mRNA processing (Danio rerio)

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Serine/Argenine Rich Proteins(SR)AGmRNA polyadenylation35AAUAAARNA helicase5(2a)CPSFU53Misc.5 G cap3exon 2(2b)Accessory ProteinsFormation of the Spliceosomal E complexRnmt (methyltransferase)exon 1Methylation of mRNA5Note: New participating members shown at each stepPrimary RNA transcriptexon 1Processing of Intron-Containing Pre-mRNACstFAG53Formation of the Spliceosomal A complexSR-phosphatasesInternal methylation of mRNAmRNA splice site selection5U6SR-binding sitesU4U1 snRNPU2 snRNPSR-repressor proteinsSR-binding sitesLariat Formation and 5’-Splice Site Cleavagedegradedexon 2U4/U63AAAAAAAU4:U5:U6 tri-snRNP complex3pre-mRNACF IhnRNPsYYYY3CACleavage at the 3’-Splice-Site and Exon LigationAdditional Factors5PiU2AFYYYYU6 snRNPmRNA cappingRNA helicase ARNAi pathwayAGACF IIhnRNP regulatorsCstF5SR-proteinssnRNP Sm core complexU4 snRNPexon 1SF3b14bYYYY5Additional SR proteinsGU(1)splicing factor SF3Bexon 1CF IIsplicing factor SF3AAlternative SplicingAGATPHOMOLOGY MAPPU2Regulatorsright click on blue text for detailed informationFormation of the Spliceosomal B complexexon 2Regulation of3Formation of pre-mRNPsCFIsnRNP Sm core complexexon 1Cleavage of mRNA at the 3’-end5exon 2Poly(A)-binding protein IIRngtt (capping enzyme)Spt55SR protein kinasesUGAPolr2amRNA CappingYYYYU5 snRNPFormation of the active Spliceosomal C complexSR-proteinsA3AG365SR protein phosphatasesAdditional FactorsmRNA splicing (major pathway)YYYYInternal methylation of mRNA5exon 2PsnRNP Sm core complexCap BindingAFormation of pre-mRNPs(3)heterogeneous nuclear ribonucleoproteinsSR-proteinsU1splicesome associated helicasesU1 snRNPexon 2Poly(A) polAdditional FactorsSR-kinasesUGCPSFU2 snRNPYYYY(2)Aexon 1U2 snRNPsPutative Alternative SplicingFormation of the Spliceosomal B complexGMPU2AFAG(2c)A3mRNA 3’-end processingFormation of the Spliceosomal A complexintron5Kinases Phosphorylating RS domains?U53P-Poly(A) polymerase alphaFormation of the Spliceosomal C complexFormation of the Spliceosomal E complexiPoPoly(A)pb IISF3B2DDX20U4 snRNAnonosfrs3POLR2Asf3a1HNRPA2B1SFRS16SF4RBM5HNRPMcpsf5SFRS6zgc:56184zgc:109706LSM7SNRPD3prpf18HNRPRcpsf3HNRPA3cugbp1prpf4snrp70sf3b5Rnu6SFRS14zgc:92484EFTUD2spopcd2bp2cstf3sfrs1CLK1zgc:103688CLK3HNRPH2U5 snRNARNPS1zgc:77093rngtthrmt1l2cugbp2zgc:103632PTBP2SSFA1prpf4HRMT1L1SNRPNDHX8zgc:85681zgc:55429zgc:55876hnrpkdhx16zgc:86860FUSIP1NXF1CSTF2Tzgc:55623FUSIP1hnrpabsnrpasrpk1SSFA1srrm1srp54HEABSNRPB2SF3B1CLK4SFRS4zgc:77449NCBP1zgc:85979wdr57ppm1gPRPF3zgc:86860SFPQBRUNOL4SNRPBnarCLK2RBMXzgc:55440zgc:56682snrpd1c20orf14DDX1DHX38PRPF8SSFA1zgc:101832HNRPDsf3b4DHX15zgc:56390DICER1snrpflzgc:77155SRPK2CSTF2smx5zgc:85960zgc:77560smx5SNRPNzgc:110689FNBP3zgc:77804hnrpa1zgc:110732nsep1pcbp2rbm17SMC1L1PSKH1rnpc2ncbp2hnrpuRNU2RNMTSF3A3SFRS5HNRPCDNAJC8sfrs10zgc:100974CPSF1sf3a2u2af1DHX9phf5aPRPF8supt5hxrn2U1 snRNA


Description

No description

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.

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Bibliography

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History

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CompareRevisionActionTimeUserComment
122797view02:12, 18 May 2022AlexanderPicocleaning up broken comments
91976view14:37, 10 April 2017LWackersUpdated human annotations to zebrafish orthologues.
91952view13:04, 6 April 2017LWackersUpdated annotations and added missing ones.
71979view00:30, 24 October 2013MaintBotremoved data source from nodes without identifier
69959view20:55, 11 July 2013MaintBotupdated to 2013 schema
67499view11:09, 26 June 2013DdiglesOntology Term : 'spliceosome pathway' added !
40828view22:18, 1 March 2011MaintBotRemoved redundant pathway information and comments
35245view19:53, 11 February 2010KhanspersModified description
34214view21:32, 9 December 2009MaintBotAutomatic update of empty xrefs
21662view11:32, 14 November 2008MaintBot[[Pathway:Danio rerio:mRNA processing Reactome]] moved to [[Pathway:WP467]]: Moved to stable identifier
12032view08:44, 15 May 2008MaintBotAdded to category $category
12030view08:44, 15 May 2008NsalomonisUploaded new pathway

External references

DataNodes

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NameTypeDatabase referenceComment
BRUNOL4GeneProduct
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.
CLK2GeneProduct
CLK3GeneProduct
CLK4GeneProduct
CPSF1GeneProduct
CSTF2GeneProduct
CSTF2TGeneProduct
DDX1GeneProduct
DDX20GeneProduct
DHX15GeneProduct
DHX38GeneProduct
DHX8GeneProduct
DHX9GeneProduct
DICER1GeneProduct
DNAJC8GeneProduct
EFTUD2GeneProduct
FNBP3GeneProduct
FUSIP1GeneProductFUSI_MOUSE PMID: 11684676
HEABGeneProduct
HNRPA2B1GeneProduct
HNRPA3GeneProduct
HNRPCGeneProduct
HNRPDGeneProduct
HNRPH2GeneProduct
HNRPMGeneProduct
HNRPRGeneProduct
HRMT1L1GeneProduct
LSM7GeneProduct
NCBP1GeneProduct
NXF1GeneProduct
POLR2AGeneProduct
PRPF3GeneProduct
PRPF8GeneProduct
PSKH1GeneProductPMID: 12466556
PTBP2GeneProduct
RBM5GeneProduct
RBMXGeneProduct
RNMTGeneProduct
RNPS1GeneProductPMID: 14729963
RNU2GeneProductGenBank sequence: K00027
Rnu6GeneProductGenBank sequence: M10329
SF3A3GeneProduct
SF3B1GeneProduct
SF3B2GeneProduct
SF4GeneProductinferred from: SURP 2, G patch protein, UniProt:O60378
SFPQGeneProduct
SFRS14GeneProduct
SFRS16GeneProduct
SFRS4GeneProduct
SFRS5GeneProduct
SFRS6GeneProduct
SMC1L1GeneProduct
SNRPB2GeneProduct
SNRPBGeneProduct
SNRPD3GeneProduct
SNRPNGeneProduct
SRPK2GeneProductPMID: 12773558
SSFA1GeneProduct
U1 snRNAGeneProductGenBank sequence: J00645
U4 snRNAGeneProductGenBank sequence: M10328, M18004
U5 snRNAGeneProductGenBank sequence: AB021173
c20orf14GeneProduct323855 (Entrez Gene)
cd2bp2GeneProduct393936 (Entrez Gene)
cpsf3GeneProduct324554 (Entrez Gene)
cpsf5GeneProduct394092 (Entrez Gene)
cstf3GeneProduct406326 (Entrez Gene)
cugbp1GeneProduct58137 (Entrez Gene)
cugbp2GeneProduct373117 (Entrez Gene)
dhx16GeneProduct336645 (Entrez Gene)
hnrpa1GeneProduct378453 (Entrez Gene)
hnrpabGeneProduct321466 (Entrez Gene)
hnrpkGeneProduct406267 (Entrez Gene)
hnrpuGeneProduct334490 (Entrez Gene)
hrmt1l2GeneProduct321974 (Entrez Gene)
narGeneProduct30203 (Entrez Gene)
ncbp2GeneProduct192325 (Entrez Gene)
nonoGeneProduct321994 (Entrez Gene)
nsep1GeneProduct58144 (Entrez Gene)
pcbp2GeneProduct321844 (Entrez Gene)
phf5aGeneProduct286774 (Entrez Gene)
ppm1gGeneProduct368275 (Entrez Gene) PMID: 12773558
prpf18GeneProduct431751 (Entrez Gene)
prpf4GeneProduct326944 (Entrez Gene)
rbm17GeneProduct393889 (Entrez Gene)
rngttGeneProduct405803 (Entrez Gene)
rnpc2GeneProduct406251 (Entrez Gene)
sf3a1GeneProduct368732 (Entrez Gene)
sf3a2GeneProduct394018 (Entrez Gene)
sf3b4GeneProduct192318 (Entrez Gene)
sf3b5GeneProduct436751 (Entrez Gene)
sfrs10GeneProduct394172 (Entrez Gene)
sfrs1GeneProduct393565 (Entrez Gene) Antagonist splicing factor
sfrs3GeneProduct368925 (Entrez Gene)
smx5GeneProduct57924 (Entrez Gene)
snrp70GeneProduct445398 (Entrez Gene)
snrpaGeneProduct324121 (Entrez Gene)
snrpd1GeneProduct192331 (Entrez Gene)
snrpflGeneProduct445404 (Entrez Gene)
spopGeneProduct394105 (Entrez Gene)
srp54GeneProduct393963 (Entrez Gene) PMID: 14729963
srpk1GeneProduct323679 (Entrez Gene) PMID: 12773558
srrm1GeneProduct406751 (Entrez Gene)
supt5hGeneProduct64275 (Entrez Gene)
u2af1GeneProduct192328 (Entrez Gene)
wdr57GeneProduct393292 (Entrez Gene)
xrn2GeneProduct321940 (Entrez Gene)
zgc:100974GeneProduct445219 (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.
zgc:101832GeneProduct492511 (Entrez Gene)
zgc:103632GeneProduct449780 (Entrez Gene)
zgc:103688GeneProduct447922 (Entrez Gene)
zgc:109706GeneProduct404041 (Entrez Gene)
zgc:110689GeneProduct323490 (Entrez Gene)
zgc:110732GeneProduct550244 (Entrez Gene)
zgc:55429GeneProduct394074 (Entrez Gene)
zgc:55440GeneProduct406824 (Entrez Gene)
zgc:55623GeneProduct406758 (Entrez Gene)
zgc:55876GeneProduct323700 (Entrez Gene)
zgc:56184GeneProduct394143 (Entrez Gene)
zgc:56390GeneProduct394058 (Entrez Gene)
zgc:56682GeneProduct393979 (Entrez Gene)
zgc:77093GeneProduct337552 (Entrez Gene)
zgc:77155GeneProduct402972 (Entrez Gene)
zgc:77449GeneProduct405835 (Entrez Gene) PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
zgc:77560GeneProduct324238 (Entrez Gene)
zgc:77804GeneProduct402989 (Entrez Gene)
zgc:85681GeneProduct326716 (Entrez Gene)
zgc:85960GeneProduct321556 (Entrez Gene)
zgc:85979GeneProduct406543 (Entrez Gene)
zgc:86860GeneProduct494534 (Entrez Gene)
zgc:92484GeneProduct436657 (Entrez Gene)

Annotated Interactions

No annotated interactions
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