mRNA processing (Rattus norvegicus)

From WikiPathways

Revision as of 02:33, 2 March 2011 by MaintBot (Talk | contribs)
Jump to: navigation, search
Polr2a5YYYYexon 1exon 2Spt5Lariat Formation and 5'-Splice Site CleavageAG3splicing factor SF3AU1 snRNPCap BindingNote: New participating members shown at each stepSF3b14b3U5P-GUYYYY(2c)3(3)Misc.3CstF3exon 2Formation of the Spliceosomal A complex3Additional Factorspre-mRNAmRNA cappingPoly(A) polymerase alphaSR protein phosphatases5 G capKinases Phosphorylating RS domains?Internal methylation of mRNAYYYYmRNA 3'-end processinghnRNP regulatorsAG5Putative Alternative SplicingRegulatorsRNAi pathwayAexon 1exon 1Formation of pre-mRNPsexon 2CF IRNA helicase Aexon 1heterogeneous nuclear ribonucleoproteinsFormation of the Spliceosomal C complexAGAG5(2b)Processing of Intron-Containing Pre-mRNASR-repressor proteinsU1 snRNPU5 snRNPCF IIexon 25YYYY(2)exon 1Cleavage at the 3'-Splice-Site and Exon LigationmRNA splice site selectionSR-proteinsPoly(A) polAU6 snRNPCPSFintron(2a)3Additional FactorsU2 snRNPssnRNP Sm core complexCPSFYYYYU6exon 23mRNA polyadenylationInternal methylation of mRNA5U2 snRNPAAAAAAAACFIAGSerine/Argenine Rich Proteins(SR)Formation of the Spliceosomal B complexsplicesome associated helicasesSR-binding sitesAGAFormation of the Spliceosomal E complexMethylation of mRNAAAUAAAsnRNP Sm core complexPRngtt (capping enzyme)Formation of the Spliceosomal E complexexon 2U465Cleavage of mRNA at the 3'-endiPoright click on blue text for detailed information5Formation of the Spliceosomal A complexU2AFPoly(A)pb IIsnRNP Sm core complex3Additional Factors3U1Formation of pre-mRNPssplicing factor SF3BAccessory ProteinsFormation of the active Spliceosomal C complexSR-phosphatasesRegulation ofAlternative SplicingU4 snRNPSR protein kinasesU2AFAdditional SR proteinsCF IISR-proteinsA3UGSR-binding sitesU5Rnmt (methyltransferase)Poly(A)-binding protein II(1)PiRNA helicaseCAUGFormation of the Spliceosomal B complexdegradedU2 snRNPmRNA splicing (major pathway)55Primary RNA transcript5YYYYmRNA CappingU2exon 1CstFU4/U65hnRNPsU4:U5:U6 tri-snRNP complexSR-proteinsSR-kinases35A5Snrpd2Supt5hPpm1gSSFA1Prmt1Smc1aFUSIP1Sf4SnrpnSfrs1Sf3b1U4 snRNASfrs14Polr2aPrpf40aSfrs3RNU2Cd2bp2Prpf18SSFA1SNRPA1HNRPH1Pskh1Prpf4LSM2ATPRbmxHnrnpuSf3a1Sf3a3Sf3b4RngttLSM2Sfrs4Srp54aTXNL4ALsm7Dhx16SFRS7Rbm5Prpf6Sfrs2Rbm39Gstt2Eftud2HnrnprCLK4Hnrnpa2b1Ptbp1SSFA1Srpk1Phf5aHnrpdRnmtU2af1l4Sf3a2SnrpelCdc40Dnajc8Dhx9U5 snRNASnrpfClk1Cstf2tSfrs12Brunol4Cpsf2Cugbp1Sfrs9Sfrs6Cpsf3FUSIP1HnrnplSnrpb2U1 snRNASrrm1Dicer1SnrpbHnrnpcSfrs8SNRPGRGD1309198Sf3b2GMPSnrp70Srpk2Dhx38HNRPA3P1Ddx1SnrpaHNRPMCugbp2LOC690372Tmed10Dhx15SfpqNxf1Pcbp2SNRPD3Sfrs10Cstf3Sfrs16SnrpnCpsf4Prmt2Dhx8HnrnpkPtbp2SpopDdx20Sf3b5Ncbp1Xrn2NCBP2Rnps1Cpsf1FusPrpf3Ybx1Prpf4NonoMettl3Clp1PapolaHnrnpabRbm17SFRS5Hnrpa1Clk3CSTF2Cstf1Sf3b3Snrpd1Prpf8Cdc40Cpsf5Hnrnph2Clk2Pabpn1Prpf8Prpf4b


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.

Try the New WikiPathways

View approved pathways at the new wikipathways.org.

Quality Tags

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)
Gstt2GeneProduct29487 (Entrez Gene) GenBank sequence: M10329
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
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
Personal tools