mRNA Processing (Canis familiaris)

From WikiPathways

Revision as of 21:53, 1 March 2011 by MaintBot (Talk | contribs)
Jump to: navigation, search
Rnmt (methyltransferase)exon 25intronU5mRNA Capping(1)exon 1PiU2 snRNPs65heterogeneous nuclear ribonucleoproteinsU6Additional FactorsCAUGSR protein kinasesYYYY5mRNA 3'-end processingexon 1Cleavage of mRNA at the 3'-endSR-kinasesexon 2CF IIexon 23Formation of the Spliceosomal A complex3hnRNPsFormation of pre-mRNPsYYYYAdditional Factors5SR-phosphatasespre-mRNA5mRNA polyadenylation355mRNA splice site selectionexon 1AGAGAmRNA splicing (major pathway)GUAGSerine/Argenine Rich Proteins(SR)YYYYInternal methylation of mRNACF IIASR-binding sitesCstF(3)Cap Bindingexon 1U4:U5:U6 tri-snRNP complexCF ICFIAAUAAA5(2b)U4/U6(2)RNAi pathwayRNA helicase3UGsnRNP Sm core complexright click on blue text for detailed informationA(2c)3splicing factor SF3BSR-proteins3Misc.5U4AGFormation of the Spliceosomal B complexCstFSR-proteins5Formation of the Spliceosomal A complexAGP-Poly(A)pb IIexon 1Internal methylation of mRNALariat Formation and 5'-Splice Site CleavageRngtt (capping enzyme)U2AF5 G capexon 2U5U2 snRNPFormation of pre-mRNPsCPSFFormation of the Spliceosomal E complexSR-proteinsKinases Phosphorylating RS domains?U1 snRNP3Formation of the Spliceosomal C complexRNA helicase ACPSFMethylation of mRNA3SR-binding sites3mRNA capping5YYYYYYYYU2 snRNPNote: New participating members shown at each stepPoly(A)-binding protein IIRegulation ofAlternative SplicingSF3b14bhnRNP regulatorsCleavage at the 3'-Splice-Site and Exon LigationSR protein phosphatasessplicing factor SF3AU5 snRNPPutative Alternative SplicingRegulators35Accessory ProteinsPoly(A) polSR-repressor proteinsexon 2Polr2aU2U1 snRNPU4 snRNPProcessing of Intron-Containing Pre-mRNA3Poly(A) polymerase alpha(2a)degradedsnRNP Sm core complexsplicesome associated helicasesYYYYU6 snRNPAdditional SR proteinsAPrimary RNA transcriptexon 2AFormation of the Spliceosomal E complexAAAAAAAAiPoU1Formation of the active Spliceosomal C complex5Formation of the Spliceosomal B complex3snRNP Sm core complexAGAdditional FactorsPU2AFexon 1Spt5SNRPFRNGTTSRP54SSFA1DICER1YBX1SNRPD2NUDT21EFTUD2SFRS3DHX38ATPSFRS12RNMTHNRNPA2B1U2AF1SRRM1SF3B3DHX9RBMXU4 snRNASF3A2HNRNPRHNRPA3P1PRPF8CSTF3RNU2SFPQSF3B1SF3A1CLK1NCBP2SFRS2SF3A3SFRS8SFRS4FUSIP1RBM39TRA2BCPSF4TXNL4ASFRS5NONOSNRPASSFA1PTBP1CDC40HNRNPCSNRNP70GMPPPM1GPRPF4HNRNPH2NCBP1SRPK2SF3B2SNRPGPRPF8PHF5ASFRS14SSFA1CSTF1HNRPABLSM7SFRS9FUSXRN2PABPN1BRUNOL4SFRS1POLR2ACPSF2U5 snRNASNRPD1SNRPA1SF3B4CLK4DHX15CD2BP2HNRNPLPSKH1CSTF2SF3B5CDC40SNRPBRNPS1DNAJC8U1 snRNAPRMT1SMC1ARHOXF2PRPF3SNRPNSFRS16PRPF4BPRPF18CUGBP1DDX20TMED10SUPT5HPAPOLASF4SFRS6SNRNP40PCBP2NXF1FUSIP1PRPF40APTBP2HNRPA1DHX8SNRPB2METTL3CUGBP2HNRNPDHNRNPUCSTF2TRBM5RBM17SNRPD3LSM2SPOPHNRNPH1DDX1PRMT2HNRNPKSRPK1CLK3U2AF2CPSF1CPSF3CLK2SNRPEPRPF4SFRS7PRPF6HNRNPMSNRPNLSM2CLP1DHX16


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
122786view00:13, 18 May 2022AlexanderPicocleaning up broken comments
95765view14:20, 19 January 2018MkutmonHomology conversion update
71483view19:18, 17 October 2013MaintBotAutomated update of data sources
69956view20:51, 11 July 2013MaintBotupdated to 2013 schema
68581view23:08, 5 July 2013MaintBotUpdated to 2013 gpml schema
67493view11:09, 26 June 2013DdiglesOntology Term : 'spliceosome pathway' added !
48160view18:58, 9 May 2012MaintBotUpdating from human to fix xrefs
40740view21:53, 1 March 2011MaintBotRemoved redundant pathway information and comments
35243view19:50, 11 February 2010KhanspersModified description
34015view18:43, 9 December 2009MaintBotAutomatic update of empty xrefs
32569view13:12, 17 August 2009MaintBotFixed text labels
32247view12:54, 15 August 2009MaintBotFixed text labels
31762view12:06, 14 August 2009MaintBotFixed group labels
31267view19:57, 13 August 2009MaintBotFixed text labels
30711view22:53, 29 July 2009MaintBotNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
ATPMetabolite
BRUNOL4GeneProduct610838 (Entrez Gene)
CD2BP2GeneProduct489937 (Entrez Gene)
CDC40GeneProduct475025 (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: [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.
CLK2GeneProduct490427 (Entrez Gene)
CLK3GeneProduct478367 (Entrez Gene)
CLK4GeneProduct474645 (Entrez Gene)
CLP1GeneProduct610161 (Entrez Gene)
CPSF1GeneProduct475126 (Entrez Gene)
CPSF2GeneProduct480230 (Entrez Gene)
CPSF3GeneProduct482962 (Entrez Gene)
CPSF4GeneProduct489859 (Entrez Gene)
CSTF1GeneProduct612933 (Entrez Gene)
CSTF2GeneProduct492015 (Entrez Gene)
CSTF2TGeneProduct
CSTF3GeneProduct475948 (Entrez Gene)
CUGBP1GeneProduct475979 (Entrez Gene)
CUGBP2GeneProduct607310 (Entrez Gene)
DDX1GeneProduct475671 (Entrez Gene)
DDX20GeneProduct475859 (Entrez Gene)
DHX15GeneProduct488856 (Entrez Gene)
DHX16GeneProduct481706 (Entrez Gene)
DHX38GeneProduct479669 (Entrez Gene)
DHX8GeneProduct480507 (Entrez Gene)
DHX9GeneProduct480032 (Entrez Gene)
DICER1GeneProduct480426 (Entrez Gene)
DNAJC8GeneProduct478166 (Entrez Gene)
EFTUD2GeneProduct490935 (Entrez Gene)
FUSGeneProduct
FUSIP1GeneProductFUSI MOUSE PMID: 11684676
GMPMetabolite
HNRNPA2B1GeneProduct475260 (Entrez Gene)
HNRNPCGeneProduct475399 (Entrez Gene)
HNRNPDGeneProduct478450 (Entrez Gene)
HNRNPH1GeneProduct481455 (Entrez Gene)
HNRNPH2GeneProduct480989 (Entrez Gene)
HNRNPKGeneProduct480979 (Entrez Gene)
HNRNPLGeneProduct476466 (Entrez Gene)
HNRNPMGeneProduct476725 (Entrez Gene)
HNRNPRGeneProduct478192 (Entrez Gene)
HNRNPUGeneProduct480100 (Entrez Gene)
HNRPA1GeneProduct
HNRPA3P1GeneProduct
HNRPABGeneProduct
LSM2GeneProduct474849 (Entrez Gene)
LSM7GeneProduct612170 (Entrez Gene)
METTL3GeneProduct475404 (Entrez Gene)
NCBP1GeneProduct474772 (Entrez Gene)
NCBP2GeneProduct478603 (Entrez Gene)
NONOGeneProduct612773 (Entrez Gene)
NUDT21GeneProduct478123 (Entrez Gene)
NXF1GeneProduct483780 (Entrez Gene)
PABPN1GeneProduct490611 (Entrez Gene)
PAPOLAGeneProduct480430 (Entrez Gene)
PCBP2GeneProduct477596 (Entrez Gene)
PHF5AGeneProduct474489 (Entrez Gene)
POLR2AGeneProduct479483 (Entrez Gene)
PPM1GGeneProduct475703 (Entrez Gene) PMID: 12773558
PRMT1GeneProduct476411 (Entrez Gene)
PRMT2GeneProduct480811 (Entrez Gene)
PRPF18GeneProduct477998 (Entrez Gene)
PRPF3GeneProduct475836 (Entrez Gene)
PRPF40AGeneProduct476152 (Entrez Gene)
PRPF4GeneProduct474807 (Entrez Gene)
PRPF4BGeneProduct488199 (Entrez Gene)
PRPF6GeneProduct477289 (Entrez Gene)
PRPF8GeneProduct480651 (Entrez Gene)
PSKH1GeneProductPMID: 12466556
PTBP1GeneProduct485097 (Entrez Gene)
PTBP2GeneProduct490149 (Entrez Gene)
RBM17GeneProduct478014 (Entrez Gene)
RBM39GeneProduct477216 (Entrez Gene)
RBM5GeneProduct476618 (Entrez Gene)
RBMXGeneProduct481063 (Entrez Gene)
RHOXF2GeneProduct611154 (Entrez Gene) GenBank sequence: M10329
RNGTTGeneProduct481914 (Entrez Gene)
RNMTGeneProduct476200 (Entrez Gene)
RNPS1GeneProduct479880 (Entrez Gene) PMID: 14729963
RNU2GeneProductGenBank sequence: K00027
SF3A1GeneProduct477538 (Entrez Gene)
SF3A2GeneProduct612188 (Entrez Gene)
SF3A3GeneProduct
SF3B1GeneProduct488456 (Entrez Gene)
SF3B2GeneProduct476015 (Entrez Gene)
SF3B3GeneProduct479659 (Entrez Gene)
SF3B4GeneProduct483177 (Entrez Gene)
SF3B5GeneProduct611736 (Entrez Gene)
SF4GeneProduct476661 (Entrez Gene) inferred from: SURP 2, G patch protein, UniProt:O60378
SFPQGeneProduct
SFRS12GeneProduct487233 (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.
SFRS14GeneProduct487882 (Entrez Gene)
SFRS1GeneProduct609693 (Entrez Gene) Antagonist splicing factor
SFRS16GeneProduct476436 (Entrez Gene)
SFRS2GeneProduct612817 (Entrez Gene)
SFRS3GeneProduct403687 (Entrez Gene)
SFRS4GeneProduct
SFRS5GeneProduct490754 (Entrez Gene)
SFRS6GeneProduct
SFRS7GeneProduct475730 (Entrez Gene)
SFRS8GeneProduct477438 (Entrez Gene)
SFRS9GeneProduct477510 (Entrez Gene) PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
SMC1AGeneProduct480928 (Entrez Gene)
SNRNP40GeneProduct611914 (Entrez Gene)
SNRNP70GeneProduct484388 (Entrez Gene)
SNRPA1GeneProduct607102 (Entrez Gene)
SNRPAGeneProduct476454 (Entrez Gene)
SNRPB2GeneProduct479267 (Entrez Gene)
SNRPBGeneProduct485806 (Entrez Gene)
SNRPD1GeneProduct480178 (Entrez Gene)
SNRPD2GeneProduct
SNRPD3GeneProduct607772 (Entrez Gene)
SNRPEGeneProduct478934 (Entrez Gene)
SNRPFGeneProduct482609 (Entrez Gene)
SNRPGGeneProduct
SNRPNGeneProduct479012 (Entrez Gene)
SPOPGeneProduct480548 (Entrez Gene)
SRP54GeneProduct403953 (Entrez Gene) PMID: 14729963
SRPK1GeneProduct474887 (Entrez Gene) PMID: 12773558
SRPK2GeneProduct475894 (Entrez Gene) PMID: 12773558
SRRM1GeneProduct478185 (Entrez Gene)
SSFA1GeneProduct
SUPT5HGeneProduct476462 (Entrez Gene)
TMED10GeneProduct610559 (Entrez Gene)
TRA2BGeneProduct478663 (Entrez Gene)
TXNL4AGeneProduct476156 (Entrez Gene)
U1 snRNAGeneProductGenBank sequence: J00645
U2AF1GeneProduct478422 (Entrez Gene)
U2AF2GeneProduct
U4 snRNAGeneProductGenBank sequence: M10328, M18004
U5 snRNAGeneProductGenBank sequence: AB021173
XRN2GeneProduct477133 (Entrez Gene)
YBX1GeneProduct479011 (Entrez Gene)

Annotated Interactions

No annotated interactions
Personal tools