EuRBPDB

Description

Ensembl ID: ENSG00000164164 (Gene tree)
Gene ID: 54726
Gene Symbol: OTUD4
Alias: HSHIN1|KIAA1046|DUBA6
Full Name: OTU deubiquitinase 4
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Minus strand
Length: 69,324 bases
Position: chr4:145,110,838-145,180,161
Accession: 24949
RBP type: non-canonical RBP
Summary: Alternatively spliced transcript variants have been found for this gene. The smaller protein isoform encoded by the shorter transcript variant is found only in HIV-1 infected cells. [provided by RefSeq, Jul 2010]

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
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
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
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & Hela	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
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
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
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & U2OS	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30352994	Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture	RIC & Jurkat	2018 Oct 23	Perez-Perri JI	DOI:10.1038/s41467-018-06557-8

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
31138677	New roles for the de-ubiquitylating enzyme OTUD4 in an RNA-protein network and RNA granules.	J Cell Sci	2019 Jun 17	Das R	doi: 10.1242/jcs.229252.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000514973	OTUD4-210	1255	-	ENSP00000425972	372 (aa)	-	D6RI06
ENST00000509985	OTUD4-209	467	-	-	- (aa)	-	-
ENST00000455611	OTUD4-203	2498	-	-	- (aa)	-	-
ENST00000454497	OTUD4-202	7069	XM_011532042	ENSP00000409279	1049 (aa)	XP_011530344	Q01804
ENST00000504501	OTUD4-205	543	-	ENSP00000423453	139 (aa)	-	D6RA27
ENST00000509620	OTUD4-208	864	-	ENSP00000424192	145 (aa)	-	Q01804
ENST00000447906	OTUD4-201	7273	XM_005263079	ENSP00000395487	1114 (aa)	XP_005263136	Q01804
ENST00000509517	OTUD4-207	617	-	-	- (aa)	-	-
ENST00000504331	OTUD4-204	591	-	-	- (aa)	-	-
ENST00000505976	OTUD4-206	671	-	-	- (aa)	-	-

Gene Model

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000164164	Hip	4E-6	25673412
ENSG00000164164	Body Mass Index	4E-6	25673412
ENSG00000164164	Hip	5E-13	25673412
ENSG00000164164	Body Mass Index	5E-13	25673412
ENSG00000164164	Angiotensin-Converting Enzyme Inhibitors	6E-7	28030426
ENSG00000164164	Hip	8E-10	25673412
ENSG00000164164	Body Mass Index	8E-10	25673412

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000164164	rs36225153	4	145160700	T	Reticulocyte count	27863252	[0.035-0.058] unit increase	0.04631483	EFO_0007986
ENSG00000164164	rs36225153	4	145160700	T	Reticulocyte fraction of red cells	27863252	[0.03-0.052] unit increase	0.04124811	EFO_0007986
ENSG00000164164	rs36225153	4	145160700	?	Red blood cell count	30595370			EFO_0004305

Protein-Protein Interaction (PPI)

Orthologs identified by RBPome

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000164164	OTUD4	100	91.034	ENSMUSG00000036990	Otud4	100	87.186	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0003723	RNA binding	22681889.	HDA	Function
GO:0004843	thiol-dependent ubiquitin-specific protease activity	21873635.	IBA	Function
GO:0004843	thiol-dependent ubiquitin-specific protease activity	23827681.	IDA	Function
GO:0005515	protein binding	25416956.	IPI	Function
GO:0005634	nucleus	-	IEA	Component
GO:0005737	cytoplasm	-	IEA	Component
GO:0016579	protein deubiquitination	21873635.	IBA	Process
GO:0034122	negative regulation of toll-like receptor signaling pathway	21873635.	IBA	Process
GO:0034122	negative regulation of toll-like receptor signaling pathway	29395066.	IDA	Process
GO:0045087	innate immune response	-	IEA	Process
GO:0060090	molecular adaptor activity	25944111.	IDA	Function
GO:0061578	Lys63-specific deubiquitinase activity	21873635.	IBA	Function
GO:0061578	Lys63-specific deubiquitinase activity	29395066.	IDA	Function
GO:0070536	protein K63-linked deubiquitination	29395066.	IDA	Process
GO:0071108	protein K48-linked deubiquitination	23827681.	IDA	Process
GO:1901537	positive regulation of DNA demethylation	25944111.	IDA	Process
GO:1903093	regulation of protein K48-linked deubiquitination	21873635.	IBA	Process
GO:1903093	regulation of protein K48-linked deubiquitination	25944111.	IDA	Process
GO:2000660	negative regulation of interleukin-1-mediated signaling pathway	21873635.	IBA	Process
GO:2000660	negative regulation of interleukin-1-mediated signaling pathway	29395066.	IDA	Process