mRNA processing (Rattus norvegicus)

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U4Cleavage of mRNA at the 3'-endexon 2RNA helicasePoly(A)pb IIexon 135SR-repressor proteinsUGmRNA polyadenylation35U4/U6Formation of the Spliceosomal B complexSR protein phosphatasesU4 snRNPSF3b14bU6 snRNP(2b)U2AFFormation of the active Spliceosomal C complexRngtt (capping enzyme)YYYYAdditional SR proteinsAG(1)U2 snRNPssplicesome associated helicasesInternal methylation of mRNASR-proteinsCstFAG(2c)Formation of the Spliceosomal A complexexon 1snRNP Sm core complex5pre-mRNAsnRNP Sm core complexCPSFAdditional Factors5CA3UGright click on blue text for detailed informationU1 snRNPGUSR-proteinsMethylation of mRNAAsplicing factor SF3BU2 snRNP3Formation of pre-mRNPsSerine/Argenine Rich Proteins(SR)AAAAAAAAAGPi(2)exon 25SR-phosphatases3AGexon 1Spt53Polr2aexon 2CF II(2a)Rnmt (methyltransferase)5Primary RNA transcriptARNAi pathway35 G capFormation of the Spliceosomal E complexAccessory Proteins5intronexon 1exon 13U2AGexon 2Formation of the Spliceosomal E complexmRNA cappinghnRNPsYYYYhnRNP regulatorsP-SR-binding sitesLariat Formation and 5'-Splice Site CleavageCF IIAAUAAAFormation of the Spliceosomal A complexU5 snRNPYYYYAdditional FactorsU1PiPomRNA CappingU4:U5:U6 tri-snRNP complexAGPoly(A)-binding protein IICF I55Note: New participating members shown at each stepRegulation ofAlternative SplicingFormation of the Spliceosomal C complexYYYYU5exon 1Cap BindingU1 snRNPmRNA splice site selectionFormation of pre-mRNPsAsplicing factor SF3Aheterogeneous nuclear ribonucleoproteinssnRNP Sm core complexSR-binding sites3SR-proteinsdegraded5Processing of Intron-Containing Pre-mRNA5A3SR protein kinasesU2 snRNP(3)CPSFCleavage at the 3'-Splice-Site and Exon LigationCFI3Internal methylation of mRNAFormation of the Spliceosomal B complexAMisc.U2AFSR-kinasesU5exon 25CstFPoly(A) polymerase alpha65exon 2mRNA splicing (major pathway)U6Putative Alternative SplicingRegulatorsKinases Phosphorylating RS domains?YYYYYYYY3RNA helicase APoly(A) polmRNA 3'-end processingAdditional FactorsHnrnpa2b1Nxf1Srpk1TXNL4APtbp2SnrpfSnrp70Sfrs4U2af1l4Dhx38Cpsf5Sf3a3Prpf4GMPSNRPA1Cstf2tSnrpd1RnmtPrpf18Dnajc8Pabpn1SNRPGCpsf3Rnu6HnrnprSf3b2Hnrnph2Clk2Sf4Prpf40aRGD1309198Polr2aPrpf6Cpsf1Srpk2SSFA1SSFA1Snrpd2LSM2Snrpb2Ybx1Cpsf2Srp54aPcbp2Supt5hHnrnpkSmc1aCugbp1LOC690372CSTF2HnrpdLsm7Clp1Prpf8SNRPD3Sf3a2U1 snRNAHNRPMPrmt2CLK4Dicer1Hnrpa1Cdc40ATPRbm17Cd2bp2Dhx16Rnps1Ptbp1U4 snRNASf3b1Prpf8Dhx8Xrn2Cstf1Dhx9Sfrs8Sfrs10Cstf3Brunol4NCBP2SnrpbSfrs9SnrpnPpm1gFusPapolaEftud2HNRPA3P1HnrnpabFUSIP1Sfrs12Sf3a1Sfrs16Srrm1FUSIP1Prpf4bRngttSfrs3Ddx20NonoSpopDhx15Mettl3Prpf3Sfrs6Prpf4Tmed10SnrpnSFRS7Cugbp2Prmt1SnrpelHnrnpcHnrnpuRbmxLSM2Sfrs14Rbm5Clk1Ncbp1HnrnplCdc40Sfrs2U5 snRNAClk3RNU2SFRS5Rbm39Sf3b5Phf5aSf3b4HNRPH1SnrpaPskh1SSFA1Ddx1Cpsf4Sf3b3SfpqSfrs1


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

View all...
NameTypeDatabase referenceComment
ATPMetaboliteHMDB01532 (HMDB)
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)
GMPMetaboliteHMDB01397 (HMDB)
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)
Hnrpa1GeneProduct29578 (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
Rnu6GeneProductGenBank sequence: M10329
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 snRNARnaGenBank sequence: J00645
U2af1l4GeneProduct361542 (Entrez Gene)
U4 snRNARnaGenBank sequence: M10328, M18004
U5 snRNARnaGenBank sequence: AB021173
Xrn2GeneProduct362229 (Entrez Gene)
Ybx1GeneProduct500538 (Entrez Gene)

Annotated Interactions

No annotated interactions
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