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OTUD3 OTU deubiquitinase 3 [ Homo sapiens (human) ]

Gene ID: 23252, updated on 25-Nov-2025
Official Symbol
OTUD3provided by HGNC
Official Full Name
OTU deubiquitinase 3provided by HGNC
Primary source
HGNC:HGNC:29038
See related
Ensembl:ENSG00000169914 MIM:611758; AllianceGenome:HGNC:29038
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DUBA4
Summary
Enables cysteine-type deubiquitinase activity. Involved in cellular response to nutrient levels and protein deubiquitination. Acts upstream of or within negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction; protein deubiquitination; and protein stabilization. Located in cytoplasm. Is active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
Expression
Broad expression in testis (RPKM 8.1), endometrium (RPKM 3.2) and 23 other tissues See more
Orthologs
all
Try the new Gene page
Try the new Transcripts and proteins table
See OTUD3 in Genome Data Viewer
Location:
1p36.13
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (19882395..19912945)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (19705780..19736328)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (20208888..20239438)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:20015541-20016055 Neighboring gene transmembrane and coiled-coil domains 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20066909-20067410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20067411-20067910 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:20076458-20077657 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:20091493-20092692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20106613-20107114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 307 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:20126577-20127077 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:20143237-20143768 Neighboring gene RNF186 antisense RNA 1 Neighboring gene ring finger protein 186 Neighboring gene uncharacterized LOC105376823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20246936-20247488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20247489-20248041 Neighboring gene phospholipase A2 group IIE Neighboring gene Sharpr-MPRA regulatory region 3300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 309 Neighboring gene RNA, 7SL, cytoplasmic 304, pseudogene

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Prevalence and clinical characteristics of T2DM patients with OTUD3 gene rs78466831 SNP at a single academic center in China. Liu JP, et al. Front Endocrinol (Lausanne), 2022. PMID 36531510, Free PMC Article
  2. MicroRNA 32 promotes cell proliferation, migration, and suppresses apoptosis in colon cancer cells by targeting OTU domain containing 3. Jin Y, et al. J Cell Biochem, 2019 Nov. PMID 31338872
  3. Distinct regulatory ribosomal ubiquitylation events are reversible and hierarchically organized. Garshott DM, et al. Elife, 2020 Feb 3. PMID 32011234, Free PMC Article
  4. The deubiquitinase OTUD3 stabilizes ACTN4 to drive growth and metastasis of hepatocellular carcinoma. Xie P, et al. Aging (Albany NY), 2021 Aug 10. PMID 34380780, Free PMC Article
  5. Silencing of LncRNA SNHG6 protects trophoblast cells through regulating miR-101-3p/OTUD3 axis in unexplained recurrent spontaneous abortion. Zhao L, et al. J Mol Histol, 2022 Dec. PMID 36173586

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Prevalence and clinical characteristics of T2DM patients with OTUD3 gene rs78466831 SNP at a single academic center in China.
    Title: Prevalence and clinical characteristics of T2DM patients with OTUD3 gene rs78466831 SNP at a single academic center in China.
  2. Silencing of LncRNA SNHG6 protects trophoblast cells through regulating miR-101-3p/OTUD3 axis in unexplained recurrent spontaneous abortion.
    Title: Silencing of LncRNA SNHG6 protects trophoblast cells through regulating miR-101-3p/OTUD3 axis in unexplained recurrent spontaneous abortion.
  3. The deubiquitinase OTUD3 stabilizes ACTN4 to drive growth and metastasis of hepatocellular carcinoma.
    Title: The deubiquitinase OTUD3 stabilizes ACTN4 to drive growth and metastasis of hepatocellular carcinoma.
  4. Nicotine-mediated OTUD3 downregulation inhibits VEGF-C mRNA decay to promote lymphatic metastasis of human esophageal cancer.
    Title: Nicotine-mediated OTUD3 downregulation inhibits VEGF-C mRNA decay to promote lymphatic metastasis of human esophageal cancer.
  5. Ubiquitin ligase CHIP regulates OTUD3 stability and suppresses tumour metastasis in lung cancer.
    Title: Ubiquitin ligase CHIP regulates OTUD3 stability and suppresses tumour metastasis in lung cancer.
  6. miR-520h Stimulates Drug Resistance to Paclitaxel by Targeting the OTUD3-PTEN Axis in Breast Cancer.
    Title: miR-520h Stimulates Drug Resistance to Paclitaxel by Targeting the OTUD3-PTEN Axis in Breast Cancer.
  7. Tumor suppressor OTUD3 induces growth inhibition and apoptosis by directly deubiquitinating and stabilizing p53 in invasive breast carcinoma cells.
    Title: Tumor suppressor OTUD3 induces growth inhibition and apoptosis by directly deubiquitinating and stabilizing p53 in invasive breast carcinoma cells.
  8. MicroRNA 32 promotes cell proliferation, migration, and suppresses apoptosis in colon cancer cells by targeting OTU domain containing 3.
    Title: MicroRNA 32 promotes cell proliferation, migration, and suppresses apoptosis in colon cancer cells by targeting OTU domain containing 3.
  9. Acetylation-Dependent Deubiquitinase OTUD3 Controls MAVS Activation in Innate Antiviral Immunity.
    Title: Acetylation-Dependent Deubiquitinase OTUD3 Controls MAVS Activation in Innate Antiviral Immunity.
  10. Knockdown of OTUD3 results in a decrease in the level of GRP78 protein, suppression of cell growth and migration, and tumorigenesis in lung cancer.
    Title: The deubiquitylase OTUD3 stabilizes GRP78 and promotes lung tumorigenesis.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
EBI GWAS Catalog
Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL).
EBI GWAS Catalog
Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
EBI GWAS Catalog
Genome-wide association study of ulcerative colitis in Koreans suggests extensive overlapping of genetic susceptibility with Caucasians.
EBI GWAS Catalog
Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study.
EBI GWAS Catalog

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Replication interactions

Interaction Pubs
Knockdown of OTU domain containing 3 (OTUD3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA0459

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type deubiquitinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables cysteine-type deubiquitinase activity IEA
Inferred from Electronic Annotation
more info
  
enables cysteine-type deubiquitinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables cysteine-type deubiquitinase activity TAS
Traceable Author Statement
more info
  
enables cysteine-type peptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to nutrient levels IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within protein K11-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K11-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within protein K27-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within protein K48-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K48-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within protein K6-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K6-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein deubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in protein deubiquitination TAS
Traceable Author Statement
more info
  
involved_in protein stabilization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within protein stabilization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein stabilization IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within protein stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
OTU domain-containing protein 3
Names
OTU domain containing 3
NP_056022.1
XP_005245849.2
XP_005245850.2
XP_024310088.1
XP_047271755.1
XP_047271762.1
XP_047271781.1
XP_054191371.1
XP_054191372.1
XP_054191373.1
XP_054191374.1
XP_054191375.1
XP_054191376.1

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_015207.2 → NP_056022.1  OTU domain-containing protein 3

    See identical proteins and their annotated locations for NP_056022.1

    Status: VALIDATED

    Source sequence(s)
    AA829387, AB007928, CV573628
    Consensus CDS
    CCDS41279.1
    UniProtKB/Swiss-Prot
    O75047, Q5T2D3
    Related
    ENSP00000364261.3, ENST00000375120.4
    Conserved Domains (1) summary
    cl19932
    Location:71 → 157
    OTU; OTU-like cysteine protease

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    19882395..19912945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005245793.5 → XP_005245850.2  OTU domain-containing protein 3 isoform X2

  2. XM_005245792.5 → XP_005245849.2  OTU domain-containing protein 3 isoform X1

    Related
    ENSP00000550313.1, ENST00000880254.1

  3. XM_047415799.1 → XP_047271755.1  OTU domain-containing protein 3 isoform X3

  4. XM_024454320.2 → XP_024310088.1  OTU domain-containing protein 3 isoform X5

  5. XM_047415806.1 → XP_047271762.1  OTU domain-containing protein 3 isoform X4

  6. XM_047415825.1 → XP_047271781.1  OTU domain-containing protein 3 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    19705780..19736328
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335397.1 → XP_054191372.1  OTU domain-containing protein 3 isoform X2

  2. XM_054335396.1 → XP_054191371.1  OTU domain-containing protein 3 isoform X1

  3. XM_054335398.1 → XP_054191373.1  OTU domain-containing protein 3 isoform X3

  4. XM_054335400.1 → XP_054191375.1  OTU domain-containing protein 3 isoform X5

  5. XM_054335399.1 → XP_054191374.1  OTU domain-containing protein 3 isoform X4

  6. XM_054335401.1 → XP_054191376.1  OTU domain-containing protein 3 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5T2D3.1 GenPept UniProtKB/Swiss-Prot:Q5T2D3

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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