mRNA processing (WP411)

Homo sapiens

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: Pathway adapted from Proteins on this pathway have targeted assays available via the [ CPTAC Assay Portal].


Nathan Salomonis , Alex Pico , Martijn Van Iersel , Kristina Hanspers , Daniela Digles , Zahra Roudbari , Martina Summer-Kutmon , Andrew Mason , Friederike Ehrhart , Eric Weitz , and Egon Willighagen


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Homo sapiens



Pathway Ontology

spliceosome pathway transcription pathway


Label Type Compact URI Comment
GMP Metabolite cas:85-32-5
ATP Metabolite cas:1927-31-7
PRPF4 GeneProduct ncbigene:9128
SNRPA1 GeneProduct ncbigene:6627
RBM17 GeneProduct ncbigene:84991
SNRPD3 GeneProduct ncbigene:6634
NCBP2 GeneProduct ncbigene:22916
DNAJC8 GeneProduct ncbigene:22826
RNGTT GeneProduct ncbigene:8732
SNRPD1 GeneProduct ncbigene:6632
SF3A2 GeneProduct ncbigene:8175
SNRPD2 GeneProduct ncbigene:6633
XRN2 GeneProduct ncbigene:22803
DHX16 GeneProduct ncbigene:8449
HNRPM GeneProduct ncbigene:4670
HNRPA1 GeneProduct ncbigene:3178
CUGBP2 GeneProduct ncbigene:10659
SPOP GeneProduct ncbigene:8405
HNRPA2B1 GeneProduct ncbigene:3181
PHF5A GeneProduct ncbigene:84844
SF3B5 GeneProduct ncbigene:83443
HNRPR GeneProduct ncbigene:10236
C20orf14 GeneProduct ncbigene:24148
NSEP1 GeneProduct ncbigene:4904
SFRS9 GeneProduct ncbigene:8683 PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
SF4 GeneProduct ncbigene:57794 inferred from: SURP 2, G patch protein, UniProt:O60378
SSFA1 GeneProduct ncbigene:4809
SF3B3 GeneProduct ncbigene:23450
FNBP3 GeneProduct ncbigene:55660
PSKH1 GeneProduct ncbigene:5681 PMID: 12466556
SNRPB2 GeneProduct ncbigene:6629
HNRPH2 GeneProduct ncbigene:3188
WDR57 GeneProduct ncbigene:9410
HNRPU GeneProduct ncbigene:3192
PCBP2 GeneProduct ncbigene:5094
LSM7 GeneProduct ncbigene:51690
DDX1 GeneProduct ncbigene:1653
SRPK1 GeneProduct ncbigene:6732 PMID: 12773558
U2AF1 GeneProduct ncbigene:7307
SFRS10 GeneProduct ncbigene:6434
SRPK2 GeneProduct ncbigene:6733 PMID: 12773558
HNRPA3P1 GeneProduct ncbigene:10151
HNRPK GeneProduct ncbigene:3190
SSFA1 GeneProduct ncbigene:4809
SUPT5H GeneProduct ncbigene:6829
SRP54 GeneProduct ncbigene:6729 PMID: 14729963
PRPF4B GeneProduct ncbigene:8899
CUGBP1 GeneProduct ncbigene:10658
SFRS1 GeneProduct ncbigene:6426 Antagonist splicing factor
HEAB GeneProduct ncbigene:10978
SNRPF GeneProduct ncbigene:6636
METTL3 GeneProduct ncbigene:56339
SFRS6 GeneProduct ncbigene:6431
NXF1 GeneProduct ncbigene:10482
SF3B2 GeneProduct ncbigene:10992
SFPQ GeneProduct ncbigene:6421
RBM5 GeneProduct ncbigene:10181
PRPF3 GeneProduct ncbigene:9129
SSFA1 GeneProduct ncbigene:4809
FUSIP1 GeneProduct ncbigene:10772 FUSI MOUSE PMID: 11684676
CSTF3 GeneProduct ncbigene:1479
PAPOLA GeneProduct ncbigene:10914
HNRPD GeneProduct ncbigene:3184
CPSF3 GeneProduct ncbigene:51692
HNRPAB GeneProduct ncbigene:3182
SFRS16 GeneProduct ncbigene:11129
POLR2A GeneProduct ncbigene:5430
DICER1 GeneProduct ncbigene:23405
PABPN1 GeneProduct ncbigene:8106
RNU2 GeneProduct ncbigene:6066 GenBank sequence: K00027
HRMT1L2 GeneProduct ncbigene:3276
CPSF4 GeneProduct ncbigene:10898
SFRS8 GeneProduct ncbigene:6433
SFRS3 GeneProduct ncbigene:6428
SF3A1 GeneProduct ncbigene:10291
CD2BP2 GeneProduct ncbigene:10421
LSM2 GeneProduct ncbigene:57819
FUSIP1 GeneProduct ncbigene:10772
TMP21 GeneProduct ncbigene:10972
CPSF2 GeneProduct ncbigene:53981
CPSF1 GeneProduct ncbigene:29894
SFRS2 GeneProduct ncbigene:6427
PPM1G GeneProduct ncbigene:5496 PMID: 12773558
NUDT21 GeneProduct ncbigene:11051
SF3B4 GeneProduct ncbigene:10262
CSTF2 GeneProduct ncbigene:1478
DHX38 GeneProduct ncbigene:9785
HNRPC GeneProduct ncbigene:3183
SFRS12 GeneProduct ncbigene:140890 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.
SFRS4 GeneProduct ncbigene:6429
CLK2 GeneProduct ncbigene:1196
PRPF8 GeneProduct ncbigene:10594
SF3A3 GeneProduct ncbigene:10946
SNRPN GeneProduct ncbigene:6638
CLK4 GeneProduct ncbigene:57396
SF3B1 GeneProduct ncbigene:23451
PRPF4 GeneProduct ncbigene:9128
HRMT1L1 GeneProduct ncbigene:3275
DDX20 GeneProduct ncbigene:11218
NONO GeneProduct ncbigene:4841
BRUNOL4 GeneProduct ncbigene:56853
SFRS5 GeneProduct ncbigene:6430
PRPF18 GeneProduct ncbigene:8559
CSTF2T GeneProduct ncbigene:23283
PTBP1 GeneProduct ncbigene:5725
SNRPN GeneProduct ncbigene:6638
CSTF1 GeneProduct ncbigene:1477
HNRPL GeneProduct ncbigene:3191
U2AF2 GeneProduct ncbigene:11338
SFRS7 GeneProduct ncbigene:6432
DHX9 GeneProduct ncbigene:1660
SFRS14 GeneProduct ncbigene:10147
SRRM1 GeneProduct ncbigene:10250
RNMT GeneProduct ncbigene:8731
SNRPE GeneProduct ncbigene:6635
CDC40 GeneProduct ncbigene:51362
SNRPG GeneProduct ncbigene:6637
RBMX GeneProduct ncbigene:27316
SNRPB GeneProduct ncbigene:6628
SMC1L1 GeneProduct ncbigene:8243
SNRP70 GeneProduct ncbigene:6625
PRPF8 GeneProduct ncbigene:10594
TXNL4A GeneProduct ncbigene:10907
NCBP1 GeneProduct ncbigene:4686
CDC40 GeneProduct ncbigene:51362
DHX8 GeneProduct ncbigene:1659
CLK1 GeneProduct ncbigene:1195
CLK3 GeneProduct ncbigene:1198
PTBP2 GeneProduct ncbigene:58155
U5-116KD GeneProduct ncbigene:9343
LSM2 GeneProduct ncbigene:57819
RNPC2 GeneProduct ncbigene:9584
SNRPA GeneProduct ncbigene:6626
HNRPH1 GeneProduct ncbigene:3187
FUS GeneProduct ncbigene:2521
RNPS1 GeneProduct ncbigene:10921 PMID: 14729963
DHX15 GeneProduct ncbigene:1665


  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