EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

GWAS

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000070495 (Gene tree)
Gene ID: 23210
Gene Symbol: JMJD6
Alias: PTDSR1|KIAA0585|PTDSR
Full Name: jumonji domain containing 6, arginine demethylase and lysine hydroxylase
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Minus strand
Length: 13,968 bases
Position: chr17:76,712,832-76,726,799
Accession: 19355
RBP type: non-canonical RBP
Summary: This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that it does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
31026779	Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation.	J Mol Graph Model	2019 Jul	Chen J	doi: 10.1016/j.jmgm.2019.04.003
25564762	A lysine-rich motif in the phosphatidylserine receptor PSR-1 mediates recognition and removal of apoptotic cells.	Nat Commun	2015 Jan 7	Yang H	doi: 10.1038/ncomms6717.
29176719	Structural Mechanism of the Oxygenase JMJD6 Recognition by the Extraterminal (ET) Domain of BRD4.	Sci Rep	2017 Nov 24	Konuma T	doi: 10.1038/s41598-017-16588-8.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000303996	JMJD6-201	1893	-	ENSP00000302916	335 (aa)	-	B2WTI3
ENST00000397625	JMJD6-202	1603	-	ENSP00000380750	403 (aa)	-	Q6NYC1
ENST00000589982	JMJD6-206	467	-	-	- (aa)	-	-
ENST00000542934	JMJD6-204	1898	-	ENSP00000442362	361 (aa)	-	B2WTI4
ENST00000585429	JMJD6-205	1330	-	ENSP00000465330	395 (aa)	-	K7EJU9
ENST00000617192	JMJD6-208	5517	-	ENSP00000483941	361 (aa)	-	B2WTI4
ENST00000591460	JMJD6-207	667	-	-	- (aa)	-	-
ENST00000445478	JMJD6-203	5303	-	ENSP00000394085	414 (aa)	-	Q6NYC1

Gene Model

Click here to download ENSG00000070495's gene model file

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000070495	rs2005827	17	76724795	A	Highest math class taken (MTAG)	30038396	[0.0062-0.0128] unit increase	0.0095	EFO_0004875
ENSG00000070495	rs2240775	17	76714046	?	White blood cell count	30595370			EFO_0004308

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000070495's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0001822	kidney development	-	IEA	Process
GO:0002040	sprouting angiogenesis	-	ISS	Process
GO:0003713	transcription coactivator activity	21555454.	IMP	Function
GO:0003723	RNA binding	21060799.	TAS	Function
GO:0003727	single-stranded RNA binding	20679243.29176719.	IDA	Function
GO:0005506	iron ion binding	20679243.	IDA	Function
GO:0005515	protein binding	19574390.21555454.23455924.24360279.24498420.24667498.25416956.29176719.	IPI	Function
GO:0005634	nucleus	14729065.17534701.	IDA	Component
GO:0005634	nucleus	21555454.	IMP	Component
GO:0005654	nucleoplasm	21060799.	IDA	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005730	nucleolus	21060799.	IDA	Component
GO:0005737	cytoplasm	24498420.	IDA	Component
GO:0005829	cytosol	-	IEA	Component
GO:0005886	plasma membrane	-	IEA	Component
GO:0006397	mRNA processing	-	IEA	Process
GO:0006482	protein demethylation	24498420.	IDA	Process
GO:0007166	cell surface receptor signaling pathway	-	IEA	Process
GO:0007507	heart development	-	IEA	Process
GO:0008380	RNA splicing	-	IEA	Process
GO:0018395	peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine	19574390.22189873.	IDA	Process
GO:0030324	lung development	-	IEA	Process
GO:0032451	demethylase activity	24498420.	IDA	Function
GO:0032452	histone demethylase activity	24498420.	IDA	Function
GO:0032452	histone demethylase activity	-	TAS	Function
GO:0033077	T cell differentiation in thymus	-	IEA	Process
GO:0033746	histone demethylase activity (H3-R2 specific)	17947579.	IDA	Function
GO:0033749	histone demethylase activity (H4-R3 specific)	17947579.24360279.	IDA	Function
GO:0035513	oxidative RNA demethylation	24360279.	IDA	Process
GO:0035515	oxidative RNA demethylase activity	24360279.	IMP	Function
GO:0038023	signaling receptor activity	-	IEA	Function
GO:0042116	macrophage activation	-	IEA	Process
GO:0042802	identical protein binding	17534701.	IDA	Function
GO:0042802	identical protein binding	24360279.	IPI	Function
GO:0042803	protein homodimerization activity	-	IEA	Function
GO:0043654	recognition of apoptotic cell	-	IEA	Process
GO:0045893	positive regulation of transcription, DNA-templated	21555454.	IMP	Process
GO:0045944	positive regulation of transcription by RNA polymerase II	24360279.	IDA	Process
GO:0048024	regulation of mRNA splicing, via spliceosome	19574390.	IMP	Process
GO:0048821	erythrocyte development	-	IEA	Process
GO:0051260	protein homooligomerization	22189873.24360279.	IDA	Process
GO:0060041	retina development in camera-type eye	-	IEA	Process
GO:0070078	histone H3-R2 demethylation	17947579.	IDA	Process
GO:0070078	histone H3-R2 demethylation	22189873.	IDA	Process
GO:0070079	histone H4-R3 demethylation	17947579.24360279.24498420.	IDA	Process
GO:0070079	histone H4-R3 demethylation	22189873.	IDA	Process
GO:0070815	peptidyl-lysine 5-dioxygenase activity	19574390.22189873.	IDA	Function
GO:0106140	P-TEFb complex binding	24360279.	IDA	Function
GO:1990904	ribonucleoprotein complex	-	IEA	Component

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
22621393	JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer.	Breast Cancer Res	2012 May 23	Lee YF	-
28882645	MiR-770 inhibits tumorigenesis and EMT by targeting JMJD6 and regulating WNT/β-catenin pathway in non-small cell lung cancer.	Life Sci	2017 Nov 1	Zhang Z	doi: 10.1016/j.lfs.2017.09.002
29229759	JMJD6 induces HOTAIR, an oncogenic lincRNA, by physically interacting with its proximal promoter.	Biochem J	2018 Jan 15	Biswas A	doi: 10.1042/BCJ20170664.
24667498	JMJD6 promotes colon carcinogenesis through negative regulation of p53 by hydroxylation.	PLoS Biol	2014 Mar 25	Wang F	doi: 10.1371/journal.pbio.1001819
25951181	Role of JMJD6 in Breast Tumourigenesis.	PLoS One	2015 May 7	Poulard C	doi: 10.1371/journal.pone.0126181
26645717	Elevated expression of JMJD6 is associated with oral carcinogenesis and maintains cancer stemness properties.	Carcinogenesis	2016 Feb	Lee CR	doi: 10.1093/carcin/bgv169
29628309	JMJD6 Licenses ERα-Dependent Enhancer and Coding Gene Activation by Modulating the Recruitment of the CARM1/MED12 Co-activator Complex.	Mol Cell	2018 Apr 19	Gao WW	doi: 10.1016/j.molcel.2018.03.006

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr17	76723926	Silent	novel	L217L	0.28
BLCA	chr17	76726445	Missense_Mutation	novel	E11Q	0.13
BLCA	chr17	76718765	Silent	rs149210415	D392D	0.24
BLCA	chr17	76726365	Silent	novel	L37L	0.33
BLCA	chr17	76726477	5'UTR	novel		0.37
BLCA	chr17	76723826	Missense_Mutation	novel	E251Q	0.11
BRCA	chr17	76716634	3'Flank	novel		0.37
BRCA	chr17	76723823	Missense_Mutation	NA	F252I	0.19
BRCA	chr17	76720496	Missense_Mutation	NA	I315S	0.52
BRCA	chr17	76716508	3'Flank	novel		0.31
CESC	chr17	76716620	3'Flank	novel		0.65
CESC	chr17	76723912	Missense_Mutation	NA	R222Q	0.46
CESC	chr17	76718634	3'UTR	novel		0.23
CESC	chr17	76718716	3'UTR	novel		0.33
CESC	chr17	76726453	Missense_Mutation	novel	R8H	0.14
CESC	chr17	76725630	Missense_Mutation	NA	E119K	0.4
COAD	chr17	76716620	3'Flank	novel		0.39
COAD	chr17	76725746	Missense_Mutation	NA	S80Y	0.39
COAD	chr17	76716579	3'Flank	novel		0.2
COAD	chr17	76716542	3'Flank	novel		0.58
COAD	chr17	76723853	Missense_Mutation	rs374399276	R242W	0.19
COAD	chr17	76718805	Missense_Mutation	rs377582812	T379M	0.26
COAD	chr17	76725804	Missense_Mutation	novel	E61K	0.34
COAD	chr17	76726429	Missense_Mutation	novel	A16V	0.51
COAD	chr17	76725781	Missense_Mutation	novel	K68N	0.08
DLBC	chr17	76718745	Missense_Mutation	rs769402176	R399H	0.42
ESCA	chr17	76718604	3'UTR	rs760707744		0.17
ESCA	chr17	76718646	3'UTR	novel		0.2
ESCA	chr17	76718845	Missense_Mutation	novel	E366Q	0.31
GBM	chr17	76725471	Missense_Mutation	novel	Y172D	0.89
GBM	chr17	76725502	Silent	novel	F161F	0.21
GBM	chr17	76721871	Missense_Mutation	novel	S290G	0.08
GBM	chr17	76725801	Missense_Mutation	NA	R62W	0.16
HNSC	chr17	76723926	Silent	NA	L217L	0.33
KIRC	chr17	76720411	Silent	NA	S343S	0.28
KIRC	chr17	76725856	Splice_Site	NA	X44_splice	0.14
KIRC	chr17	76723866	Missense_Mutation	NA	N237K	0.32
KIRP	chr17	76716663	3'Flank	novel		0.16
LGG	chr17	76726463	Missense_Mutation	novel	S5G	0.44
LGG	chr17	76720407	Missense_Mutation	NA	D345N	0.11
LGG	chr17	76718746	Missense_Mutation	NA	R399C	0.4
LIHC	chr17	76725839	Missense_Mutation	novel	A49V	0.08
LIHC	chr17	76726471	Missense_Mutation	novel	N2T	0.55
LUAD	chr17	76725720	Missense_Mutation	novel	R89C	0.16
LUAD	chr17	76718828	Silent	novel	V371V	0.14
LUAD	chr17	76718776	Missense_Mutation	novel	T389S	0.2
LUAD	chr17	76725482	Missense_Mutation	novel	R168L	0.19
LUAD	chr17	76726591	5'Flank	novel		0.56
LUAD	chr17	76721869	Silent	novel	S290S	0.13
LUAD	chr17	76721870	Missense_Mutation	NA	S290I	0.13
LUAD	chr17	76725678	Missense_Mutation	NA	E103K	0.1
LUAD	chr17	76724037	Silent	NA	P180P	0.14
LUAD	chr17	76723926	Silent	NA	L217L	0.53
LUSC	chr17	76718683	3'UTR	rs201523447		0.43
LUSC	chr17	76718684	3'UTR	novel		0.44
LUSC	chr17	76716612	3'Flank	novel		0.3
LUSC	chr17	76716563	3'Flank	novel		0.33
LUSC	chr17	76721827	Silent	NA	G304G	0.11
LUSC	chr17	76721926	Missense_Mutation	NA	W271C	0.13
OV	chr17	76725497	Missense_Mutation	novel	Y163F	0.08
OV	chr17	76725800	Missense_Mutation	NA	R62L	0.85
OV	chr17	76725550	Silent	novel	K145K	0.19
OV	chr17	76725501	Missense_Mutation	novel	Q162E	0.08
OV	chr17	76725720	Missense_Mutation	novel	R89C	0.08
OV	chr17	76725547	Silent	novel	L146L	0.15
OV	chr17	76725490	Silent	novel	G165G	0.12
OV	chr17	76724036	Missense_Mutation	novel	R181C	0.09
OV	chr17	76725719	Missense_Mutation	novel	R89H	0.32
OV	chr17	76726454	Missense_Mutation	NA	R8S	0.28
READ	chr17	76725522	Missense_Mutation	novel	F155I	0.13
READ	chr17	76726448	Missense_Mutation	NA	R10G	0.44
READ	chr17	76725540	Frame_Shift_Ins	NA	*D149Rfs10**	0.16
READ	chr17	76716658	3'Flank	novel		0.21
READ	chr17	76716694	3'Flank	novel		0.28
SKCM	chr17	76716667	3'Flank	novel		0.54
SKCM	chr17	76724006	Silent	rs780787949	L191L	0.22
SKCM	chr17	76724025	Silent	NA	T184T	0.08
SKCM	chr17	76723775	Missense_Mutation	NA	P268S	0.3
SKCM	chr17	76718718	3'UTR	novel		0.66
SKCM	chr17	76723914	Silent	NA	T221T	0.29
SKCM	chr17	76718773	Missense_Mutation	novel	S390A	0.07
SKCM	chr17	76718774	Silent	novel	T389T	0.08
SKCM	chr17	76723816	Missense_Mutation	novel	P254L	0.29
STAD	chr17	76718786	Silent	rs372217669	N385N	0.11
STAD	chr17	76725615	Missense_Mutation	NA	T124A	0.11
STAD	chr17	76718690	3'UTR	novel		0.07
STAD	chr17	76723887	Silent	rs778506056	D230D	0.29
STAD	chr17	76718713	3'UTR	novel		0.28
STAD	chr17	76718746	Missense_Mutation	NA	R399C	0.37
STAD	chr17	76718826	Missense_Mutation	rs537527655	H372R	0.19
TGCT	chr17	76726480	5'UTR	rs567489133		0.18
UCEC	chr17	76725599	Missense_Mutation	rs369981508	P129L	0.32
UCEC	chr17	76718537	3'UTR	novel		0.35
UCEC	chr17	76718692	3'UTR	rs374027972		0.28
UCEC	chr17	76716618	3'Flank	rs774265044		0.32
UCEC	chr17	76716594	3'Flank	novel		0.2
UCEC	chr17	76725761	Missense_Mutation	NA	A75V	0.27
UCEC	chr17	76725467	Missense_Mutation	NA	R173M	0.45
UCEC	chr17	76723989	Missense_Mutation	NA	W196C	0.28
UCEC	chr17	76723853	Missense_Mutation	rs374399276	R242W	0.44
UCEC	chr17	76725720	Missense_Mutation	novel	R89C	0.4
UCEC	chr17	76724029	Missense_Mutation	NA	G183E	0.17
UCEC	chr17	76725589	Silent	novel	I132I	0.55
UCEC	chr17	76723915	Missense_Mutation	novel	T221I	0.35
UCEC	chr17	76718692	3'UTR	rs374027972		0.44
UCEC	chr17	76716590	3'Flank	novel		0.65
UCEC	chr17	76721880	Missense_Mutation	novel	N287H	0.13
UCEC	chr17	76720379	Missense_Mutation	rs753793238	S354L	0.26
UCEC	chr17	76725814	Nonsense_Mutation	novel	*E57Dfs4**	0.14
UCEC	chr17	76725847	Silent	novel	V46V	0.36
UCEC	chr17	76718765	Silent	rs149210415	D392D	0.35
UCEC	chr17	76726485	5'UTR	novel		0.36
UCEC	chr17	76716651	3'Flank	rs758833224		0.37
UCEC	chr17	76718824	Missense_Mutation	rs563924240	R373C	0.18
UCEC	chr17	76720462	Silent	rs375092056	L326L	0.37
UCEC	chr17	76721870	Missense_Mutation	novel	S290N	0.35
UCS	chr17	76726519	5'UTR	novel		0.22

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
BLCA	AMP	0.3873	0.00012456
KIRP	AMP	0.6701	0.14801
LGG	AMP	0.0682	1.52e-05
LUSC	AMP	0.3453	0.001059
SARC	AMP	0.2257	0.032181
SKCM	AMP	0.2916	7.0388e-08
THCA	DEL	0.002	0.221
UVM	AMP	0.15	0.054583

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.00011	Kaplan-Meier Survival Analysis
MESO	0.00011	Kaplan-Meier Survival Analysis
ACC	0.0058	Kaplan-Meier Survival Analysis
HNSC	0.022	Kaplan-Meier Survival Analysis
ESCA	0.0017	Kaplan-Meier Survival Analysis
KIRP	0.00077	Kaplan-Meier Survival Analysis
COAD	0.037	Kaplan-Meier Survival Analysis
PAAD	0.00068	Kaplan-Meier Survival Analysis
GBM	0.037	Kaplan-Meier Survival Analysis
LIHC	0.00012	Kaplan-Meier Survival Analysis
UVM	0.048	Kaplan-Meier Survival Analysis
OV	0.033	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

GWAS

PPI

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742