entrez Gene)
GMPMetabolite
Gstt2GeneProduct29487 (Entrez Gene) GenBank sequence: M10329
HNRPA1GeneProduct
HNRPA3P1GeneProduct
HNRPH1GeneProduct140931 (Entrez Gene)
HNRPMGeneProduct116655 (Entrez Gene)
Hnrnpa2b1GeneProduct362361 (Entrez Gene)
HnrnpabGeneProduct83498 (Entrez Gene)
HnrnpcGeneProduct290046 (Entrez Gene)
Hnrnph2GeneProduct308650 (Entrez Gene)
HnrnpkGeneProduct117282 (Entrez Gene)
HnrnplGeneProduct80846 (Entrez Gene)
HnrnprGeneProduct319110 (Entrez Gene)
HnrnpuGeneProduct117280 (Entrez Gene)
HnrpdGeneProduct79256 (Entrez Gene)
LOC690372GeneProduct690372 (Entrez Gene)
LSM2GeneProduct684148 (Entrez Gene)
Lsm7GeneProduct362829 (Entrez Gene)
Mettl3GeneProduct361035 (Entrez Gene)
NCBP2GeneProduct288040 (Entrez Gene)
Ncbp1GeneProduct298075 (Entrez Gene)
NonoGeneProduct317259 (Entrez Gene)
Nxf1GeneProduct59087 (Entrez Gene)
Pabpn1GeneProduct116697 (Entrez Gene)
PapolaGeneProduct314417 (Entrez Gene)
Pcbp2GeneProduct363005 (Entrez Gene)
Phf5aGeneProduct192246 (Entrez Gene)
Polr2aGeneProduct363633 (Entrez Gene)
Ppm1gGeneProduct259229 (Entrez Gene) PMID: 12773558
Prmt1GeneProduct60421 (Entrez Gene)
Prmt2GeneProduct499420 (Entrez Gene)
Prpf18GeneProduct171552 (Entrez Gene)
Prpf3GeneProduct361995 (Entrez Gene)
Prpf40aGeneProduct295607 (Entrez Gene)
Prpf4GeneProduct298095 (Entrez Gene)
Prpf4bGeneProduct291078 (Entrez Gene)
Prpf6GeneProduct366276 (Entrez Gene)
Prpf8GeneProduct287530 (Entrez Gene)
Pskh1GeneProduct364993 (Entrez Gene) PMID: 12466556
Ptbp1GeneProduct29497 (Entrez Gene)
Ptbp2GeneProduct310820 (Entrez Gene)
RGD1309198GeneProduct313056 (Entrez Gene)
RNU2GeneProductGenBank sequence: K00027
Rbm17GeneProduct291295 (Entrez Gene)
Rbm39GeneProduct362251 (Entrez Gene)
Rbm5GeneProduct300996 (Entrez Gene)
RbmxGeneProduct302855 (Entrez Gene)
RngttGeneProduct313131 (Entrez Gene)
RnmtGeneProduct291534 (Entrez Gene)
Rnps1GeneProduct287113 (Entrez Gene) PMID: 14729963
SFRS5GeneProduct29667 (Entrez Gene)
SFRS7GeneProduct362687 (Entrez Gene)
SNRPA1GeneProduct292997 (Entrez Gene)
SNRPD3GeneProduct
SNRPGGeneProduct681031 (Entrez Gene)
SSFA1GeneProduct366501 (Entrez Gene)
Sf3a1GeneProduct305479 (Entrez Gene)
Sf3a2GeneProduct299620 (Entrez Gene)
Sf3a3GeneProduct313583 (Entrez Gene)
Sf3b1GeneProduct84486 (Entrez Gene)
Sf3b2GeneProduct293671 (Entrez Gene)
Sf3b3GeneProduct292019 (Entrez Gene)
Sf3b4GeneProduct295270 (Entrez Gene)
Sf3b5GeneProduct680891 (Entrez Gene)
Sf4GeneProduct290666 (Entrez Gene) inferred from: SURP 2, G patch protein, UniProt:O60378
SfpqGeneProduct252855 (Entrez Gene)
Sfrs10GeneProduct117259 (Entrez Gene)
Sfrs12GeneProduct56763 (Entrez Gene) PMID: 14559993. SRrp86 is a unique member of the SR protein superfamily containing one RNA recognition motif and two serine-arginine (SR)-rich domains separated by an unusual glutamic acid-lysine (EK)-rich region. Previously, we showed that SRrp86 could regulate alternative splicing by both positively and negatively modulating the activity of other SR proteins and that the unique EK domain could inhibit both constitutive and alternative splicing. These functions were most consistent with the model in which SRrp86 functions by interacting with and thereby modulating the activity of target proteins. To identify the specific proteins that interact with SRrp86, we used a yeast two-hybrid library screen and immunoprecipitation coupled to mass spectrometry. We show that SRrp86 interacts with all of the core SR proteins, as well as a subset of other splicing regulatory proteins, including SAF-B, hnRNP G, YB-1, and p72. In contrast to previous results that showed activation of SRp20 by SRrp86, we now show that SAF-B, hnRNP G, and 9G8 all antagonize the activity of SRrp86. Overall, we conclude that not only does SRrp86 regulate SR protein activity but that it is, in turn, regulated by other splicing factors to control alternative splice site selection.
Sfrs14GeneProduct361126 (Entrez Gene)
Sfrs16GeneProduct499390 (Entrez Gene)
Sfrs1GeneProduct689890 (Entrez Gene) Antagonist splicing factor
Sfrs2GeneProduct494445 (Entrez Gene)
Sfrs3GeneProduct361814 (Entrez Gene)
Sfrs4GeneProduct362612 (Entrez Gene)
Sfrs6GeneProduct362264 (Entrez Gene)
Sfrs8GeneProduct304431 (Entrez Gene)
Sfrs9GeneProduct288701 (Entrez Gene) PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
Smc1aGeneProduct63996 (Entrez Gene)
Snrp70GeneProduct361574 (Entrez Gene)
SnrpaGeneProduct292729 (Entrez Gene)
SnrpbGeneProduct171365 (Entrez Gene)
Snrpb2GeneProduct362223 (Entrez Gene)
Snrpd1GeneProduct291794 (Entrez Gene)
Snrpd2GeneProduct680309 (Entrez Gene)
SnrpelGeneProduct360844 (Entrez Gene)
SnrpfGeneProduct680737 (Entrez Gene)
SnrpnGeneProduct81781 (Entrez Gene)
SpopGeneProduct287643 (Entrez Gene)
Srp54aGeneProduct116650 (Entrez Gene) PMID: 14729963
Srpk1GeneProduct361811 (Entrez Gene) PMID: 12773558
Srpk2GeneProduct296753 (Entrez Gene) PMID: 12773558
Srrm1GeneProduct313620 (Entrez Gene)
Supt5hGeneProduct308472 (Entrez Gene)
TXNL4AGeneProduct291415 (Entrez Gene)
Tmed10GeneProduct84599 (Entrez Gene)
U1 snRNAGeneProductGenBank sequence: J00645
U2AF1GeneProduct
U4 snRNAGeneProductGenBank sequence: M10328, M18004
U5 snRNAGeneProductGenBank sequence: AB021173
Xrn2GeneProduct362229 (Entrez Gene)
Ybx1GeneProduct500538 (Entrez Gene)

Annotated Interactions

No annotated interactions
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