mRNA Processing (Bos taurus)

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YYYY65Poly(A) polMisc.Internal methylation of mRNAProcessing of Intron-Containing Pre-mRNAUG3SF3b14bexon 13exon 2splicing factor SF3B5 G capSR protein kinasesPoly(A)-binding protein II35CFImRNA 3'-end processingexon 2AGAdditional SR proteins5AAFormation of pre-mRNPsAhnRNPsU5Pisplicesome associated helicasesAAUAAAGU3YYYYSerine/Argenine Rich Proteins(SR)(2c)exon 1P-YYYYFormation of the Spliceosomal E complexPrimary RNA transcript5iPoAdditional FactorsCF IIU5 snRNPSR-phosphatasessnRNP Sm core complexdegradedU2 snRNPs(3)U6 snRNPU2AFSR-binding sites5mRNA capping5Kinases Phosphorylating RS domains?Lariat Formation and 5'-Splice Site CleavageAAAAAAAright click on blue text for detailed informationCF IIU4SR-proteinsU2 snRNPexon 1Poly(A) polymerase alphaInternal methylation of mRNAAGSR protein phosphatasesCAmRNA splicing (major pathway)exon 2YYYYAG5Formation of the active Spliceosomal C complexACF I3U2AF3PFormation of the Spliceosomal E complex5Rnmt (methyltransferase)Regulation ofAlternative SplicingCPSFexon 2Formation of the Spliceosomal A complexYYYYSpt5Methylation of mRNAU4/U63SR-proteins(2b)U4 snRNPexon 1ACap Binding3U1 snRNPYYYY5CPSFSR-kinasesPutative Alternative SplicingRegulators(1)3mRNA Capping3splicing factor SF3AFormation of pre-mRNPsFormation of the Spliceosomal A complexAGsnRNP Sm core complexU5exon 1CstFAGCleavage of mRNA at the 3'-endexon 1RNAi pathwayPolr2aU2 snRNPCstF(2a)3Additional FactorsRNA helicase AU1 snRNP(2)U1Poly(A)pb IIFormation of the Spliceosomal C complexApre-mRNAAccessory ProteinsSR-repressor proteinsRNA helicaseUGmRNA polyadenylationAdditional Factorsexon 2U2Cleavage at the 3'-Splice-Site and Exon LigationFormation of the Spliceosomal B complexU4:U5:U6 tri-snRNP complexhnRNP regulatorsexon 2Formation of the Spliceosomal B complex3SR-binding sitesU6Note: New participating members shown at each step55heterogeneous nuclear ribonucleoproteinsRngtt (capping enzyme)5intronAGsnRNP Sm core complex5SR-proteinsmRNA splice site selectionNUDT21LOC615374CUGBP2SMC1AFUSIP1DHX9METTL3SF3A2LOC100124428CPSF1CSTF2TPTBP2RNU2NCBP2SFRS16PHF5APCBP2SNRPGCPSF4SSFA1DDX20HNRNPH2PRPF4TMED10ATPSF3B3SRPK1SNRPNSF3B4PAPOLASFRS14RNGTTU1 snRNADICER1TRA2BSFRS2SFPQGMPHNRNPDSNRPD1SRRM1SF3B2SRPK2PRPF6EFTUD2HNRPA3P1PRPF3SNRPASNRPA1HNRNPMCPSF3NONOSPOPSNRPBPRPF4CPSF2CSTF2HNRNPH1DHX15CSTF3CDC40HNRNPCPOLR2ASRP54SF3A3DHX38SNRPD3U2AF1SFRS4SF3A1U5 snRNADHX16RBM17TXNL4AFUSCLP1SNRNP70NXF1BRUNOL4PTBP1HNRNPRFUSIP1HNRNPKSFRS12SFRS3SNRPD2LSM7SFRS5CLK2RBM39SUPT5HSFRS8CLK1DDX1SNRPB2XRN2SF3B1PRPF8LSM2CD2BP2SSFA1PRPF4BCLK3SFRS7SF3B5U4 snRNADHX8PABPN1RNPS1HNRNPUHRMT1L1SSFA1HNRNPABYBX1CSTF1CDC40SFRS9SF4LSM2RBMXSNRPNPPM1GHNRNPLCLK4RBM5PRPF8CUGBP1PRMT1RNMTLOC789375SFRS6PRPF18SNRNP40DNAJC8FNBP3HNRPA1HNRNPA2B1SFRS1U2AF2PSKH1SNRPF


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 85% conversion rate.

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
95764view14:18, 19 January 2018MkutmonHomology conversion update
80888view15:29, 30 June 2015Mkutmonhomology conversion
71421view19:02, 17 October 2013MaintBotAutomated update of data sources
67492view11:08, 26 June 2013DdiglesOntology Term : 'spliceosome pathway' added !
63389view00:03, 10 May 2013MaintBotUpdated to 2013 gpml schema
48124view05:41, 9 May 2012KhanspersUpdating from human to fix xref duplication
40562view19:32, 1 March 2011MaintBotRemoved redundant pathway information and comments
35238view19:44, 11 February 2010Khanspersupdated xrefs
35235view19:37, 11 February 2010KhanspersModified description
33800view00:16, 9 December 2009MaintBotAutomatic update of empty xrefs
32497view12:47, 17 August 2009MaintBotFixed text labels
32189view12:34, 15 August 2009MaintBotFixed text labels
31663view11:39, 14 August 2009MaintBotFixed group labels
31195view19:31, 13 August 2009MaintBotFixed text labels
30592view22:13, 29 July 2009MaintBotNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
ATPMetaboliteHMDB01532 (HMDB)
BRUNOL4GeneProduct535177 (Entrez Gene)
CD2BP2GeneProduct513857 (Entrez Gene)
CDC40GeneProduct514003 (Entrez Gene)
CLK1GeneProduct613808 (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: John.Bell@orcc.on.ca 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.
CLK2GeneProduct512737 (Entrez Gene)
CLK3GeneProduct505499 (Entrez Gene)
CLK4GeneProduct529633 (Entrez Gene)
CLP1GeneProduct506507 (Entrez Gene)
CPSF1GeneProduct282703 (Entrez Gene)
CPSF2GeneProduct327689 (Entrez Gene)
CPSF3GeneProduct281712 (Entrez Gene)
CPSF4GeneProduct280875 (Entrez Gene)
CSTF1GeneProduct507051 (Entrez Gene)
CSTF2GeneProduct282588 (Entrez Gene)
CSTF2TGeneProduct783569 (Entrez Gene)
CSTF3GeneProduct508491 (Entrez Gene)
CUGBP1GeneProduct540475 (Entrez Gene)
CUGBP2GeneProduct777790 (Entrez Gene)
DDX1GeneProduct510816 (Entrez Gene)
DDX20GeneProduct528433 (Entrez Gene)
DHX15GeneProduct512327 (Entrez Gene)
DHX16GeneProduct506405 (Entrez Gene)
DHX38GeneProduct520046 (Entrez Gene)
DHX8GeneProduct536093 (Entrez Gene)
DHX9GeneProduct281115 (Entrez Gene)
DICER1GeneProduct337871 (Entrez Gene)
DNAJC8GeneProduct614259 (Entrez Gene)
EFTUD2GeneProduct509425 (Entrez Gene)
FNBP3GeneProduct
FUSGeneProduct280796 (Entrez Gene)
FUSIP1GeneProduct782389 (Entrez Gene) FUSI MOUSE PMID: 11684676
GMPMetaboliteHMDB01397 (HMDB)
HNRNPA2B1GeneProduct507564 (Entrez Gene)
HNRNPABGeneProduct513410 (Entrez Gene)
HNRNPCGeneProduct510852 (Entrez Gene)
HNRNPDGeneProduct527471 (Entrez Gene)
HNRNPH1GeneProduct541202 (Entrez Gene)
HNRNPH2GeneProduct534001 (Entrez Gene)
HNRNPKGeneProduct528135 (Entrez Gene)
HNRNPLGeneProduct504520 (Entrez Gene)
HNRNPMGeneProduct515290 (Entrez Gene)
HNRNPRGeneProduct512479 (Entrez Gene)
HNRNPUGeneProduct539950 (Entrez Gene)
HNRPA1GeneProduct
HNRPA3P1GeneProduct
HRMT1L1GeneProduct
LOC100124428GeneProduct100124428 (Entrez Gene)
LOC615374GeneProduct615374 (Entrez Gene) GenBank sequence: M10329
LOC789375GeneProduct789375 (Entrez Gene)
LSM2GeneProduct538662 (Entrez Gene)
LSM7GeneProduct509920 (Entrez Gene)
METTL3GeneProduct540339 (Entrez Gene)
NCBP2GeneProduct510872 (Entrez Gene)
NONOGeneProduct615175 (Entrez Gene)
NUDT21GeneProduct518859 (Entrez Gene)
NXF1GeneProduct512136 (Entrez Gene)
PABPN1GeneProduct282298 (Entrez Gene)
PAPOLAGeneProduct338051 (Entrez Gene)
PCBP2GeneProduct540653 (Entrez Gene)
PHF5AGeneProduct507180 (Entrez Gene)
POLR2AGeneProduct282312 (Entrez Gene)
PPM1GGeneProduct286880 (Entrez Gene) PMID: 12773558
PRMT1GeneProduct520388 (Entrez Gene)
PRPF18GeneProduct507639 (Entrez Gene)
PRPF3GeneProduct510322 (Entrez Gene)
PRPF4GeneProduct508735 (Entrez Gene)
PRPF4BGeneProduct512236 (Entrez Gene)
PRPF6GeneProduct534228 (Entrez Gene)
PRPF8GeneProduct507371 (Entrez Gene)
PSKH1GeneProduct509656 (Entrez Gene) PMID: 12466556
PTBP1GeneProduct282018 (Entrez Gene)
PTBP2GeneProduct537341 (Entrez Gene)
RBM17GeneProduct512694 (Entrez Gene)
RBM39GeneProduct508722 (Entrez Gene)
RBM5GeneProduct534216 (Entrez Gene)
RBMXGeneProduct509591 (Entrez Gene)
RNGTTGeneProduct511408 (Entrez Gene)
RNMTGeneProduct511555 (Entrez Gene)
RNPS1GeneProduct504506 (Entrez Gene) PMID: 14729963
RNU2GeneProductGenBank sequence: K00027
SF3A1GeneProduct504381 (Entrez Gene)
SF3A2GeneProduct789082 (Entrez Gene)
SF3A3GeneProduct523250 (Entrez Gene)
SF3B1GeneProduct510177 (Entrez Gene)
SF3B2GeneProduct531931 (Entrez Gene)
SF3B3GeneProduct504962 (Entrez Gene)
SF3B4GeneProduct506123 (Entrez Gene)
SF3B5GeneProduct574400 (Entrez Gene)
SF4GeneProduct533971 (Entrez Gene) inferred from: SURP 2, G patch protein, UniProt:O60378
SFPQGeneProduct618226 (Entrez Gene)
SFRS12GeneProduct507801 (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.
SFRS14GeneProduct516567 (Entrez Gene)
SFRS1GeneProduct615796 (Entrez Gene) Antagonist splicing factor
SFRS16GeneProduct509208 (Entrez Gene)
SFRS2GeneProduct508312 (Entrez Gene)
SFRS3GeneProduct540276 (Entrez Gene)
SFRS4GeneProduct614310 (Entrez Gene)
SFRS5GeneProduct510474 (Entrez Gene)
SFRS6GeneProduct507828 (Entrez Gene)
SFRS7GeneProduct507066 (Entrez Gene)
SFRS8GeneProduct512326 (Entrez Gene)
SFRS9GeneProduct509905 (Entrez Gene) PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
SMC1AGeneProduct282370 (Entrez Gene)
SNRNP40GeneProduct534645 (Entrez Gene)
SNRNP70GeneProduct535113 (Entrez Gene)
SNRPA1GeneProduct512584 (Entrez Gene)
SNRPAGeneProduct509802 (Entrez Gene)
SNRPB2GeneProduct767873 (Entrez Gene)
SNRPBGeneProduct613304 (Entrez Gene)
SNRPD1GeneProduct508788 (Entrez Gene)
SNRPD2GeneProduct514932 (Entrez Gene)
SNRPD3GeneProduct617823 (Entrez Gene)
SNRPFGeneProduct615240 (Entrez Gene)
SNRPGGeneProduct783499 (Entrez Gene)
SNRPNGeneProduct780877 (Entrez Gene)
SPOPGeneProduct530618 (Entrez Gene)
SRP54GeneProduct614017 (Entrez Gene) PMID: 14729963
SRPK1GeneProduct512631 (Entrez Gene) PMID: 12773558
SRPK2GeneProduct505945 (Entrez Gene) PMID: 12773558
SRRM1GeneProduct784123 (Entrez Gene)
SSFA1GeneProduct
SUPT5HGeneProduct519808 (Entrez Gene)
TMED10GeneProduct529761 (Entrez Gene)
TRA2BGeneProduct615156 (Entrez Gene)
TXNL4AGeneProduct535457 (Entrez Gene)
U1 snRNARnaGenBank sequence: J00645
U2AF1GeneProduct512680 (Entrez Gene)
U2AF2GeneProduct507895 (Entrez Gene)
U4 snRNARnaGenBank sequence: M10328, M18004
U5 snRNARnaGenBank sequence: AB021173
XRN2GeneProduct517417 (Entrez Gene)
YBX1GeneProduct287023 (Entrez Gene)

Annotated Interactions

No annotated interactions
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