mRNA processing (Danio rerio)

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U2 snRNP35YYYY(3)U5 snRNP5Cleavage of mRNA at the 3'-endexon 2U1 snRNP(2b)hnRNP regulators5Additional FactorsSR protein kinasesAMisc.CPSFHOMOLOGY MAPPYYYYAGYYYYSR protein phosphatasesYYYYU4:U5:U6 tri-snRNP complexCleavage at the 3'-Splice-Site and Exon LigationAU5GU3P-Rnmt (methyltransferase)Formation of the Spliceosomal B complex5Accessory Proteins5Kinases Phosphorylating RS domains?SR-proteinsPi3SR-binding sitesmRNA 3'-end processingCFIPU5U2AFU1AGexon 1snRNP Sm core complexU4/U63Poly(A)pb IIU1 snRNPexon 1AiPoexon 15Formation of the Spliceosomal E complexFormation of pre-mRNPsPoly(A) pol(1)CAFormation of the Spliceosomal A complexSF3b14bsplicesome associated helicasesPutative Alternative SplicingFormation of the Spliceosomal B complexGMPAG(2a)Serine/Argenine Rich Proteins(SR)5UGLariat Formation and 5'-Splice Site CleavageU4 snRNPCstFRngtt (capping enzyme)U2 snRNPexon 2AGFormation of pre-mRNPsmRNA Capping5SR-proteinsexon 1CstFsnRNP Sm core complexFormation of the active Spliceosomal C complex3SR-phosphatasesU6RNAi pathway3SR-binding sites3AGPoly(A) polymerase alpha5 G cap5pre-mRNAexon 23Methylation of mRNAProcessing of Intron-Containing Pre-mRNACF IIPrimary RNA transcripthnRNPsAdditional SR proteinssplicing factor SF3Bexon 235AYYYYFormation of the Spliceosomal E complexU2exon 1RNA helicase AInternal methylation of mRNAATPright click on blue text for detailed informationRegulatorsAGU6 snRNPCF IU2AFheterogeneous nuclear ribonucleoproteinsCap BindingUGsnRNP Sm core complexSR-kinasesU2 snRNPsexon 2Polr2a3exon 23ACF IImRNA cappingAdditional FactorsAlternative SplicingmRNA polyadenylationFormation of the Spliceosomal A complexSpt5intronSR-proteinsRNA helicaseInternal methylation of mRNAAdditional FactorsSR-repressor proteinsRegulation of3mRNA splicing (major pathway)splicing factor SF3AFormation of the Spliceosomal C complexdegraded(2c)AU4CPSFAAUAAA5Poly(A)-binding protein IIexon 1mRNA splice site selection5YYYY65Note: New participating members shown at each stepAAAAAAA(2)fusrnpc2SNRPBhnrnpa3cstf1prmt1DNAJC8srsf9cpsf5SRPK2RNU2snrpezgc:55440smx5PRPF8dhx16sfrs16prpf4bbppm1gnonoNCBP1prpf40ahnrpuprpf4snrpgpcbp2srsf2brbm5hnrnpcPRPF8xrn2POLR2Ahnrplprpf3tmed10sf3a2hnrnprsrrm1sugp1cpsf3ddx20U1 snRNAPSKH1srpk1sfrs5aphf5aEFTUD2ddx1snrp70supt5hspopsnrpd2RNMThnrpa1CLK1HEABcd2bp2ssfa1ybx1snrpbssfa1HNRPA2B1lsm7sfswapprpf4nxf1hnrnpmsfrs3clk4aCLK3ptbp2asnrpd1hnrnph1lsnrpb2narRBMXU4 snRNAsfpqprpf18SFRS4sfrs6asmx5SF3A3c20orf14srp54snrpaptbp1aprmt2ssfa1dhx8zgc:77804txnl4aDHX9hnrnpdsfrs10hnrnpkpabn1u2af1cstf2rbm17CSTF2Trnps1dicer1papolasnrpbDHX38snrpflsrek1sfrs1U5 snRNASNRPD3sf3b2srsf7acdc40sf3b5srsf10ancbp2HNRPH2rngttcpsf1Rnu6cugbp2sf3b4SFRS14snrpa1wdr57dhx15sf3a1sf3b1cstf3clk2acugbp1mettl3cpsf2smc1alhnrpabcelf4clk2bclk4bptbp2bsrsf10bsrsf10asrsf10bsfrs5bsfrs6b


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.

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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

View all...
NameTypeDatabase referenceComment
CLK1GeneProduct
CLK3GeneProduct
CSTF2TGeneProduct
DHX38GeneProduct393850 (Entrez Gene)
DHX9GeneProductENSDARG00000079725 (Ensembl)
DNAJC8GeneProductENSDARG00000059373 (Ensembl)
EFTUD2GeneProduct393480 (Entrez Gene)
HEABGeneProductENSDARG00000063663 (Ensembl)
HNRPA2B1GeneProduct
HNRPH2GeneProduct
NCBP1GeneProduct101885456 (Entrez Gene)
POLR2AGeneProduct553347 (Entrez Gene)
PRPF8GeneProduct393951 (Entrez Gene)
PSKH1GeneProduct554840 (Entrez Gene) PMID: 12466556
RBMXGeneProduct321860 (Entrez Gene)
RNMTGeneProductENSDARG00000070553 (Ensembl)
RNU2GeneProductGenBank sequence: K00027
Rnu6GeneProductGenBank sequence: M10329
SF3A3GeneProduct446168 (Entrez Gene)
SFRS14GeneProductNo zebrafish ortholog for this gene on NCBI, maybe remove?
SFRS4GeneProduct321872 (Entrez Gene)
SNRPBGeneProduct402966 (Entrez Gene)
SNRPD3GeneProduct415171 (Entrez Gene)
SRPK2GeneProduct100333293 (Entrez Gene) PMID: 12773558
U1 snRNAGeneProductGenBank sequence: J00645
U4 snRNAGeneProductGenBank sequence: M10328, M18004
U5 snRNAGeneProductGenBank sequence: AB021173
c20orf14GeneProduct323855 (Entrez Gene)
cd2bp2GeneProduct393936 (Entrez Gene)
cdc40GeneProduct494534 (Entrez Gene)
celf4GeneProductENSDARG00000070045 (Ensembl) Alias for BRUNOL4
clk2aGeneProductENSDARG00000062954 (Ensembl)
clk2bGeneProductENSDARG00000059870 (Ensembl)
clk4aGeneProductENSDARG00000089372 (Ensembl)
clk4bGeneProductENSDARG00000005908 (Ensembl)
cpsf1GeneProduct432372 (Entrez Gene)
cpsf2GeneProduct436657 (Entrez Gene)
cpsf3GeneProduct324554 (Entrez Gene)
cpsf5GeneProduct394092 (Entrez Gene)
cstf1GeneProduct324238 (Entrez Gene)
cstf2GeneProduct386806 (Entrez Gene)
cstf3GeneProduct406326 (Entrez Gene)
cugbp1GeneProduct58137 (Entrez Gene)
cugbp2GeneProduct373117 (Entrez Gene)
ddx1GeneProductENSDARG00000032117 (Ensembl)
ddx20GeneProduct556273 (Entrez Gene)
dhx15GeneProduct321931 (Entrez Gene)
dhx16GeneProduct336645 (Entrez Gene)
dhx8GeneProductENSDARG00000054707 (Ensembl)
dicer1GeneProduct324724 (Entrez Gene)
fusGeneProduct394058 (Entrez Gene)
hnrnpa3GeneProductENSDARG00000059351 (Ensembl) HNRPA3 is old identifier for HNRNPA3
hnrnpcGeneProductENSDARG00000053810 (Ensembl) HNRPC is old identifier for hnrnpc
hnrnpdGeneProductENSDARG00000059246 (Ensembl)
hnrnph1lGeneProduct321556 (Entrez Gene)
hnrnpkGeneProduct406267 (Entrez Gene)
hnrnpmGeneProductENSDARG00000061735 (Ensembl)
hnrnprGeneProductENSDARG00000014569 (Ensembl)
hnrpa1GeneProduct378453 (Entrez Gene)
hnrpabGeneProduct321466 (Entrez Gene)
hnrplGeneProduct394074 (Entrez Gene)
hnrpuGeneProduct334490 (Entrez Gene)
lsm7GeneProduct573047 (Entrez Gene)
mettl3 GeneProduct100004398 (Entrez Gene)
narGeneProduct30203 (Entrez Gene)
ncbp2GeneProduct192325 (Entrez Gene)
nonoGeneProduct321994 (Entrez Gene)
nxf1GeneProduct323865 (Entrez Gene)
pabn1GeneProduct406543 (Entrez Gene)
papolaGeneProduct404041 (Entrez Gene)
pcbp2GeneProduct321844 (Entrez Gene)
phf5aGeneProduct286774 (Entrez Gene)
ppm1gGeneProduct368275 (Entrez Gene) PMID: 12773558
prmt1GeneProduct321974 (Entrez Gene)
prmt2GeneProduct558841 (Entrez Gene)
prpf18GeneProduct431751 (Entrez Gene)
prpf3GeneProduct403072 (Entrez Gene)
prpf40aGeneProduct321555 (Entrez Gene) Alias for FNBP3
prpf4GeneProduct326944 (Entrez Gene)
prpf4bbGeneProduct406758 (Entrez Gene)
ptbp1aGeneProduct323490 (Entrez Gene)
ptbp2aGeneProductENSDARG00000101947 (Ensembl)
ptbp2bGeneProductENSDARG00000015901 (Ensembl)
rbm17GeneProduct393889 (Entrez Gene)
rbm5GeneProductENSDARG00000098280 (Ensembl)
rngttGeneProduct405803 (Entrez Gene)
rnpc2GeneProduct406251 (Entrez Gene)
rnps1GeneProduct327020 (Entrez Gene) PMID: 14729963
sf3a1GeneProductENSDARG00000041887 (Ensembl)
sf3a2GeneProduct394018 (Entrez Gene)
sf3b1GeneProduct446117 (Entrez Gene)
sf3b2GeneProductENSDARG00000018049 (Ensembl)
sf3b4GeneProduct192318 (Entrez Gene)
sf3b5GeneProduct436751 (Entrez Gene)
sfpqGeneProduct406564 (Entrez Gene)
sfrs10GeneProduct394172 (Entrez Gene)
sfrs16GeneProduct555304 (Entrez Gene)
sfrs1GeneProductENSDARG00000017843 (Ensembl) Antagonist splicing factor
sfrs3GeneProduct368925 (Entrez Gene)
sfrs5aGeneProductENSDARG00000029818 (Ensembl)
sfrs5bGeneProductENSDARG00000027734 (Ensembl)
sfrs6aGeneProductENSDARG00000013729 (Ensembl)
sfrs6bGeneProductENSDARG00000016783 (Ensembl)
sfswapGeneProduct394143 (Entrez Gene)
smc1alGeneProductENSDARG00000058203 (Ensembl)
smx5GeneProduct57924 (Entrez Gene)
snrp70GeneProduct445398 (Entrez Gene)
snrpa1GeneProduct492511 (Entrez Gene)
snrpaGeneProduct324121 (Entrez Gene)
snrpb2GeneProduct402896 (Entrez Gene)
snrpbGeneProduct402966 (Entrez Gene) snrpb is the zebrafish homolog of human SNRPN
snrpd1GeneProduct192331 (Entrez Gene)
snrpd2GeneProduct550244 (Entrez Gene)
snrpeGeneProduct393979 (Entrez Gene)
snrpflGeneProduct445404 (Entrez Gene)
snrpgGeneProduct447922 (Entrez Gene)
spopGeneProduct100005514 (Entrez Gene)
srek1GeneProduct445219 (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.
srp54GeneProduct393963 (Entrez Gene) PMID: 14729963
srpk1GeneProduct323679 (Entrez Gene) PMID: 12773558
srrm1GeneProduct406751 (Entrez Gene)
srsf10aGeneProductENSDARG00000022415 (Ensembl)
srsf10bGeneProductENSDARG00000086411 (Ensembl)
srsf2bGeneProduct323700 (Entrez Gene)
srsf7aGeneProduct402972 (Entrez Gene)
srsf9GeneProduct405835 (Entrez Gene) PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
ssfa1GeneProductENSDARG00000023299 (Ensembl) Alias of snu13b
sugp1GeneProductENSDARG00000075936 (Ensembl)
  • inferred from: SURP 2, G patch protein, UniProt:O60378
  • SF4 is alias for sugp1; added annotation
supt5hGeneProduct64275 (Entrez Gene)
tmed10GeneProduct326716 (Entrez Gene)
txnl4aGeneProduct449780 (Entrez Gene)
u2af1GeneProduct192328 (Entrez Gene)
wdr57GeneProduct393292 (Entrez Gene)
xrn2GeneProduct321940 (Entrez Gene)
ybx1GeneProductENSDARG00000004757 (Ensembl)
zgc:55440GeneProduct406824 (Entrez Gene)
zgc:77804GeneProduct402989 (Entrez Gene)

Annotated Interactions

No annotated interactions
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