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    OTUD4 OTU deubiquitinase 4 [ Homo sapiens (human) ]

    Gene ID: 54726, updated on 3-Nov-2024

    Summary

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    Official Symbol
    OTUD4provided by HGNC
    Official Full Name
    OTU deubiquitinase 4provided by HGNC
    Primary source
    HGNC:HGNC:24949
    See related
    Ensembl:ENSG00000164164 MIM:611744; AllianceGenome:HGNC:24949
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HIN1; DUBA6; HSHIN1
    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]
    Expression
    Ubiquitous expression in testis (RPKM 19.7), bone marrow (RPKM 11.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See OTUD4 in Genome Data Viewer
    Location:
    4q31.21
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (145133650..145180589, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (148451040..148497987, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (146054802..146101741, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene anaphase promoting complex subunit 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15722 Neighboring gene RN7SK pseudogene 235 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:146018722-146019921 Neighboring gene ATP binding cassette subfamily E member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21962 Neighboring gene MPRA-validated peak5130 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21963 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:146100843-146101672 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:146101673-146102502 Neighboring gene uncharacterized LOC124900794 Neighboring gene uncharacterized LOC105377465

    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. OTUD4 enhances TGFβ signalling through regulation of the TGFβ receptor complex. Jaynes PW, et al. Sci Rep, 2020 Sep 24. PMID 32973272, Free PMC Article
    2. HIV-1 promotor insertion revealed by selective detection of chimeric provirus-host gene transcripts. Raineri I, et al. Nucleic Acids Res, 1992 Dec 11. PMID 1475186, Free PMC Article
    3. Deubiquitinating enzyme OTUD4 regulates metastasis in triple-negative breast cancer by stabilizing Snail1. Ma X, et al. Exp Cell Res, 2024 Jan 1. PMID 38040050
    4. Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes. Fodder K, et al. Acta Neuropathol, 2023 Jul. PMID 37149835, Free PMC Article
    5. OTUD4 promotes the progression of glioblastoma by deubiquitinating CDK1 and activating MAPK signaling pathway. Ci M, et al. Cell Death Dis, 2024 Mar 1. PMID 38429268, Free PMC Article

    See all (109) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deubiquitinating enzyme OTUD4 stabilizes RBM47 to induce ATF3 transcription: a novel mechanism underlying the restrained malignant properties of ccRCC cells.
      Title: Deubiquitinating enzyme OTUD4 stabilizes RBM47 to induce ATF3 transcription: a novel mechanism underlying the restrained malignant properties of ccRCC cells.
    2. NRF2 regulates EGF stability through OTUD4 in lung adenocarcinoma.
      Title: NRF2 regulates EGF stability through OTUD4 in lung adenocarcinoma.
    3. OTUD4 promotes the progression of glioblastoma by deubiquitinating CDK1 and activating MAPK signaling pathway.
      Title: OTUD4 promotes the progression of glioblastoma by deubiquitinating CDK1 and activating MAPK signaling pathway.
    4. Deubiquitinating enzyme OTUD4 regulates metastasis in triple-negative breast cancer by stabilizing Snail1.
      Title: Deubiquitinating enzyme OTUD4 regulates metastasis in triple-negative breast cancer by stabilizing Snail1.
    5. OTUD4 regulates metastasis and chemoresistance in melanoma by stabilizing Snail1.
      Title: OTUD4 regulates metastasis and chemoresistance in melanoma by stabilizing Snail1.
    6. Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes.
      Title: Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes.
    7. OTUD4 enhances TGFbeta signalling through regulation of the TGFbeta receptor complex.
      Title: OTUD4 enhances TGFβ signalling through regulation of the TGFβ receptor complex.
    8. Knockdown of OTUD4 in HeLa cells resulted in defects in stress granule formation and led to apoptotic cell death
      Title: New roles for the de-ubiquitylating enzyme OTUD4 in an RNA-protein network and RNA granules.
    9. Authors demonstrate that the deubiquitinase OTUD4, which nominally encodes a K48-specific deubiquitinase, is phosphorylated near its catalytic domain, activating a latent K63-specific deubiquitinase. Besides phosphorylation, this latter activity requires an adjacent ubiquitin-interacting motif, which increases the affinity of OTUD4 for K63-linked chains.
      Title: OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling.
    10. There is an evolutionary loss of activity in de-ubiquitylating enzymes of the OTU family, OTUD4, otu, and CG3251.
      Title: Evolutionary Loss of Activity in De-Ubiquitylating Enzymes of the OTU Family.
    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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1046, DKFZp434I0721

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K63-linked deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables K63-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    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 molecular adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA alkylation repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of interleukin-1-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of interleukin-1-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of toll-like receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of toll-like receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K11-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K48-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K63-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of protein K48-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    OTU domain-containing protein 4
    Names
    HIV-1 induced protein HIN-1
    NP_001096123.1
    NP_001352986.1
    NP_001352987.1
    NP_059963.1
    XP_011530342.2
    XP_011530343.2
    XP_011530344.1
    XP_047271794.1
    XP_054206243.1
    XP_054206244.1
    XP_054206245.1
    XP_054206246.1

    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.

    Genomic

    1. NG_047157.1 RefSeqGene

      Range
      4385..51324
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001102653.1 → NP_001096123.1  OTU domain-containing protein 4 isoform 3

      See identical proteins and their annotated locations for NP_001096123.1

      Status: REVIEWED

      Source sequence(s)
      AC096757, BC118572, DB446926
      Consensus CDS
      CCDS47139.1
      UniProtKB/Swiss-Prot
      Q01804
      Related
      ENSP00000409279.2, ENST00000454497.6
      Conserved Domains (1) summary
      cl19932
      Location:3 → 56
      OTU; OTU-like cysteine protease

    2. NM_001366057.1 → NP_001352986.1  OTU domain-containing protein 4 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC096757
      Consensus CDS
      CCDS93644.1
      UniProtKB/Swiss-Prot
      B4DYS4, Q01804, Q147U2, Q1ZYK1, Q6PG39, Q96MQ5, Q9NT94, Q9UPV6
      Related
      ENSP00000395487.2, ENST00000447906.8
      Conserved Domains (2) summary
      cl19932
      Location:42 → 121
      OTU; OTU-like cysteine protease
      cl26464
      Location:543 → 886
      Atrophin-1; Atrophin-1 family

    3. NM_001366058.1 → NP_001352987.1  OTU domain-containing protein 4 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC096757
      Conserved Domains (1) summary
      cl19932
      Location:42 → 121
      OTU; OTU-like cysteine protease

    4. NM_017493.7 → NP_059963.1  OTU domain-containing protein 4 isoform 2

      See identical proteins and their annotated locations for NP_059963.1

      Status: REVIEWED

      Source sequence(s)
      AC096757, X68242
      Consensus CDS
      CCDS3764.1
      UniProtKB/TrEMBL
      D6RA27
      Related
      ENSP00000424192.2, ENST00000509620.6
      Conserved Domains (1) summary
      cl19932
      Location:3 → 56
      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      145133650..145180589 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047415838.1 → XP_047271794.1  OTU domain-containing protein 4 isoform X3

    2. XM_011532041.3 → XP_011530343.2  OTU domain-containing protein 4 isoform X2

    3. XM_011532040.3 → XP_011530342.2  OTU domain-containing protein 4 isoform X1

    4. XM_011532042.4 → XP_011530344.1  OTU domain-containing protein 4 isoform X4

      See identical proteins and their annotated locations for XP_011530344.1

      Conserved Domains (1) summary
      cl19932
      Location:3 → 63
      OTU; OTU-like cysteine protease

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      148451040..148497987 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350270.1 → XP_054206245.1  OTU domain-containing protein 4 isoform X3

    2. XM_054350269.1 → XP_054206244.1  OTU domain-containing protein 4 isoform X2

    3. XM_054350268.1 → XP_054206243.1  OTU domain-containing protein 4 isoform X1

    4. XM_054350271.1 → XP_054206246.1  OTU domain-containing protein 4 isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_199324.2: Suppressed sequence

      Description
      NM_199324.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q01804.4 GenPept UniProtKB/Swiss-Prot:Q01804

    Gene LinkOut

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

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