mRNA processing (Rattus norvegicus)

From WikiPathways

Revision as of 02:33, 2 March 2011 by MaintBot (Talk | contribs)
Jump to: navigation, search
Spt5exon 1AGexon 2U4/U6Rnmt (methyltransferase)Cleavage at the 3'-Splice-Site and Exon Ligation5AAAAAAAsplicing factor SF3BU2AFMethylation of mRNAUGSR-proteinsAAUAAANote: New participating members shown at each stepdegradedAAG(3)UGmRNA 3'-end processingRngtt (capping enzyme)exon 1CFIexon 1AFormation of the Spliceosomal E complex5Primary RNA transcriptInternal methylation of mRNACF ISR-repressor proteins3PmRNA splicing (major pathway)AGCleavage of mRNA at the 3'-endRNAi pathwayA3Accessory Proteins3YYYYYYYYexon 2Internal methylation of mRNAintronYYYYU2AFexon 2Formation of pre-mRNPsPoly(A)-binding protein II55exon 2(2c)iPoAdditional Factors3snRNP Sm core complexPoly(A) polymerase alphaCstF3AG(2a)exon 2(1)hnRNP regulatorsAdditional Factors53U5 snRNPCstFGU(2b)5splicing factor SF3ASF3b14bU1 snRNPsplicesome associated helicasesAGU2YYYYexon 1CPSFFormation of pre-mRNPs3snRNP Sm core complexYYYYPiCF II5mRNA cappingFormation of the active Spliceosomal C complexMisc.U1 snRNP53Formation of the Spliceosomal A complexheterogeneous nuclear ribonucleoproteinsCAFormation of the Spliceosomal A complexSR-phosphatasesSR-kinasessnRNP Sm core complexAU135mRNA polyadenylationCap Binding5SR-binding sitesU2 snRNPSerine/Argenine Rich Proteins(SR)Poly(A) polU4:U5:U6 tri-snRNP complexARNA helicaseU5Formation of the Spliceosomal C complexSR-proteinsU2 snRNPsmRNA splice site selectionLariat Formation and 5'-Splice Site CleavageSR-proteinsAdditional FactorsU6 snRNPAdditional SR proteins65Putative Alternative SplicingRegulatorsPoly(A)pb IISR protein phosphatases55U6SR-binding sitesFormation of the Spliceosomal B complexmRNA Capping5 G capCF II(2)P-U2 snRNPCPSFexon 1U4 snRNPSR protein kinases3pre-mRNAexon 1exon 2hnRNPs3AGProcessing of Intron-Containing Pre-mRNAU4Formation of the Spliceosomal B complexright click on blue text for detailed informationU5AFormation of the Spliceosomal E complexYYYYRegulation ofAlternative SplicingKinases Phosphorylating RS domains?RNA helicase A3Polr2aSnrpelRnmtRnps1SSFA1Pcbp2Cd2bp2Snrpd1Rbm5FUSIP1Sfrs2Sf3b2GMPTmed10Supt5hRbm17SFRS5Sf3b4Ybx1HNRPA3P1SSFA1Sf3a1Hnrnph2Prpf18LSM2Prpf8U1 snRNASfrs8Sf3a2SNRPA1Sf3b3Ncbp1Sfrs1Snrpb2HnrnpuSf3b5SnrpnCugbp1Sfrs6Cpsf5RGD1309198Sfrs3Brunol4Snrp70U5 snRNAHNRPMLOC690372HnrnpabGstt2U4 snRNASrpk2Prpf4HNRPH1RngttSrpk1Sf3b1Hnrpa1SnrpfDnajc8Prpf8SNRPD3SSFA1SNRPGHnrnpa2b1Clk2Pabpn1Sfrs16NonoCstf2tRbm39LSM2Sfrs10Cpsf1Eftud2FUSIP1Sf3a3RNU2Clk3Ddx20Smc1aHnrnpkSfpqCstf1TXNL4ADhx38ATPSnrpaPpm1gCdc40RbmxPrmt2SnrpbPtbp1Ptbp2Cdc40Sfrs12Dhx8Pskh1Dhx16Dicer1Sfrs14Polr2aClp1FusSFRS7Prpf6Prmt1Prpf4bHnrnplPrpf3Cugbp2Dhx15Sfrs4NCBP2SpopMettl3Srp54aCpsf2Sf4Prpf40aDhx9Prpf4Xrn2HnrpdPapolaDdx1HnrnpcU2af1l4Srrm1CLK4Cpsf3CSTF2Clk1Snrpd2Phf5aSnrpnCpsf4HnrnprLsm7Sfrs9Cstf3Nxf1


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