mRNA processing (WP529)

Rattus norvegicus

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 Pathway adapted from http://www.reactome.org.

Authors

Nathan Salomonis , Kristina Hanspers , Daniela Digles , Martina Summer-Kutmon , and Eric Weitz

Activity

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Organisms

Rattus norvegicus

Communities

Annotations

Pathway Ontology

transcription pathway spliceosome pathway

Participants

Label Type Compact URI Comment
GMP Metabolite cas:85-32-5
ATP Metabolite cas:1927-31-7
Prpf4 GeneProduct ensembl:ENSRNOG00000014777 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:9128
Snrpa1 GeneProduct ensembl:ENSRNOG00000011932 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6627
Rbm17 GeneProduct ensembl:ENSRNOG00000018767 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:84991
Snrpd3 GeneProduct ensembl:ENSRNOG00000050410 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6634
Ncbp2 GeneProduct ensembl:ENSRNOG00000001746 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:22916
Rngtt GeneProduct ensembl:ENSRNOG00000007867 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8732
Snrpd1 GeneProduct ensembl:ENSRNOG00000013714 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6632
Sf3a2 GeneProduct ensembl:ENSRNOG00000019349 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8175
Xrn2 GeneProduct ensembl:ENSRNOG00000011785 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:22803
Dhx16 GeneProduct ensembl:ENSRNOG00000030157 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8449
Hnrnpm GeneProduct ensembl:ENSRNOG00000007921 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:4670
AABR07060628.1 GeneProduct ensembl:ENSRNOG00000051748 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3178
Celf2 GeneProduct ensembl:ENSRNOG00000023661 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10659
Spop GeneProduct ensembl:ENSRNOG00000004686 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8405
Hnrnpa2b1 GeneProduct ensembl:ENSRNOG00000011175 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3181
Phf5a GeneProduct ensembl:ENSRNOG00000024170 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:84844
Sf3b5 GeneProduct ensembl:ENSRNOG00000014908 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:83443
Hnrnpr GeneProduct ensembl:ENSRNOG00000011910 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10236
Prpf6 GeneProduct ensembl:ENSRNOG00000051498 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:24148
Ybx1 GeneProduct ensembl:ENSRNOG00000023786 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:4904
Srsf9 GeneProduct ensembl:ENSRNOG00000001163 PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8683
Sugp1 GeneProduct ensembl:ENSRNOG00000052111 inferred from: SURP 2, G patch protein, UniProt:O60378
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:57794
Snu13 GeneProduct ensembl:ENSRNOG00000025154 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:4809
Sf3b3 GeneProduct ensembl:ENSRNOG00000017724 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:23450
Prpf40a GeneProduct ensembl:ENSRNOG00000004864 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:55660
Pskh1 GeneProduct ensembl:ENSRNOG00000019290 PMID: 12466556
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:5681
Snrpb2 GeneProduct ensembl:ENSRNOG00000004967 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6629
Hnrnph2 GeneProduct ensembl:ENSRNOG00000011661 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3188
Snrnp40 GeneProduct ensembl:ENSRNOG00000012219 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:9410
Hnrnpu GeneProduct ensembl:ENSRNOG00000033790 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3192
Lsm7 GeneProduct ensembl:ENSRNOG00000019552 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:51690
Ddx1 GeneProduct ensembl:ENSRNOG00000006652 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1653
Srpk1 GeneProduct ensembl:ENSRNOG00000000511 PMID: 12773558
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6732
U2af1 GeneProduct ensembl:ENSRNOG00000045860 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:7307
Tra2b GeneProduct ensembl:ENSRNOG00000001783 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6434
Hnrnpk GeneProduct ensembl:ENSRNOG00000019113 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3190
Snu13 GeneProduct ensembl:ENSRNOG00000025154 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:4809
Supt5h GeneProduct ensembl:ENSRNOG00000032034 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6829
Srp54a GeneProduct ensembl:ENSRNOG00000032776 PMID: 14729963
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6729
Prpf4b GeneProduct ensembl:ENSRNOG00000016705 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8899
Celf1 GeneProduct ensembl:ENSRNOG00000010379 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10658
Srsf1 GeneProduct ensembl:ENSRNOG00000050323 Antagonist splicing factor
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6426
Clp1 GeneProduct ensembl:ENSRNOG00000007416 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10978
Snrpf GeneProduct ensembl:ENSRNOG00000005556 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6636
Mettl3 GeneProduct ensembl:ENSRNOG00000013111 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:56339
Srsf6 GeneProduct ensembl:ENSRNOG00000006380 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6431
Nxf1 GeneProduct ensembl:ENSRNOG00000019069 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10482
Sf3b2 GeneProduct ensembl:ENSRNOG00000020412 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10992
Sfpq GeneProduct ensembl:ENSRNOG00000058461 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6421
Rbm5 GeneProduct ensembl:ENSRNOG00000018153 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10181
Prpf3 GeneProduct ensembl:ENSRNOG00000025629 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:9129
Snu13 GeneProduct ensembl:ENSRNOG00000025154 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:4809
Srsf10 GeneProduct ensembl:ENSRNOG00000007992 FUSI MOUSE PMID: 11684676
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10772
Cstf3 GeneProduct ensembl:ENSRNOG00000012089 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1479
Papola GeneProduct ensembl:ENSRNOG00000004827 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10914
Hnrnpd GeneProduct ensembl:ENSRNOG00000002292 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3184
Cpsf3 GeneProduct ensembl:ENSRNOG00000052418 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:51692
LOC103689931 GeneProduct ensembl:ENSRNOG00000003645 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3182
Clasrp GeneProduct ensembl:ENSRNOG00000046000 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:11129
Dicer1 GeneProduct ensembl:ENSRNOG00000010711 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:23405
Pabpn1 GeneProduct ensembl:ENSRNOG00000042195 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8106
U2 GeneProduct ensembl:ENSRNOG00000061106 GenBank sequence: K00027
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6066
Prmt1 GeneProduct ensembl:ENSRNOG00000026109 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3276
Cpsf4 GeneProduct ensembl:ENSRNOG00000000985 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10898
Sfswap GeneProduct ensembl:ENSRNOG00000000931 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6433
Srsf3 GeneProduct ensembl:ENSRNOG00000000520 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6428
Sf3a1 GeneProduct ensembl:ENSRNOG00000005218 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10291
Cd2bp2 GeneProduct ensembl:ENSRNOG00000017201 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10421
AC126899.1 GeneProduct ensembl:ENSRNOG00000011065 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:57819
Srsf10 GeneProduct ensembl:ENSRNOG00000007992 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10772
Tmed10 GeneProduct ensembl:ENSRNOG00000007901 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10972
Cpsf2 GeneProduct ensembl:ENSRNOG00000005733 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:53981
Cpsf1 GeneProduct ensembl:ENSRNOG00000030705 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:29894
Srsf2 GeneProduct ensembl:ENSRNOG00000000248 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6427
Ppm1g GeneProduct ensembl:ENSRNOG00000026905 PMID: 12773558
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:5496
Nudt21 GeneProduct ensembl:ENSRNOG00000042983 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:11051
Sf3b4 GeneProduct ensembl:ENSRNOG00000021181 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10262
Cstf2 GeneProduct ensembl:ENSRNOG00000048025 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1478
Dhx38 GeneProduct ensembl:ENSRNOG00000014619 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:9785
Srek1 GeneProduct ensembl:ENSRNOG00000032735 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.
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:140890
Srsf4 GeneProduct ensembl:ENSRNOG00000010007 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6429
Clk2 GeneProduct ensembl:ENSRNOG00000020500 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1196
Prpf8 GeneProduct ensembl:ENSRNOG00000003495 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10594
Sf3a3 GeneProduct ensembl:ENSRNOG00000007629 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10946
Snrpn GeneProduct ensembl:ENSRNOG00000059764 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6638
Clk4 GeneProduct ensembl:ENSRNOG00000003714 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:57396
Sf3b1 GeneProduct ensembl:ENSRNOG00000013516 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:23451
Prpf4 GeneProduct ensembl:ENSRNOG00000014777 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:9128
Prmt2 GeneProduct ensembl:ENSRNOG00000001297 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3275
Ddx20 GeneProduct ensembl:ENSRNOG00000015274 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:11218
Nono GeneProduct ensembl:ENSRNOG00000003689 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:4841
Celf4 GeneProduct ensembl:ENSRNOG00000014503 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:56853
Srsf5 GeneProduct ensembl:ENSRNOG00000005513 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6430
Prpf18 GeneProduct ensembl:ENSRNOG00000018396 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8559
Cstf2t GeneProduct ensembl:ENSRNOG00000050289 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:23283
Ptbp1 GeneProduct ensembl:ENSRNOG00000010448 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:5725
Snrpn GeneProduct ensembl:ENSRNOG00000059764 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6638
Cstf1 GeneProduct ensembl:ENSRNOG00000004775 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1477
AABR07051190.1 GeneProduct ensembl:ENSRNOG00000005062 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3191
U2af2 GeneProduct ensembl:ENSRNOG00000015914 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:11338
Srsf7 GeneProduct ensembl:ENSRNOG00000027360 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6432
Dhx9 GeneProduct ensembl:ENSRNOG00000002735 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1660
Sugp2 GeneProduct ensembl:ENSRNOG00000020269 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10147
Srrm1 GeneProduct ensembl:ENSRNOG00000018194 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10250
Rnmt GeneProduct ensembl:ENSRNOG00000016698 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8731
Snrpep2 GeneProduct ensembl:ENSRNOG00000034206 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6635
Cdc40 GeneProduct ensembl:ENSRNOG00000000581 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:51362
Rbmx GeneProduct ensembl:ENSRNOG00000000866 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:27316
Snrpb GeneProduct ensembl:ENSRNOG00000006961 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6628
Smc1a GeneProduct ensembl:ENSRNOG00000003139 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:8243
Snrnp70 GeneProduct ensembl:ENSRNOG00000020763 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6625
Prpf8 GeneProduct ensembl:ENSRNOG00000003495 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10594
Txnl4a GeneProduct ensembl:ENSRNOG00000052004 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10907
Ncbp1 GeneProduct ensembl:ENSRNOG00000023605 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:4686
Cdc40 GeneProduct ensembl:ENSRNOG00000000581 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:51362
Dhx8 GeneProduct ensembl:ENSRNOG00000020772 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1659
Clk1 GeneProduct ensembl:ENSRNOG00000025768 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: [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.
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1195
Clk3 GeneProduct ensembl:ENSRNOG00000030126 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1198
Ptbp2 GeneProduct ensembl:ENSRNOG00000010827 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:58155
Eftud2 GeneProduct ensembl:ENSRNOG00000002818 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:9343
AC126899.1 GeneProduct ensembl:ENSRNOG00000011065 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:57819
Rbm39 GeneProduct ensembl:ENSRNOG00000019848 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:9584
Snrpa GeneProduct ensembl:ENSRNOG00000001501 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:6626
Hnrnph1 GeneProduct ensembl:ENSRNOG00000003399 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:3187
Fus GeneProduct ensembl:ENSRNOG00000023360 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:2521
LOC688526 GeneProduct ensembl:ENSRNOG00000027239 PMID: 14729963
Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:10921
Dhx15 GeneProduct ensembl:ENSRNOG00000003844 Homology Mapping from Homo sapiens to Rattus norvegicus: Original ID = L:1665

References

  1. mRNA nuclear export at a glance. Carmody SR, Wente SR. J Cell Sci. 2009 Jun 15;122(Pt 12):1933–7. PubMed Europe PMC Scholia