Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	7375
Gene name	Ubiquitin specific peptidase 4
Gene symbol	USP4
Synonyms (NCBI Gene)	UNPUnph
Chromosome	3
Chromosome location	3p21.31
Summary	The protein encoded by this gene is a protease that deubiquitinates target proteins such as ADORA2A and TRIM21. The encoded protein shuttles between the nucleus and cytoplasm and is involved in maintaining operational fidelity in the endoplasmic reticulum

Show/Hide all (47)

miRTarBase ID	miRNA	Experiments	Reference
MIRT438752	hsa-miR-148a-3p	Hep3B	24798342
MIRT438752	hsa-miR-148a-3p	Hep3B	24798342
MIRT739953	hsa-miR-1324	CLIP-seq
MIRT739950	hsa-miR-136	CLIP-seq
MIRT1479727	hsa-miR-28-3p	CLIP-seq
MIRT739952	hsa-miR-3145-5p	CLIP-seq
MIRT1479728	hsa-miR-3175	CLIP-seq
MIRT1479729	hsa-miR-320a	CLIP-seq
MIRT1479730	hsa-miR-320b	CLIP-seq
MIRT1479731	hsa-miR-320c	CLIP-seq
MIRT1479732	hsa-miR-320d	CLIP-seq
MIRT1479733	hsa-miR-320e	CLIP-seq
MIRT1479734	hsa-miR-4321	CLIP-seq
MIRT1479735	hsa-miR-4429	CLIP-seq
MIRT1479736	hsa-miR-4704-5p	CLIP-seq
MIRT1479737	hsa-miR-4706	CLIP-seq
MIRT739954	hsa-miR-4713-3p	CLIP-seq
MIRT1479738	hsa-miR-4749-5p	CLIP-seq
MIRT1479739	hsa-miR-4781-5p	CLIP-seq
MIRT739951	hsa-miR-508-5p	CLIP-seq
MIRT1479740	hsa-miR-875-3p	CLIP-seq
MIRT2144435	hsa-miR-193a-5p	CLIP-seq
MIRT2144436	hsa-miR-3925-3p	CLIP-seq
MIRT2144437	hsa-miR-4645-5p	CLIP-seq
MIRT2144438	hsa-miR-4673	CLIP-seq
MIRT1479736	hsa-miR-4704-5p	CLIP-seq
MIRT2144439	hsa-miR-766	CLIP-seq
MIRT739950	hsa-miR-136	CLIP-seq
MIRT2144435	hsa-miR-193a-5p	CLIP-seq
MIRT2364651	hsa-miR-3183	CLIP-seq
MIRT2364652	hsa-miR-342-5p	CLIP-seq
MIRT2364653	hsa-miR-3665	CLIP-seq
MIRT2144436	hsa-miR-3925-3p	CLIP-seq
MIRT2364654	hsa-miR-4326	CLIP-seq
MIRT2144437	hsa-miR-4645-5p	CLIP-seq
MIRT2364655	hsa-miR-4651	CLIP-seq
MIRT2364656	hsa-miR-4664-5p	CLIP-seq
MIRT2144438	hsa-miR-4673	CLIP-seq
MIRT2364657	hsa-miR-4723-3p	CLIP-seq
MIRT2364658	hsa-miR-510	CLIP-seq
MIRT2364659	hsa-miR-512-5p	CLIP-seq
MIRT2364660	hsa-miR-608	CLIP-seq
MIRT2364661	hsa-miR-657	CLIP-seq
MIRT2144439	hsa-miR-766	CLIP-seq
MIRT2463055	hsa-miR-3157-5p	CLIP-seq
MIRT2463056	hsa-miR-4760-3p	CLIP-seq
MIRT2463057	hsa-miR-548c-3p	CLIP-seq

Show/Hide all (35)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000244	Process	Spliceosomal tri-snRNP complex assembly	IMP	20595234
GO:0002181	Process	Cytoplasmic translation	IDA	8706699, 34314702
GO:0004843	Function	Cysteine-type deubiquitinase activity	IDA	16316627, 16472766, 18728397, 30514904
GO:0004843	Function	Cysteine-type deubiquitinase activity	IEA
GO:0004843	Function	Cysteine-type deubiquitinase activity	TAS
GO:0005515	Function	Protein binding	IPI	11461834, 16339847, 20595234, 21522127, 23313255, 28604766
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	16339847, 20595234
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	16316627, 16339847, 20595234
GO:0005737	Component	Cytoplasm	IEA
GO:0005764	Component	Lysosome	TAS	9827704
GO:0005829	Component	Cytosol	TAS
GO:0006508	Process	Proteolysis	IEA
GO:0008233	Function	Peptidase activity	IEA
GO:0008234	Function	Cysteine-type peptidase activity	IEA
GO:0009267	Process	Cellular response to starvation	IDA	24529379
GO:0016579	Process	Protein deubiquitination	IDA	16316627, 16339847, 16472766
GO:0016579	Process	Protein deubiquitination	IEA
GO:0016579	Process	Protein deubiquitination	IMP	20595234
GO:0016579	Process	Protein deubiquitination	TAS
GO:0016787	Function	Hydrolase activity	IEA
GO:0031397	Process	Negative regulation of protein ubiquitination	IMP	16472766
GO:0031647	Process	Regulation of protein stability	IDA	16472766
GO:0031669	Process	Cellular response to nutrient levels	IDA	29236692, 29750193
GO:0031685	Function	Adenosine receptor binding	IPI	16339847
GO:0034394	Process	Protein localization to cell surface	IDA	16339847
GO:0038202	Process	TORC1 signaling	IDA	12087098, 29750193
GO:0042802	Function	Identical protein binding	IPI	22001210
GO:0045947	Process	Negative regulation of translational initiation	IDA	22578813
GO:0045948	Process	Positive regulation of translational initiation	IDA	1922062, 29750193
GO:0046872	Function	Metal ion binding	IEA
GO:1904262	Process	Negative regulation of TORC1 signaling	IDA	9045618, 12906785
GO:1904263	Process	Positive regulation of TORC1 signaling	IDA	29236692
GO:1904263	Process	Positive regulation of TORC1 signaling	IDA	30514904

MIM	HGNC	e!Ensembl
603486	12627	ENSG00000114316

Q13107

Protein name

Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.4.19.12) (Deubiquitinating enzyme 4) (Ubiquitin thioesterase 4) (Ubiquitin-specific-processing protease 4) (Ubiquitous nuclear protein homolog)

Protein function

Deubiquitinating enzyme that removes conjugated ubiquitin from target proteins (PubMed:16316627, PubMed:16339847, PubMed:16472766, PubMed:20595234, PubMed:22347420, PubMed:25404403, PubMed:28604766, PubMed:30514904). Deubiquitinates PDPK1 (PubMe

PDB

2Y6E , 5CTR

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF06337	DUSP	31 → 123	DUSP domain	Domain
PF14836	Ubiquitin_3	139 → 226	Ubiquitin-like domain	Domain
PF00443	UCH	302 → 920	Ubiquitin carboxyl-terminal hydrolase	Family

Tissue specificity

TISSUE SPECIFICITY: Overexpressed in small cell tumors and adenocarcinomas of the lung compared to wild-type lung (at protein level). Expressed in the hippocampal neurons. {ECO:0000269|PubMed:16339847, ECO:0000269|PubMed:7784062}.

Sequence

MAEGGGCRERPDAETQKSELGPLMRTTLQRGAQWYLIDSRWFKQWKKYVGFDSWDMYNVG
EHNLFPGPIDNSGLFSDPESQTLKEHLIDELDYVLVPTEAWNKLLNWYGCVEGQQPIVRK
VVEHGLFVKHCKVEVYLLELKLCENSDPTNVLSCHFSKADTIATIEKEMRKLFNIPAERE
TRLWNKYMSNTYEQLSKLDNTVQDAGLYQGQVLVIEPQNEDGTWPRQTLQSKSSTAPSRN
FTTSPKSSASPYSSVSASLIANGDSTSTCGMHSSGVSRGGSGFSASYNCQEPPSSHIQPG
LCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIK
QMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLEL
KDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLP
LPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYN
HRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASAL
YGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGED
EEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADI
NSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRD
CIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDT
VVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDS
NVSLASEDQIVTKAAYVLFYQRRDDEFYKTPSLSSSGSSDGGTRPSSSQQGFGDDEACSM
DTN

Sequence length

963

Interactions

View interactions

	Reactome
			TNFR1-induced proapoptotic signaling Regulation of TNFR1 signaling TNFR1-induced NFkappaB signaling pathway Ub-specific processing proteases

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CANNABIS DEPENDENCE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOOD DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (17)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	29667299	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Associate	27060135, 27990632	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Inhibit	29667299	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	26189775	★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Associate	28946564	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Associate	35774799	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoalphalipoproteinemias	Associate	28473662	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Associate	40311306	★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma	Associate	29542252	★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Associate	33531688, 36762777	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	29542252	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	23313255	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	26189775, 26411366, 28946564, 36336860, 37624791	★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteitis Deformans	Associate	25115182	★★★★★ ★☆☆☆☆ Found in Text Mining only
Rheumatic Heart Disease	Associate	28791349	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Associate	23313255, 37308746	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Associate	36336860, 37624791	★★★★★ ★☆☆☆☆ Found in Text Mining only

USP4 (ubiquitin specific peptidase 4)