EuRBPDB

Description

RBDs

RBPome

Literatures

Expression

Transcripts

Gene Model

GWAS

PPI

Paralogs

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000135870 (Gene tree)
Gene ID: 149041
Gene Symbol: RC3H1
Alias: KIAA2025|roquin|RP5-1198E17.5|RNF198
Full Name: ring finger and CCCH-type domains 1
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Minus strand
Length: 91,214 bases
Position: chr1:173,931,084-174,022,297
Accession: 29434
RBP type: canonical RBP
Summary: This gene encodes a protein containing RING-type and C3H1-type zinc finger motifs. The encoded protein recognizes and binds to a constitutive decay element (CDE) in the 3' UTR of mRNAs, leading to mRNA deadenylation and degradation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

RNA binding domains(RBDs)

Protein ID	Domain	Pfam ID	E-value	Domain number	Total number
ENSP00000356667	zf-CCCH	PF00642.24	0.00078	1	1
ENSP00000258349	zf-CCCH	PF00642.24	0.00078	1	1
ENSP00000356669	zf-CCCH	PF00642.24	0.00078	1	1

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
22681889	The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts	4SURIC & HEK293	2012 May	Baltz AG	DOI: 10.1016/j.molcel.2012.05.021
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & HEK293	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
29431736	Capturing the interactome of newly transcribed RNA	RIC & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
22658674	Insights into RNA biology from an atlas of mammalian mRNA-binding proteins	RIC & Hela	2012 May 31	Castello A	DOI: 10.1016/j.cell.2012.04.031
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & MCF7	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
15917799	A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity.	Nature	2005 May 26	Vinuesa CG	-
23601678	Roquin paralogs add a new dimension to ICOS regulation.	Immunity	2013 Apr 18	Bertino SA	doi: 10.1016/j.immuni.2013.03.007.
26489670	New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins.	Sci Rep	2015 Oct 22	Zhang Q	doi: 10.1038/srep15660.
29352114	Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA.	Nat Commun	2018 Jan 19	Rehage N	doi: 10.1038/s41467-017-02582-1.
31236273	Post-transcriptional control of immune responses and its potential application.	Clin Transl Immunology	2019 Jun 17	Yoshinaga M	doi: 10.1002/cti2.1063
28929622	Endonuclease Regnase-1/Monocyte chemotactic protein-1-induced protein-1 (MCPIP1) in controlling immune responses and beyond.	Wiley Interdiscip Rev RNA	2018 Jan	Takeuchi O	doi: 10.1002/wrna.1449
30295819	Identification of new high affinity targets for Roquin based on structural conservation.	Nucleic Acids Res	2018 Dec 14	Braun J	doi: 10.1093/nar/gky908.
20412057	The ROQUIN family of proteins localizes to stress granules via the ROQ domain and binds target mRNAs.	FEBS J	2010 May	Athanasopoulos V	doi: 10.1111/j.1742-4658.2010.07628.x.
25697406	Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis.	Nat Commun	2015 Feb 20	Srivastava M	doi: 10.1038/ncomms7253.
25282160	Cleavage of roquin and regnase-1 by the paracaspase MALT1 releases their cooperatively repressed targets to promote T(H)17 differentiation.	Nat Immunol	2014 Nov	Jeltsch KM	doi: 10.1038/ni.3008
23583642	Roquin-2 shares functions with its paralog Roquin-1 in the repression of mRNAs controlling T follicular helper cells and systemic inflammation.	Immunity	2013 Apr 18	Pratama A	doi: 10.1016/j.immuni.2013.01.011
23550652	Molecular control of Tfh-cell differentiation by Roquin family proteins.	Immunol Rev	2013 May	Heissmeyer V	doi: 10.1111/imr.12056.
28155712	Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs.	BMC Genomics	2016 Dec 22	Kumagai Y	doi: 10.1186/s12864-016-3325-7.
26871597	Regulation of T cell signaling and autoimmunity by RNA-binding proteins.	Curr Opin Immunol	2016 Apr	Jeltsch KM	doi: 10.1016/j.coi.2016.01.011
27060455	ROQUIN signalling pathways in innate and adaptive immunity.	Eur J Immunol	2016 May	Athanasopoulos V	doi: 10.1002/eji.201545956
27010430	Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.	Nat Commun	2016 Mar 24	Janowski R	doi: 10.1038/ncomms11032.
26432764	Posttranscriptional T cell gene regulation to limit Tfh cells and autoimmunity.	Curr Opin Immunol	2015 Dec	Jiang SH	doi: 10.1016/j.coi.2015.09.003
26249698	Structure of human Roquin-2 and its complex with constitutive-decay element RNA.	Acta Crystallogr F Struct Biol Commun	2015 Aug	Sakurai S	doi: 10.1107/S2053230X15011887
26170170	RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kB pathway.	Nat Commun	2015 Jul 14	Murakawa Y	doi: 10.1038/ncomms8367.
26000482	Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms.	Cell	2015 May 21	Mino T	doi: 10.1016/j.cell.2015.04.029.
29114069	BAG3 directly stabilizes Hexokinase 2 mRNA and promotes aerobic glycolysis in pancreatic cancer cells.	J Cell Biol	2017 Dec 4	An MX	doi: 10.1083/jcb.201701064
29127149	Regnase-1 and Roquin Nonredundantly Regulate Th1 Differentiation Causing Cardiac Inflammation and Fibrosis.	J Immunol	2017 Dec 15	Cui X	doi: 10.4049/jimmunol.1701211
29799562	How T cells go rogue in the absence of Roquins.	Noncoding RNA Investig	2018 Apr	Akef A	doi: 10.21037/ncri.2018.03.08
30232334	Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation.	Nat Commun	2018 Sep 19	Essig K	doi: 10.1038/s41467-018-06184-3.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000479099	RC3H1-204	481	-	-	- (aa)	-	-
ENST00000531594	RC3H1-206	303	-	-	- (aa)	-	-
ENST00000367694	RC3H1-202	3775	XM_011509231	ENSP00000356667	1125 (aa)	XP_011507533	Q5TC82
ENST00000484867	RC3H1-205	368	-	-	- (aa)	-	-
ENST00000367696	RC3H1-203	11261	-	ENSP00000356669	1133 (aa)	-	Q5TC82
ENST00000258349	RC3H1-201	10988	XM_005244921	ENSP00000258349	1133 (aa)	XP_005244978	Q5TC82

Gene Model

Click here to download ENSG00000135870's gene model file

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000135870	rs41304550	1	173937797	T	Feeling miserable	29500382	z score decrease	5.88	EFO_0009598

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000135870's network

* RBP PPI network refers to all genes directly bind to RBP

Paralogs

Ensembl ID	Gene Symbol	Coverage	Identiy	Paralog	Gene Symbol	Coverage	Identiy
ENSG00000135870	RC3H1	96	52.323	ENSG00000056586	RC3H2	94	83.223

Orthologs

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000135870	RC3H1	100	96.911	ENSAMEG00000015657	RC3H1	100	96.911	Ailuropoda_melanoleuca
ENSG00000135870	RC3H1	100	88.056	ENSAPLG00000005341	RC3H1	100	88.056	Anas_platyrhynchos
ENSG00000135870	RC3H1	100	85.253	ENSACAG00000015271	RC3H1	100	85.253	Anolis_carolinensis
ENSG00000135870	RC3H1	100	98.941	ENSANAG00000036716	RC3H1	100	98.941	Aotus_nancymaae
ENSG00000135870	RC3H1	100	96.533	ENSBTAG00000052708	RC3H1	100	96.533	Bos_taurus
ENSG00000135870	RC3H1	100	98.588	ENSCJAG00000009106	RC3H1	100	98.588	Callithrix_jacchus
ENSG00000135870	RC3H1	100	96.999	ENSCAFG00000014434	RC3H1	100	96.999	Canis_familiaris
ENSG00000135870	RC3H1	100	96.914	ENSCAFG00020017112	RC3H1	99	98.202	Canis_lupus_dingo
ENSG00000135870	RC3H1	100	96.889	ENSCHIG00000002873	RC3H1	100	96.889	Capra_hircus
ENSG00000135870	RC3H1	99	95.322	ENSTSYG00000003913	RC3H1	99	95.322	Carlito_syrichta
ENSG00000135870	RC3H1	100	91.534	ENSCPOG00000004349	RC3H1	100	91.446	Cavia_porcellus
ENSG00000135870	RC3H1	100	96.558	ENSCCAG00000025652	RC3H1	100	96.558	Cebus_capucinus
ENSG00000135870	RC3H1	100	99.294	ENSCATG00000033497	RC3H1	100	99.294	Cercocebus_atys
ENSG00000135870	RC3H1	100	94.974	ENSCLAG00000011267	RC3H1	100	94.974	Chinchilla_lanigera
ENSG00000135870	RC3H1	96	99.079	ENSCSAG00000011823	RC3H1	85	99.079	Chlorocebus_sabaeus
ENSG00000135870	RC3H1	100	89.737	ENSCPBG00000014670	RC3H1	100	89.737	Chrysemys_picta_bellii
ENSG00000135870	RC3H1	100	99.295	ENSCANG00000032120	RC3H1	100	99.295	Colobus_angolensis_palliatus
ENSG00000135870	RC3H1	100	94.263	ENSCGRG00001020812	Rc3h1	100	93.822	Cricetulus_griseus_chok1gshd
ENSG00000135870	RC3H1	100	94.263	ENSCGRG00000011952	Rc3h1	100	93.822	Cricetulus_griseus_crigri
ENSG00000135870	RC3H1	55	95.484	ENSDNOG00000011494	RC3H1	99	95.484	Dasypus_novemcinctus
ENSG00000135870	RC3H1	100	96.028	ENSDORG00000004855	Rc3h1	100	96.028	Dipodomys_ordii
ENSG00000135870	RC3H1	82	96.527	ENSETEG00000012064	RC3H1	87	96.527	Echinops_telfairi
ENSG00000135870	RC3H1	100	96.622	ENSEASG00005017000	RC3H1	100	96.622	Equus_asinus_asinus
ENSG00000135870	RC3H1	100	96.444	ENSECAG00000021208	RC3H1	100	96.444	Equus_caballus
ENSG00000135870	RC3H1	83	97.059	ENSEEUG00000014861	RC3H1	93	83.302	Erinaceus_europaeus
ENSG00000135870	RC3H1	100	97.352	ENSFCAG00000014924	RC3H1	100	97.352	Felis_catus
ENSG00000135870	RC3H1	100	87.424	ENSFALG00000002947	RC3H1	100	86.900	Ficedula_albicollis
ENSG00000135870	RC3H1	100	94.974	ENSFDAG00000013303	RC3H1	100	94.974	Fukomys_damarensis
ENSG00000135870	RC3H1	100	87.898	ENSGALG00000004587	RC3H1	100	87.898	Gallus_gallus
ENSG00000135870	RC3H1	100	88.703	ENSGAGG00000018194	RC3H1	100	88.967	Gopherus_agassizii
ENSG00000135870	RC3H1	100	92.876	ENSGGOG00000005735	RC3H1	100	92.876	Gorilla_gorilla
ENSG00000135870	RC3H1	88	88.846	ENSHGLG00000004183	-	99	88.846	Heterocephalus_glaber_female
ENSG00000135870	RC3H1	100	94.444	ENSHGLG00100008577	RC3H1	100	94.444	Heterocephalus_glaber_male
ENSG00000135870	RC3H1	100	96.649	ENSSTOG00000016033	RC3H1	100	96.649	Ictidomys_tridecemlineatus
ENSG00000135870	RC3H1	100	95.322	ENSJJAG00000018915	Rc3h1	100	95.146	Jaculus_jaculus
ENSG00000135870	RC3H1	100	75.217	ENSLACG00000016186	RC3H1	100	78.279	Latimeria_chalumnae
ENSG00000135870	RC3H1	97	97.541	ENSLAFG00000004367	RC3H1	100	97.541	Loxodonta_africana
ENSG00000135870	RC3H1	100	99.206	ENSMFAG00000033725	RC3H1	100	99.206	Macaca_fascicularis
ENSG00000135870	RC3H1	100	99.117	ENSMMUG00000000630	RC3H1	100	99.117	Macaca_mulatta
ENSG00000135870	RC3H1	100	99.294	ENSMNEG00000035968	RC3H1	100	99.294	Macaca_nemestrina
ENSG00000135870	RC3H1	100	99.206	ENSMLEG00000037455	RC3H1	100	99.206	Mandrillus_leucophaeus
ENSG00000135870	RC3H1	97	94.254	ENSMAUG00000020864	Rc3h1	100	93.750	Mesocricetus_auratus
ENSG00000135870	RC3H1	100	97.440	ENSMICG00000003000	RC3H1	100	97.440	Microcebus_murinus
ENSG00000135870	RC3H1	93	92.898	ENSMOCG00000016587	Rc3h1	98	92.519	Microtus_ochrogaster
ENSG00000135870	RC3H1	100	92.240	ENSMODG00000004289	RC3H1	100	92.328	Monodelphis_domestica
ENSG00000135870	RC3H1	100	93.822	MGP_CAROLIEiJ_G0014756	Rc3h1	100	93.380	Mus_caroli
ENSG00000135870	RC3H1	100	93.645	ENSMUSG00000040423	Rc3h1	100	93.204	Mus_musculus
ENSG00000135870	RC3H1	100	93.469	MGP_PahariEiJ_G0027992	Rc3h1	100	93.027	Mus_pahari
ENSG00000135870	RC3H1	100	93.469	MGP_SPRETEiJ_G0015563	Rc3h1	100	93.027	Mus_spretus
ENSG00000135870	RC3H1	100	96.649	ENSMPUG00000004747	RC3H1	100	96.649	Mustela_putorius_furo
ENSG00000135870	RC3H1	100	95.587	ENSMLUG00000011127	RC3H1	100	95.587	Myotis_lucifugus
ENSG00000135870	RC3H1	100	95.852	ENSNGAG00000011135	Rc3h1	100	95.410	Nannospalax_galili
ENSG00000135870	RC3H1	100	99.382	ENSNLEG00000015327	RC3H1	100	99.382	Nomascus_leucogenys
ENSG00000135870	RC3H1	99	82.935	ENSOPRG00000013068	RC3H1	99	83.024	Ochotona_princeps
ENSG00000135870	RC3H1	100	94.533	ENSODEG00000014185	RC3H1	100	94.533	Octodon_degus
ENSG00000135870	RC3H1	100	91.441	ENSOANG00000000924	RC3H1	100	91.354	Ornithorhynchus_anatinus
ENSG00000135870	RC3H1	99	96.150	ENSOCUG00000004930	RC3H1	98	96.150	Oryctolagus_cuniculus
ENSG00000135870	RC3H1	100	90.220	ENSOGAG00000004044	RC3H1	100	90.220	Otolemur_garnettii
ENSG00000135870	RC3H1	100	96.491	ENSOARG00000013011	RC3H1	100	96.491	Ovis_aries
ENSG00000135870	RC3H1	100	99.824	ENSPPAG00000039253	RC3H1	100	99.824	Pan_paniscus
ENSG00000135870	RC3H1	100	97.333	ENSPPRG00000009007	RC3H1	100	97.333	Panthera_pardus
ENSG00000135870	RC3H1	100	97.012	ENSPTIG00000015326	RC3H1	100	97.012	Panthera_tigris_altaica
ENSG00000135870	RC3H1	100	99.824	ENSPTRG00000001702	RC3H1	100	99.824	Pan_troglodytes
ENSG00000135870	RC3H1	100	99.206	ENSPANG00000008886	RC3H1	100	99.206	Papio_anubis
ENSG00000135870	RC3H1	100	89.497	ENSPSIG00000016181	RC3H1	100	89.762	Pelodiscus_sinensis
ENSG00000135870	RC3H1	100	93.822	ENSPEMG00000011966	Rc3h1	100	93.469	Peromyscus_maniculatus_bairdii
ENSG00000135870	RC3H1	70	94.051	ENSPCIG00000002058	RC3H1	95	98.430	Phascolarctos_cinereus
ENSG00000135870	RC3H1	100	96.028	ENSPPYG00000000490	RC3H1	98	99.421	Pongo_abelii
ENSG00000135870	RC3H1	81	100.000	ENSPCAG00000010775	RC3H1	87	100.000	Procavia_capensis
ENSG00000135870	RC3H1	83	96.902	ENSPCOG00000021795	RC3H1	96	96.902	Propithecus_coquereli
ENSG00000135870	RC3H1	100	88.173	ENSPVAG00000007593	RC3H1	100	88.173	Pteropus_vampyrus
ENSG00000135870	RC3H1	97	62.422	ENSPNAG00000023439	rc3h1a	95	90.991	Pygocentrus_nattereri
ENSG00000135870	RC3H1	100	99.206	ENSRBIG00000037743	RC3H1	100	99.206	Rhinopithecus_bieti
ENSG00000135870	RC3H1	100	99.117	ENSRROG00000036546	RC3H1	100	99.117	Rhinopithecus_roxellana
ENSG00000135870	RC3H1	93	93.702	ENSSBOG00000010664	RC3H1	100	93.702	Saimiri_boliviensis_boliviensis
ENSG00000135870	RC3H1	100	91.454	ENSSHAG00000007589	RC3H1	100	91.542	Sarcophilus_harrisii
ENSG00000135870	RC3H1	87	86.712	ENSSARG00000004660	RC3H1	86	86.712	Sorex_araneus
ENSG00000135870	RC3H1	100	84.501	ENSSPUG00000018472	RC3H1	100	83.961	Sphenodon_punctatus
ENSG00000135870	RC3H1	100	97.529	ENSSSCG00000015498	RC3H1	100	97.529	Sus_scrofa
ENSG00000135870	RC3H1	100	87.895	ENSTGUG00000004090	RC3H1	100	87.895	Taeniopygia_guttata
ENSG00000135870	RC3H1	89	97.561	ENSTBEG00000005015	RC3H1	89	97.561	Tupaia_belangeri
ENSG00000135870	RC3H1	100	96.564	ENSTTRG00000008572	RC3H1	100	96.564	Tursiops_truncatus
ENSG00000135870	RC3H1	100	96.293	ENSUAMG00000019525	RC3H1	100	96.293	Ursus_americanus
ENSG00000135870	RC3H1	100	96.825	ENSUMAG00000020087	RC3H1	100	96.825	Ursus_maritimus
ENSG00000135870	RC3H1	91	98.649	ENSVPAG00000002591	RC3H1	92	98.649	Vicugna_pacos
ENSG00000135870	RC3H1	100	96.658	ENSVVUG00000014201	RC3H1	100	96.658	Vulpes_vulpes
ENSG00000135870	RC3H1	100	79.199	ENSXETG00000020030	rc3h1	100	78.746	Xenopus_tropicalis

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000209	protein polyubiquitination	26489670.	IDA	Process
GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	-	ISS	Process
GO:0000932	P-body	-	ISS	Component
GO:0000956	nuclear-transcribed mRNA catabolic process	25026078.	IDA	Process
GO:0000956	nuclear-transcribed mRNA catabolic process	-	ISS	Process
GO:0001782	B cell homeostasis	-	IEA	Process
GO:0002634	regulation of germinal center formation	-	ISS	Process
GO:0002635	negative regulation of germinal center formation	-	ISS	Process
GO:0003723	RNA binding	22658674.22681889.	HDA	Function
GO:0003725	double-stranded RNA binding	25026078.25504471.	IDA	Function
GO:0003730	mRNA 3'-UTR binding	-	ISS	Function
GO:0004842	ubiquitin-protein transferase activity	26489670.	IDA	Function
GO:0005515	protein binding	25697406.	IPI	Function
GO:0008270	zinc ion binding	-	ISS	Function
GO:0010494	cytoplasmic stress granule	-	ISS	Component
GO:0010608	posttranscriptional regulation of gene expression	-	ISS	Process
GO:0030889	negative regulation of B cell proliferation	-	ISS	Process
GO:0033962	cytoplasmic mRNA processing body assembly	-	ISS	Process
GO:0035198	miRNA binding	-	ISS	Function
GO:0035613	RNA stem-loop binding	25504471.	IDA	Function
GO:0035613	RNA stem-loop binding	-	ISS	Function
GO:0042098	T cell proliferation	-	IEA	Process
GO:0043029	T cell homeostasis	-	IEA	Process
GO:0043488	regulation of mRNA stability	-	ISS	Process
GO:0045623	negative regulation of T-helper cell differentiation	-	ISS	Process
GO:0046007	negative regulation of activated T cell proliferation	-	ISS	Process
GO:0048535	lymph node development	-	IEA	Process
GO:0048536	spleen development	-	IEA	Process
GO:0050852	T cell receptor signaling pathway	-	ISS	Process
GO:0050856	regulation of T cell receptor signaling pathway	-	ISS	Process
GO:0061014	positive regulation of mRNA catabolic process	-	ISS	Process
GO:0061158	3'-UTR-mediated mRNA destabilization	-	ISS	Process
GO:0061470	T follicular helper cell differentiation	-	IEA	Process
GO:0061630	ubiquitin protein ligase activity	19217324.	TAS	Function
GO:0071347	cellular response to interleukin-1	-	ISS	Process
GO:1901224	positive regulation of NIK/NF-kappaB signaling	-	IEA	Process
GO:2000320	negative regulation of T-helper 17 cell differentiation	-	ISS	Process
GO:2000628	regulation of miRNA metabolic process	-	ISS	Process