mRNA processing (Caenorhabditis elegans)

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U4:U5:U6 tri-snRNP complexFormation of the Spliceosomal A complexPoly(A)pb IIYYYYexon 1SR-proteinsU6U2 snRNPsAAGPoly(A) polSF3b14bU4 snRNPPolr2aPoly(A) polymerase alphaAGexon 1YYYYProcessing of Intron-Containing Pre-mRNARnmt (methyltransferase)AU2 snRNPYYYYU5P-Formation of pre-mRNPsmRNA Capping3U4/U6splicing factor SF3BFormation of the active Spliceosomal C complex5Alternative Splicingheterogeneous nuclear ribonucleoproteinsU2AFhnRNP regulatorsAdditional FactorsFormation of the Spliceosomal E complexRNA helicase AU4degradedAGMethylation of mRNAexon 153Note: New participating members shown at each stepFormation of the Spliceosomal A complexGUCstFCF IIACF I5YYYYintronRNA helicase53exon 2Internal methylation of mRNAmRNA splicing (major pathway)Additional FactorsPutative Alternative SplicingU5U1exon 2GMPPiAUG5 G capAGAAAAAAAexon 1U6 snRNPAU2 snRNPYYYYexon 2Cap BindingFormation of the Spliceosomal E complexsnRNP Sm core complexhnRNPspre-mRNAFormation of the Spliceosomal B complex653snRNP Sm core complex355RegulatorsmRNA splice site selectionUG3CFIU2CF IISR-binding sitesAGexon 2U2AFSR-proteinsexon 2exon 15Additional SR proteinsAccessory Proteinsexon 1Internal methylation of mRNA5exon 23Formation of the Spliceosomal C complexSR-binding sitesU5 snRNPAGFormation of the Spliceosomal B complexSR protein kinasesPrimary RNA transcriptSerine/Argenine Rich Proteins(SR)snRNP Sm core complex5AYYYYsplicing factor SF3ASpt5U1 snRNPRegulation of35Poly(A)-binding protein II533Formation of pre-mRNPsU1 snRNPmRNA cappingRNAi pathwayiPo3DDX20rsp-7dnj-30pab-3ptb-1rsp-6cpf-2Rnu6rnp-3RNU2spt-5rsp-1prp-8tag-72U1 snRNASF3B5prp-17SSFA1snr-7CLK1Y59A8B.6Y113G7B.17cpf-1F58B3.7F43G9.5hrp-2C27H5.3HNRPABC36B1.5FUSIP1HNRPA2B1HNRPA1suf-1CLK3him-1snr-6PTBP2METTL3SFRS9PCBP2mog-4phf-5F56D2.6F11A10.2gut-2prp-4Y55F3AM.3C25A1.4nxf-1prp-17lsm-7F28C1.1HNRPH2CSTF2F59A2.4W03F9.10HNRPCSFRS3CLK4U5 snRNAC36B1.5F43G6.5SF4Y48B6A.3Y76B12C.7uaf-1SFRS5T13H5.4cel-1M03C11.7F11A10.8Y73B6BL.33NONOHNRPA3P1SFRS10RBMXbath-43rha-1rsp-3F47G9.1gut-2rsr-1F09G2.4HNRPDsap-1snr-4SNRPNetr-1rnp-2ama-1eft-1F37E3.1prp-21snr-1SF3B4rsp-4mog-5T08A11.2tag-203FNBP3rsp-2TXNL4Ateg-1dcr-1snr-5HRMT1L1rnp-7SFRS14T08B2.5SSFA1SNRPBprp-8SNRPNNCBP2snr-3HNRPKC44B7.2Y67H2A.1unc-75NSEP1mog-1F08G12.2Y55F3BR.1CUGBP2tag-172U4 snRNA


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

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71848view20:09, 18 October 2013MaintBotremoved data source from nodes without identifier
69960view20:58, 11 July 2013MaintBotupdating to 2013 schema
67495view11:09, 26 June 2013DdiglesOntology Term : 'spliceosome pathway' added !
40645view19:58, 1 March 2011MaintBotRemoved redundant pathway information and comments
35240view19:45, 11 February 2010KhanspersModified description
20941view11:30, 14 November 2008MaintBot[[Pathway:Caenorhabditis elegans:mRNA processing Reactome]] moved to [[Pathway:WP123]]: Moved to stable identifier
8507view14:01, 7 January 2008MaintBotAdded to category $category
8505view14:01, 7 January 2008NsalomonisUploaded new pathway

External references


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NameTypeDatabase referenceComment
C25A1.4GeneProduct172881 (Entrez Gene)
C27H5.3GeneProduct174175 (Entrez Gene)
C36B1.5GeneProduct183250 (Entrez Gene)
C44B7.2GeneProduct3565706 (Entrez Gene)
CLK1GeneProductPMID: 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.
F08G12.2GeneProduct181319 (Entrez Gene)
F09G2.4GeneProduct179103 (Entrez Gene)
F11A10.2GeneProduct178147 (Entrez Gene)
F11A10.8GeneProduct178151 (Entrez Gene)
F28C1.1GeneProduct179705 (Entrez Gene)
F37E3.1GeneProduct172345 (Entrez Gene)
F43G6.5GeneProduct174816 (Entrez Gene)
F43G9.5GeneProduct172657 (Entrez Gene)
F47G9.1GeneProduct179567 (Entrez Gene)
F56D2.6GeneProduct175771 (Entrez Gene)
F58B3.7GeneProduct178091 (Entrez Gene)
F59A2.4GeneProduct175442 (Entrez Gene)
M03C11.7GeneProduct176461 (Entrez Gene)
RNU2GeneProductGenBank sequence: K00027
Rnu6GeneProductGenBank sequence: M10329
SF4GeneProductinferred from: SURP 2, G patch protein, UniProt:O60378
SFRS9GeneProductPMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
T08A11.2GeneProduct175549 (Entrez Gene)
T08B2.5GeneProduct172312 (Entrez Gene)
T13H5.4GeneProduct174364 (Entrez Gene)
U1 snRNAGeneProductGenBank sequence: J00645
U4 snRNAGeneProductGenBank sequence: M10328, M18004
U5 snRNAGeneProductGenBank sequence: AB021173
W03F9.10GeneProduct178542 (Entrez Gene)
Y113G7B.17GeneProduct180326 (Entrez Gene)
Y48B6A.3GeneProduct175071 (Entrez Gene)
Y55F3AM.3GeneProduct176922 (Entrez Gene)
Y55F3BR.1GeneProduct176913 (Entrez Gene)
Y59A8B.6GeneProduct180180 (Entrez Gene)
Y67H2A.1GeneProduct178285 (Entrez Gene)
Y73B6BL.33GeneProduct177398 (Entrez Gene)
Y76B12C.7GeneProduct177003 (Entrez Gene)
ama-1GeneProduct177190 (Entrez Gene)
bath-43GeneProduct176422 (Entrez Gene)
cel-1GeneProduct172814 (Entrez Gene)
cpf-1GeneProduct174378 (Entrez Gene)
cpf-2GeneProduct176742 (Entrez Gene)
dcr-1GeneProduct176138 (Entrez Gene)
dnj-30GeneProduct171833 (Entrez Gene)
eft-1GeneProduct175851 (Entrez Gene)
etr-1GeneProduct173401 (Entrez Gene)
gut-2GeneProduct179833 (Entrez Gene)
him-1GeneProduct172116 (Entrez Gene)
hrp-2GeneProduct173086 (Entrez Gene)
lsm-7GeneProduct177988 (Entrez Gene)
mog-1GeneProduct176409 (Entrez Gene)
mog-4GeneProduct175117 (Entrez Gene)
mog-5GeneProduct173920 (Entrez Gene)
nxf-1GeneProduct191736 (Entrez Gene)
pab-3GeneProduct172768 (Entrez Gene)
phf-5GeneProduct3564851 (Entrez Gene)
prp-17GeneProduct172999 (Entrez Gene)
prp-21GeneProduct173440 (Entrez Gene)
prp-4GeneProduct172443 (Entrez Gene)
prp-8GeneProduct176153 (Entrez Gene)
ptb-1GeneProduct174647 (Entrez Gene)
rha-1GeneProduct174417 (Entrez Gene)
rnp-2GeneProduct177181 (Entrez Gene)
rnp-3GeneProduct177182 (Entrez Gene)
rnp-7GeneProduct176002 (Entrez Gene)
rsp-1GeneProduct174748 (Entrez Gene)
rsp-2GeneProduct174747 (Entrez Gene)
rsp-3GeneProduct176688 (Entrez Gene) Antagonist splicing factor
rsp-4GeneProduct173915 (Entrez Gene)
rsp-6GeneProduct177566 (Entrez Gene)
rsp-7GeneProduct174646 (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.
rsr-1GeneProduct173013 (Entrez Gene)
sap-1GeneProduct173767 (Entrez Gene)
snr-1GeneProduct178483 (Entrez Gene)
snr-3GeneProduct174072 (Entrez Gene)
snr-4GeneProduct179639 (Entrez Gene)
snr-5GeneProduct176103 (Entrez Gene)
snr-6GeneProduct176668 (Entrez Gene)
snr-7GeneProduct171834 (Entrez Gene)
spt-5GeneProduct178143 (Entrez Gene)
suf-1GeneProduct174380 (Entrez Gene)
tag-172GeneProduct3565068 (Entrez Gene)
tag-203GeneProduct172406 (Entrez Gene)
tag-72GeneProduct182875 (Entrez Gene)
teg-1GeneProduct176561 (Entrez Gene)
uaf-1GeneProduct175270 (Entrez Gene)
unc-75GeneProduct182722 (Entrez Gene)

Annotated Interactions

No annotated interactions
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