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	10713
Gene name	Ubiquitin specific peptidase 39
Gene symbol	USP39
Synonyms (NCBI Gene)	65KCGI-21HSPC332SAD1SNRNP65
Chromosome	2
Chromosome location	2p11.2

Show/Hide all (95)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016575	hsa-miR-193b-3p	Microarray	20304954
MIRT1479604	hsa-miR-1252	CLIP-seq
MIRT1479605	hsa-miR-3202	CLIP-seq
MIRT1479606	hsa-miR-4533	CLIP-seq
MIRT2658435	hsa-miR-1226	CLIP-seq
MIRT2658436	hsa-miR-1273d	CLIP-seq
MIRT2658437	hsa-miR-1587	CLIP-seq
MIRT2658438	hsa-miR-1915	CLIP-seq
MIRT2658439	hsa-miR-2116	CLIP-seq
MIRT2658440	hsa-miR-300	CLIP-seq
MIRT2658441	hsa-miR-3135	CLIP-seq
MIRT2658442	hsa-miR-3151	CLIP-seq
MIRT2658443	hsa-miR-3157-5p	CLIP-seq
MIRT2658444	hsa-miR-3176	CLIP-seq
MIRT2658445	hsa-miR-3182	CLIP-seq
MIRT2658446	hsa-miR-3194-3p	CLIP-seq
MIRT2658447	hsa-miR-3194-5p	CLIP-seq
MIRT2658448	hsa-miR-320e	CLIP-seq
MIRT2658449	hsa-miR-378g	CLIP-seq
MIRT2658450	hsa-miR-381	CLIP-seq
MIRT2658451	hsa-miR-3907	CLIP-seq
MIRT2658452	hsa-miR-3922-3p	CLIP-seq
MIRT2658453	hsa-miR-4299	CLIP-seq
MIRT2658454	hsa-miR-4302	CLIP-seq
MIRT2658455	hsa-miR-4417	CLIP-seq
MIRT2658456	hsa-miR-4437	CLIP-seq
MIRT2658457	hsa-miR-4447	CLIP-seq
MIRT2658458	hsa-miR-4456	CLIP-seq
MIRT2658459	hsa-miR-4472	CLIP-seq
MIRT2658460	hsa-miR-4476	CLIP-seq
MIRT2658461	hsa-miR-4492	CLIP-seq
MIRT2658462	hsa-miR-4498	CLIP-seq
MIRT2658463	hsa-miR-4529-5p	CLIP-seq
MIRT2658464	hsa-miR-4645-3p	CLIP-seq
MIRT2658465	hsa-miR-4645-5p	CLIP-seq
MIRT2658466	hsa-miR-4656	CLIP-seq
MIRT2658467	hsa-miR-4673	CLIP-seq
MIRT2658468	hsa-miR-4674	CLIP-seq
MIRT2658469	hsa-miR-4675	CLIP-seq
MIRT2658470	hsa-miR-4676-5p	CLIP-seq
MIRT2658471	hsa-miR-4677-5p	CLIP-seq
MIRT2658472	hsa-miR-4691-3p	CLIP-seq
MIRT2658473	hsa-miR-4699-3p	CLIP-seq
MIRT2658474	hsa-miR-4726-3p	CLIP-seq
MIRT2658475	hsa-miR-4741	CLIP-seq
MIRT2658476	hsa-miR-4742-5p	CLIP-seq
MIRT2658477	hsa-miR-491-5p	CLIP-seq
MIRT2658478	hsa-miR-548q	CLIP-seq
MIRT2658479	hsa-miR-548v	CLIP-seq
MIRT2658480	hsa-miR-575	CLIP-seq
MIRT2658481	hsa-miR-671-5p	CLIP-seq
MIRT2658482	hsa-miR-762	CLIP-seq
MIRT2658435	hsa-miR-1226	CLIP-seq
MIRT2658436	hsa-miR-1273d	CLIP-seq
MIRT2658437	hsa-miR-1587	CLIP-seq
MIRT2658438	hsa-miR-1915	CLIP-seq
MIRT2658440	hsa-miR-300	CLIP-seq
MIRT2658441	hsa-miR-3135	CLIP-seq
MIRT2658442	hsa-miR-3151	CLIP-seq
MIRT2658444	hsa-miR-3176	CLIP-seq
MIRT2658445	hsa-miR-3182	CLIP-seq
MIRT2658446	hsa-miR-3194-3p	CLIP-seq
MIRT2658447	hsa-miR-3194-5p	CLIP-seq
MIRT2658448	hsa-miR-320e	CLIP-seq
MIRT2658449	hsa-miR-378g	CLIP-seq
MIRT2658450	hsa-miR-381	CLIP-seq
MIRT2658451	hsa-miR-3907	CLIP-seq
MIRT2658452	hsa-miR-3922-3p	CLIP-seq
MIRT2658453	hsa-miR-4299	CLIP-seq
MIRT2658454	hsa-miR-4302	CLIP-seq
MIRT2658455	hsa-miR-4417	CLIP-seq
MIRT2658456	hsa-miR-4437	CLIP-seq
MIRT2658457	hsa-miR-4447	CLIP-seq
MIRT2658458	hsa-miR-4456	CLIP-seq
MIRT2658459	hsa-miR-4472	CLIP-seq
MIRT2658460	hsa-miR-4476	CLIP-seq
MIRT2658461	hsa-miR-4492	CLIP-seq
MIRT2658462	hsa-miR-4498	CLIP-seq
MIRT2658463	hsa-miR-4529-5p	CLIP-seq
MIRT2658464	hsa-miR-4645-3p	CLIP-seq
MIRT2658465	hsa-miR-4645-5p	CLIP-seq
MIRT2658466	hsa-miR-4656	CLIP-seq
MIRT2658467	hsa-miR-4673	CLIP-seq
MIRT2658468	hsa-miR-4674	CLIP-seq
MIRT2658469	hsa-miR-4675	CLIP-seq
MIRT2658470	hsa-miR-4676-5p	CLIP-seq
MIRT2658474	hsa-miR-4726-3p	CLIP-seq
MIRT2658475	hsa-miR-4741	CLIP-seq
MIRT2658476	hsa-miR-4742-5p	CLIP-seq
MIRT2658477	hsa-miR-491-5p	CLIP-seq
MIRT2658478	hsa-miR-548q	CLIP-seq
MIRT2658479	hsa-miR-548v	CLIP-seq
MIRT2658480	hsa-miR-575	CLIP-seq
MIRT2658481	hsa-miR-671-5p	CLIP-seq
MIRT2658482	hsa-miR-762	CLIP-seq

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000245	Process	Spliceosomal complex assembly	IBA
GO:0000245	Process	Spliceosomal complex assembly	IEA
GO:0000245	Process	Spliceosomal complex assembly	IMP	11350945
GO:0000245	Process	Spliceosomal complex assembly	TAS	10022888
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	11350945
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	30975767
GO:0004843	Function	Cysteine-type deubiquitinase activity	IDA	18728397
GO:0005515	Function	Protein binding	IPI	23602568, 29513927, 31046837, 32707033
GO:0005634	Component	Nucleus	IDA	11350945, 26912367
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	IPI	30975767
GO:0006397	Process	MRNA processing	IEA
GO:0006397	Process	MRNA processing	TAS	10022888
GO:0008270	Function	Zinc ion binding	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	10022888
GO:0016579	Process	Protein deubiquitination	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	11350945, 26912367
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IPI	30975767
GO:0046872	Function	Metal ion binding	IEA
GO:0051301	Process	Cell division	IEA

MIM	HGNC	e!Ensembl
611594	20071	ENSG00000168883

Q53GS9

Protein name

Ubiquitin carboxyl-terminal hydrolase 39 (EC 3.4.19.12) (SAD1 homolog) (U4/U6.U5 tri-snRNP-associated 65 kDa protein)

Protein function

Deubiquitinating enzyme that plays a role in many cellular processes including cellular antiviral response, epithelial morphogenesis, DNA repair or B-cell development (PubMed:33127822, PubMed:34614178). Plays a role in pre-mRNA splicing as a com

PDB

3JCR , 6AH0 , 6QW6 , 6QX9 , 8H6E , 8H6J , 8QOZ , 8QP8 , 8QP9 , 8QPA , 8QPB , 8QPE , 8QPK , 8QXD , 8QZS , 8R08 , 8R09 , 8R0A , 8R0B , 8RM5 , 8Y6O

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02148	zf-UBP	123 → 186	Zn-finger in ubiquitin-hydrolases and other protein	Domain
PF00443	UCH	225 → 552	Ubiquitin carboxyl-terminal hydrolase	Family

Sequence

MSGRSKRESRGSTRGKRESESRGSSGRVKRERDREREPEAASSRGSPVRVKREFEPASAR
EAPASVVPFVRVKREREVDEDSEPEREVRAKNGRVDSEDRRSRHCPYLDTINRSVLDFDF
EKLCSISLSHINAYACLVCGKYFQGRGLKSHAYIHSVQFSHHVFLNLHTLKFYCLPDNYE
IIDSSLEDITYVLKPTFTKQQIANLDKQAKLSRAYDGTTYLPGIVGLNNIKANDYANAVL
QALSNVPPLRNYFLEEDNYKNIKRPPGDIMFLLVQRFGELMRKLWNPRNFKAHVSPHEML
QAVVLCSKKTFQITKQGDGVDFLSWFLNALHSALGGTKKKKKTIVTDVFQGSMRIFTKKL
PHPDLPAEEKEQLLHNDEYQETMVESTFMYLTLDLPTAPLYKDEKEQLIIPQVPLFNILA
KFNGITEKEYKTYKENFLKRFQLTKLPPYLIFCIKRFTKNNFFVEKNPTIVNFPITNVDL
REYLSEEVQAVHKNTTYDLIANIVHDGKPSEGSYRIHVLHHGTGKWYELQDLQVTDILPQ
MITLSEAYIQIWKRRDNDETNQQGA

Sequence length

565

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		mRNA Splicing - Major Pathway

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 (2)

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.
COLONIC NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (39)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Breast Carcinoma	Breast Carcinoma	BEFREE	24126978, 30675193		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	25889525	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	25889525, 34197957	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	25889525, 34197957, 35748266, 36707504	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	27629785, 30675193		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	36582601	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	37957720	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	31180526, 31637536		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	28259917, 29556295		★★★★★ ★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	29328477		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	35627203	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Fibrosis, Liver	Liver Fibrosis	BEFREE	30282980		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	31332287		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	37005321	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	30898977		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	30898977	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	25889525, 26081192, 28413501, 29933754, 31637536		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	36046375	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	24126978, 30675193		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	27629785, 30675193		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	31180526, 31637536		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	28286270		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	26959883		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	27175747, 29805563		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	26959883, 27629785, 28154181, 28403900, 29328477, 29556295, 30898977, 31180526, 31637536		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	31754952		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	27456357		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	26081192, 26835714, 27629785, 28413501, 31180526, 31332287		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	28403900, 30323969		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	28403900	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	31180526, 31637536		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	28286270		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	26959883		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	26959883	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	29328477		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	26835714		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	26835714	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	27175747, 29805563		★★★★★ ★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	25812575		★★★★★ ★☆☆☆☆ Found in Text Mining only

USP39 (ubiquitin specific peptidase 39)