mRNA processing (WP793)

Gallus gallus

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

Kristina Hanspers , Daniela Digles , Egon Willighagen , Martina Summer-Kutmon , and Eric Weitz

Activity

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Cited In

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Organisms

Gallus gallus

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:ENSGALG00000008857 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:9128
SNRPA1 GeneProduct ensembl:ENSGALG00000007170 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6627
RBM17 GeneProduct ensembl:ENSGALG00000006332 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:84991
SNRPD3 GeneProduct ensembl:ENSGALG00000006596 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6634
NCBP2 GeneProduct ensembl:ENSGALG00000006843 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:22916
DNAJC8 GeneProduct ensembl:ENSGALG00000000790 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:22826
RNGTT GeneProduct ensembl:ENSGALG00000015787 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8732
SNRPD1 GeneProduct ensembl:ENSGALG00000041334 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6632
SF3A2 GeneProduct ensembl:ENSGALG00000021679 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8175
SNRPD2 GeneProduct ensembl:ENSGALG00000042282 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6633
XRN2 GeneProduct ensembl:ENSGALG00000008372 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:22803
DHX16 GeneProduct ensembl:ENSGALG00000029334 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8449
HNRNPM GeneProduct ensembl:ENSGALG00000000377 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:4670
HNRPA1 GeneProduct ensembl:ENSGALG00000042011 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3178
CELF2 GeneProduct ensembl:ENSGALG00000034590 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10659
SPOP GeneProduct ensembl:ENSGALG00000009939 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8405
HNRNPA2B1 GeneProduct ensembl:ENSGALG00000011036 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3181
PHF5A GeneProduct ensembl:ENSGALG00000011953 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:84844
SF3B5 GeneProduct ensembl:ENSGALG00000030824 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:83443
HNRNPR GeneProduct ensembl:ENSGALG00000000814 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10236
PRPF6 GeneProduct ensembl:ENSGALG00000006001 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:24148
YBX1 GeneProduct ensembl:ENSGALG00000004848 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:4904
SUGP1 GeneProduct ensembl:ENSGALG00000042132 inferred from: SURP 2, G patch protein, UniProt:O60378
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:57794
SNU13 GeneProduct ensembl:ENSGALG00000011931 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:4809
SF3B3 GeneProduct ensembl:ENSGALG00000037508 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:23450
PRPF40A GeneProduct ensembl:ENSGALG00000012526 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:55660
PSKH1 GeneProduct ensembl:ENSGALG00000001647 PMID: 12466556
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:5681
SNRPB2 GeneProduct ensembl:ENSGALG00000026999 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6629
HNRNPH1 GeneProduct ensembl:ENSGALG00000031120 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3188
SNRNP40 GeneProduct ensembl:ENSGALG00000000615 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:9410
HNRNPU GeneProduct ensembl:ENSGALG00000010671 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3192
LSM7 GeneProduct ensembl:ENSGALG00000000408 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:51690
DDX1 GeneProduct ensembl:ENSGALG00000016461 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:1653
SRPK1 GeneProduct ensembl:ENSGALG00000037546 PMID: 12773558
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6732
U2AF1 GeneProduct ensembl:ENSGALG00000016198 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:7307
TRA2B GeneProduct ensembl:ENSGALG00000006531 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6434
SRPK2 GeneProduct ensembl:ENSGALG00000008154 PMID: 12773558
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6733
HNRNPK GeneProduct ensembl:ENSGALG00000012591 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3190
SUPT5H GeneProduct ensembl:ENSGALG00000039160 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6829
SRP54 GeneProduct ensembl:ENSGALG00000023135 PMID: 14729963
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6729
PRPF4B GeneProduct ensembl:ENSGALG00000043751 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8899
CELF1 GeneProduct ensembl:ENSGALG00000008097 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10658
SRSF1 GeneProduct ensembl:ENSGALG00000005525 Antagonist splicing factor
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6426
CLP1 GeneProduct ensembl:ENSGALG00000007370 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10978
SNRPF GeneProduct ensembl:ENSGALG00000011409 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6636
METTL3 GeneProduct ensembl:ENSGALG00000044213 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:56339
SRSF6 GeneProduct ensembl:ENSGALG00000000990 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6431
NXF1 GeneProduct ensembl:ENSGALG00000032057 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10482
SFPQ GeneProduct ensembl:ENSGALG00000002514 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6421
RBM5 GeneProduct ensembl:ENSGALG00000039288 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10181
PRPF3 GeneProduct ensembl:ENSGALG00000028205 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:9129
SRSF10 GeneProduct ensembl:ENSGALG00000004133 FUSI MOUSE PMID: 11684676
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10772
CSTF3 GeneProduct ensembl:ENSGALG00000011685 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:1479
PAPOLA GeneProduct ensembl:ENSGALG00000030578 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10914
HNRNPD GeneProduct ensembl:ENSGALG00000011184 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3184
CPSF3 GeneProduct ensembl:ENSGALG00000016424 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:51692
HNRNPAB GeneProduct ensembl:ENSGALG00000014381 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3182
POLR2A GeneProduct ensembl:ENSGALG00000032698 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:5430
DICER1 GeneProduct ensembl:ENSGALG00000010999 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:23405
CPSF4 GeneProduct ensembl:ENSGALG00000004714 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10898
SFSWAP GeneProduct ensembl:ENSGALG00000002487 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6433
SRSF3 GeneProduct ensembl:ENSGALG00000000533 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6428
SF3A1 GeneProduct ensembl:ENSGALG00000007937 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10291
SRSF10 GeneProduct ensembl:ENSGALG00000004133 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10772
TMED10 GeneProduct ensembl:ENSGALG00000010318 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10972
CPSF2 GeneProduct ensembl:ENSGALG00000010783 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:53981
PPM1G GeneProduct ensembl:ENSGALG00000016513 PMID: 12773558
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:5496
NUDT21 GeneProduct ensembl:ENSGALG00000003084 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:11051
SF3B4 GeneProduct ensembl:ENSGALG00000013352 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10262
CSTF2 GeneProduct ensembl:ENSGALG00000006760 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:1478
DHX38 GeneProduct ensembl:ENSGALG00000000787 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:9785
SREK1 GeneProduct ensembl:ENSGALG00000014775 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 Gallus gallus: Original ID = L:140890
SFRS4 GeneProduct ensembl:ENSGALG00000037539 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6429
CLK2 GeneProduct ensembl:ENSGALG00000029444 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:1196
PRPF8 GeneProduct ensembl:ENSGALG00000002943 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10594
SF3A3 GeneProduct ensembl:ENSGALG00000001540 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10946
SNRPB GeneProduct ensembl:ENSGALG00000035421 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6638
CLK4 GeneProduct ensembl:ENSGALG00000006057 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:57396
SF3B1 GeneProduct ensembl:ENSGALG00000008038 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:23451
DDX20 GeneProduct ensembl:ENSGALG00000001504 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:11218
NONO GeneProduct ensembl:ENSGALG00000005507 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:4841
CELF4 GeneProduct ensembl:ENSGALG00000002413 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:56853
SRSF5 GeneProduct ensembl:ENSGALG00000009421 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6430
PRPF18 GeneProduct ensembl:ENSGALG00000043593 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8559
CSTF2T GeneProduct ensembl:ENSGALG00000006760 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:23283
PTBP1 GeneProduct ensembl:ENSGALG00000001962 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:5725
CSTF1 GeneProduct ensembl:ENSGALG00000007757 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:1477
HNRPL GeneProduct ensembl:ENSGALG00000043929 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3191
SRSF7 GeneProduct ensembl:ENSGALG00000033120 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6432
SUGP2 GeneProduct ensembl:ENSGALG00000003047 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10147
SRRM1 GeneProduct ensembl:ENSGALG00000001283 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10250
RNMT GeneProduct ensembl:ENSGALG00000013889 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8731
CDC40 GeneProduct ensembl:ENSGALG00000015061 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:51362
SNRPG GeneProduct ensembl:ENSGALG00000028409 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6637
RBMX GeneProduct ensembl:ENSGALG00000006457 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:27316
SNRPB GeneProduct ensembl:ENSGALG00000035421 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6628
SMC1L1 GeneProduct ensembl:ENSGALG00000041777 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:8243
SNRNP70 GeneProduct ensembl:ENSGALG00000034738 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:6625
TXNL4A GeneProduct ensembl:ENSGALG00000040739 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10907
NCBP1 GeneProduct ensembl:ENSGALG00000002087 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:4686
DHX8 GeneProduct ensembl:ENSGALG00000032305 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:1659
CLK1 GeneProduct ensembl:ENSGALG00000028438 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 Gallus gallus: Original ID = L:1195
CLK3 GeneProduct ensembl:ENSGALG00000001362 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:1198
PTBP2 GeneProduct ensembl:ENSGALG00000005552 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:58155
EFTUD2 GeneProduct ensembl:ENSGALG00000000988 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:9343
RBM39 GeneProduct ensembl:ENSGALG00000001550 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:9584
HNRNPH1 GeneProduct ensembl:ENSGALG00000031120 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:3187
FUS GeneProduct ensembl:ENSGALG00000032219 Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:2521
RNPS1 GeneProduct ensembl:ENSGALG00000009288 PMID: 14729963
Homology Mapping from Homo sapiens to Gallus gallus: Original ID = L:10921
DHX15 GeneProduct ensembl:ENSGALG00000014395 Homology Mapping from Homo sapiens to Gallus gallus: 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