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    OTUD3 OTU deubiquitinase 3 [ Homo sapiens (human) ]

    Gene ID: 23252, updated on 2-Nov-2024

    Summary

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    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, Nov 2024]
    Expression
    Broad expression in testis (RPKM 8.1), endometrium (RPKM 3.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See OTUD3 in Genome Data Viewer
    Location:
    1p36.13
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (19882395..19912945)
    RS_2024_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

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    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. 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
    5. Tumor suppressor OTUD3 induces growth inhibition and apoptosis by directly deubiquitinating and stabilizing p53 in invasive breast carcinoma cells. Pu Q, et al. BMC Cancer, 2020 Jun 22. PMID 32571254, Free PMC Article

    See all (42) 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)

    Phenotypes

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    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity TAS
    Traceable Author Statement
    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 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 cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    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

    NCBI Reference Sequences (RefSeq)

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    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_2024_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

    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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