mRNA Processing (Bos taurus)

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RNAi pathwayintron5Note: New participating members shown at each stepCleavage at the 3'-Splice-Site and Exon Ligation5Formation of the Spliceosomal A complex35Primary RNA transcriptCleavage of mRNA at the 3'-end5UGheterogeneous nuclear ribonucleoproteinsASR-phosphatasesAG(3)CF ICap BindingU4/U63exon 13Spt5Additional Factorsexon 1(1)Additional FactorsU1 snRNPSR-binding sitesMisc.YYYYCstFsplicing factor SF3APi65splicing factor SF3BYYYYFormation of the Spliceosomal C complex3Formation of the active Spliceosomal C complexAAUAAAexon 25Additional SR proteinsACPSFU5U6CF IImRNA 3'-end processing5hnRNP regulatorsFormation of pre-mRNPsAccessory Proteinsexon 2SR-binding sitesLariat Formation and 5'-Splice Site CleavageRNA helicase Aexon 2U2 snRNP(2)CPSFPPoly(A)-binding protein IIAGSR protein kinases3AU5 snRNPFormation of the Spliceosomal B complexsnRNP Sm core complexpre-mRNAPoly(A) polFormation of the Spliceosomal B complexYYYYCFIexon 1Kinases Phosphorylating RS domains?exon 2YYYY(2a)SF3b14bU4 snRNPCAdegradedAexon 13exon 1SR-proteinsiPohnRNPsU2AF5Regulation ofAlternative SplicingAAdditional FactorsRNA helicaseU2 snRNPs5 G capP-3mRNA splice site selectionRngtt (capping enzyme)5AG3Methylation of mRNASerine/Argenine Rich Proteins(SR)5AGsplicesome associated helicases(2c)YYYY35SR protein phosphatasesU6 snRNPSR-kinasesUGright click on blue text for detailed informationSR-proteinssnRNP Sm core complexFormation of pre-mRNPsU23SR-proteinsU5U2 snRNPInternal methylation of mRNAU4:U5:U6 tri-snRNP complexFormation of the Spliceosomal E complexProcessing of Intron-Containing Pre-mRNAU1exon 1Poly(A)pb IIPolr2aU2AFInternal methylation of mRNAPoly(A) polymerase alpha3mRNA capping5U4CstFmRNA Capping(2b)SR-repressor proteinsFormation of the Spliceosomal A complexRnmt (methyltransferase)YYYYPutative Alternative SplicingRegulatorsFormation of the Spliceosomal E complexAGGUU1 snRNPAGexon 23snRNP Sm core complexexon 2AAAAAAACF II5mRNA splicing (major pathway)mRNA polyadenylationASF3A1SSFA1HNRNPH2HNRNPH1PABPN1EFTUD2RBM17SRPK1U5 snRNAHNRNPDCSTF3RBM5CUGBP2SNRPD2PRMT1SNRPFPAPOLACSTF2SF4HNRNPKU4 snRNALSM2CSTF1SFRS12CPSF2SNRPARNU2HRMT1L1FUSIP1CPSF3POLR2ASF3A3CLK1DHX15HNRNPUSNRPNSSFA1HNRPA1BRUNOL4CSTF2TPSKH1DDX20SNRPB2CPSF1SNRPA1ATPFNBP3PTBP1SNRPD3PRPF4U2AF1CPSF4PRPF3LOC100124428SSFA1SRRM1PRPF8RNMTFUSIP1U1 snRNANXF1CLK2SFRS5LOC789375SNRPGDDX1HNRNPABDNAJC8NUDT21LOC615374HNRNPRSFRS16RNGTTHNRNPLCDC40DICER1SF3B1HNRNPCGMPRBM39DHX16SFRS8PRPF4SFRS3NONOU2AF2DHX38SFRS6SFPQSF3B5HNRNPMTRA2BSNRPD1LSM7SUPT5HSFRS4CD2BP2CLK4TXNL4ASNRNP70RNPS1TMED10SMC1APRPF6FUSPRPF18SFRS7SF3B4SFRS2SF3B2SRPK2SFRS1PRPF4BNCBP2PTBP2LSM2PPM1GMETTL3CDC40CUGBP1HNRPA3P1SNRNP40SFRS14SNRPNCLP1XRN2SF3B3CLK3SNRPBSFRS9YBX1PHF5APRPF8DHX8SRP54RBMXSF3A2DHX9HNRNPA2B1PCBP2SPOP


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:


GenMAPP notes 
Gene lists from obtained from InterPro 9-23-2003: Mm RNA-binding region RNP-1 (RNA recognition motif)
GenMAPP remarks 
Adapted from
This pathway was inferred from Homo sapiens pathway WP411(r30272) with a 85% conversion rate.

Quality Tags

Ontology Terms



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


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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


View all...
NameTypeDatabase referenceComment
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: 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)
FUSGeneProduct280796 (Entrez Gene)
FUSIP1GeneProduct782389 (Entrez Gene) FUSI MOUSE PMID: 11684676
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)
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)
SUPT5HGeneProduct519808 (Entrez Gene)
TMED10GeneProduct529761 (Entrez Gene)
TRA2BGeneProduct615156 (Entrez Gene)
TXNL4AGeneProduct535457 (Entrez Gene)
U1 snRNAGeneProductGenBank sequence: J00645
U2AF1GeneProduct512680 (Entrez Gene)
U2AF2GeneProduct507895 (Entrez Gene)
U4 snRNAGeneProductGenBank sequence: M10328, M18004
U5 snRNAGeneProductGenBank sequence: AB021173
XRN2GeneProduct517417 (Entrez Gene)
YBX1GeneProduct287023 (Entrez Gene)

Annotated Interactions

No annotated interactions
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