mRNA processing (WP467)

Danio rerio

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:


Nathan Salomonis , Kristina Hanspers , Daniela Digles , Levi Wackers , and Alex Pico


last edited

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Danio rerio



Pathway Ontology

spliceosome pathway


Label Type Compact URI Comment
c20orf14 GeneProduct ncbigene:323855
RBMX GeneProduct ncbigene:321860
rbm17 GeneProduct ncbigene:393889
ssfa1 GeneProduct ensembl:ENSDARG00000023299
snrpb GeneProduct ncbigene:402966 snrpb is the zebrafish homolog of human SNRPN
hnrpu GeneProduct ncbigene:334490
sf3b1 GeneProduct ncbigene:446117
prpf3 GeneProduct ncbigene:403072
ptbp2a GeneProduct ensembl:ENSDARG00000101947
supt5h GeneProduct ncbigene:64275
smx5 GeneProduct ncbigene:57924
snrpfl GeneProduct ncbigene:445404
srek1 GeneProduct ncbigene:445219 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.
SNRPB GeneProduct ncbigene:402966
SRPK2 GeneProduct ncbigene:100333293 PMID: 12773558
sugp1 GeneProduct ensembl:ENSDARG00000075936 inferred from: SURP 2, G patch protein, UniProt:O60378
SF4 is alias for sugp1; added annotation
DHX38 GeneProduct ncbigene:393850
SNRPD3 GeneProduct ncbigene:415171
rbm5 GeneProduct ensembl:ENSDARG00000098280
ddx20 GeneProduct ncbigene:556273
srsf10a GeneProduct ensembl:ENSDARG00000022415
smx5 GeneProduct ncbigene:57924
clk4a GeneProduct ensembl:ENSDARG00000089372
cstf3 GeneProduct ncbigene:406326
txnl4a GeneProduct ncbigene:449780
phf5a GeneProduct ncbigene:286774
zgc:77804 GeneProduct ncbigene:402989
dicer1 GeneProduct ncbigene:324724
prpf18 GeneProduct ncbigene:431751
hnrnph1l GeneProduct ncbigene:321556
DHX9 GeneProduct ensembl:ENSDARG00000079725
cstf1 GeneProduct ncbigene:324238
sf3a2 GeneProduct ncbigene:394018
ptbp1a GeneProduct ncbigene:323490
SFRS4 GeneProduct ncbigene:321872
clk2a GeneProduct ensembl:ENSDARG00000062954
hnrnpk GeneProduct ncbigene:406267
HEAB GeneProduct ensembl:ENSDARG00000063663
ssfa1 GeneProduct ensembl:ENSDARG00000023299 Alias of snu13b
ncbp2 GeneProduct ncbigene:192325
hnrpl GeneProduct ncbigene:394074
prpf4 GeneProduct ncbigene:326944
smc1al GeneProduct ensembl:ENSDARG00000058203
srsf7a GeneProduct ncbigene:402972
hnrnpm GeneProduct ensembl:ENSDARG00000061735
cpsf5 GeneProduct ncbigene:394092
sfrs16 GeneProduct ncbigene:555304
mettl3 GeneProduct ncbigene:100004398
pcbp2 GeneProduct ncbigene:321844
snrpa GeneProduct ncbigene:324121
sfpq GeneProduct ncbigene:406564
cd2bp2 GeneProduct ncbigene:393936
tmed10 GeneProduct ncbigene:326716
wdr57 GeneProduct ncbigene:393292
sfrs5a GeneProduct ensembl:ENSDARG00000029818
ssfa1 GeneProduct ensembl:ENSDARG00000023299 Alias of snu13b
srpk1 GeneProduct ncbigene:323679 PMID: 12773558
rnpc2 GeneProduct ncbigene:406251
dhx16 GeneProduct ncbigene:336645
sf3b2 GeneProduct ensembl:ENSDARG00000018049
sfrs3 GeneProduct ncbigene:368925
hnrnpc GeneProduct ensembl:ENSDARG00000053810 HNRPC is old identifier for hnrnpc
EFTUD2 GeneProduct ncbigene:393480
hnrnpa3 GeneProduct ensembl:ENSDARG00000059351 HNRPA3 is old identifier for HNRNPA3
NCBP1 GeneProduct ncbigene:101885456
spop GeneProduct ncbigene:100005514
snrpb2 GeneProduct ncbigene:402896
sfrs10 GeneProduct ncbigene:394172
zgc:55440 GeneProduct ncbigene:406824
srsf9 GeneProduct ncbigene:405835 PMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
celf4 GeneProduct ensembl:ENSDARG00000070045 Alias for BRUNOL4
hnrnpr GeneProduct ensembl:ENSDARG00000014569
rngtt GeneProduct ncbigene:405803
papola GeneProduct ncbigene:404041
u2af1 GeneProduct ncbigene:192328
pabn1 GeneProduct ncbigene:406543
POLR2A GeneProduct ncbigene:553347
snrpd2 GeneProduct ncbigene:550244
hnrnpd GeneProduct ensembl:ENSDARG00000059246
prpf40a GeneProduct ncbigene:321555 Alias for FNBP3
dhx8 GeneProduct ensembl:ENSDARG00000054707
snrpd1 GeneProduct ncbigene:192331
RNMT GeneProduct ensembl:ENSDARG00000070553
snrpe GeneProduct ncbigene:393979
sfrs6a GeneProduct ensembl:ENSDARG00000013729
cstf2 GeneProduct ncbigene:386806
sf3b4 GeneProduct ncbigene:192318
SF3A3 GeneProduct ncbigene:446168
PSKH1 GeneProduct ncbigene:554840 PMID: 12466556
srrm1 GeneProduct ncbigene:406751
cpsf3 GeneProduct ncbigene:324554
xrn2 GeneProduct ncbigene:321940
lsm7 GeneProduct ncbigene:573047
hnrpab GeneProduct ncbigene:321466
PRPF8 GeneProduct ncbigene:393951
ybx1 GeneProduct ensembl:ENSDARG00000004757
prpf4 GeneProduct ncbigene:326944
prmt2 GeneProduct ncbigene:558841
snrpg GeneProduct ncbigene:447922
sf3a1 GeneProduct ensembl:ENSDARG00000041887
cpsf1 GeneProduct ncbigene:432372
dhx15 GeneProduct ncbigene:321931
cugbp2 GeneProduct ncbigene:373117
snrp70 GeneProduct ncbigene:445398
cdc40 GeneProduct ncbigene:494534
sf3b5 GeneProduct ncbigene:436751
PRPF8 GeneProduct ncbigene:393951
ddx1 GeneProduct ensembl:ENSDARG00000032117
hnrpa1 GeneProduct ncbigene:378453
nxf1 GeneProduct ncbigene:323865
srsf2b GeneProduct ncbigene:323700
prpf4bb GeneProduct ncbigene:406758
cugbp1 GeneProduct ncbigene:58137
nar GeneProduct ncbigene:30203
ppm1g GeneProduct ncbigene:368275 PMID: 12773558
DNAJC8 GeneProduct ensembl:ENSDARG00000059373
prmt1 GeneProduct ncbigene:321974
srp54 GeneProduct ncbigene:393963 PMID: 14729963
snrpb GeneProduct ncbigene:402966 snrpb is the zebrafish homolog of human SNRPN
cpsf2 GeneProduct ncbigene:436657
sfswap GeneProduct ncbigene:394143
nono GeneProduct ncbigene:321994
sfrs1 GeneProduct ensembl:ENSDARG00000017843 Antagonist splicing factor
rnps1 GeneProduct ncbigene:327020 PMID: 14729963
snrpa1 GeneProduct ncbigene:492511
fus GeneProduct ncbigene:394058
clk2b GeneProduct ensembl:ENSDARG00000059870
clk4b GeneProduct ensembl:ENSDARG00000005908
ptbp2b GeneProduct ensembl:ENSDARG00000015901
srsf10b GeneProduct ensembl:ENSDARG00000086411
srsf10a GeneProduct ensembl:ENSDARG00000022415
srsf10b GeneProduct ensembl:ENSDARG00000086411
sfrs5b GeneProduct ensembl:ENSDARG00000027734
sfrs6b GeneProduct ensembl:ENSDARG00000016783