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    YOD1 YOD1 deubiquitinase [ Homo sapiens (human) ]

    Gene ID: 55432, updated on 28-Oct-2024

    Summary

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    Official Symbol
    YOD1provided by HGNC
    Official Full Name
    YOD1 deubiquitinaseprovided by HGNC
    Primary source
    HGNC:HGNC:25035
    See related
    Ensembl:ENSG00000180667 MIM:612023; AllianceGenome:HGNC:25035
    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
    DUBA8; OTUD2; PRO0907
    Summary
    Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. The protein encoded by this gene belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
    Expression
    Broad expression in bone marrow (RPKM 24.5), esophagus (RPKM 15.7) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YOD1 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (207043849..207053116, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (206309040..206318351, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (207217194..207226461, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:207192892-207194091 Neighboring gene chromosome 1 open reading frame 116 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 4428 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207224117-207224687 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207225911-207226550 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:207240869-207241100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2439 Neighboring gene complement component 4 binding protein beta Neighboring gene uncharacterized LOC107985251 Neighboring gene complement component 4 binding protein alpha

    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. Deubiquitinase YOD1: the potent activator of YAP in hepatomegaly and liver cancer. Kim Y, et al. BMB Rep, 2017 Jun. PMID 28502290, Free PMC Article
    2. Lys11- and Lys48-linked ubiquitin chains interact with p97 during endoplasmic-reticulum-associated degradation. Locke M, et al. Biochem J, 2014 Apr 1. PMID 24417208, Free PMC Article
    3. Deubiquitylase YOD1 regulates CDK1 stability and drives triple-negative breast cancer tumorigenesis. Han Z, et al. J Exp Clin Cancer Res, 2023 Sep 4. PMID 37667382, Free PMC Article
    4. Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes α-synuclein. Park SS, et al. Biochem Biophys Res Commun, 2023 Feb 19. PMID 36682332
    5. Blockade of deubiquitinase YOD1 degrades oncogenic PML/RARα and eradicates acute promyelocytic leukemia cells. Shao X, et al. Acta Pharm Sin B, 2022 Apr. PMID 35847510, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. YOD1 protects against MRSA sepsis-induced DIC through Lys33-linked deubiquitination of NLRP3.
      Title: YOD1 protects against MRSA sepsis-induced DIC through Lys33-linked deubiquitination of NLRP3.
    2. Deubiquitylase YOD1 regulates CDK1 stability and drives triple-negative breast cancer tumorigenesis.
      Title: Deubiquitylase YOD1 regulates CDK1 stability and drives triple-negative breast cancer tumorigenesis.
    3. YY1-induced LncRNA-TUG1 elevates YOD1 to promote cell proliferation and inhibit bortezomib sensitivity in multiple myeloma.
      Title: YY1-induced LncRNA-TUG1 elevates YOD1 to promote cell proliferation and inhibit bortezomib sensitivity in multiple myeloma.
    4. Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes alpha-synuclein.
      Title: Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes α-synuclein.
    5. findings thus provided novel insights into the regulatory cascade of the cellular antiviral response through YOD1-mediated K63-linked deubiquitination and aggregation of MAVS.
      Title: The Otubain YOD1 Suppresses Aggregation and Activation of the Signaling Adaptor MAVS through Lys63-Linked Deubiquitination.
    6. YOD1 RNAi may inhibit cell proliferation and migration associated with the pathogenesis of NSCL/P through TGF-beta3 signaling. The study indicates a novel role of YOD1 in regulating TGF-beta3 signaling to affect cell proliferation and migration resulting in cleft lip with or without cleft palate.
      Title: Targeting YOD1 by RNA Interference Inhibits Proliferation and Migration of Human Oral Keratinocytes through Transforming Growth Factor-β3 Signaling Pathway.
    7. This study showed that YOD1 overexpression enhances cell migration by promoting TGF-beta3 signaling which may play an important role in lip and palate formation.
      Title: Overexpression of YOD1 Promotes the Migration of Human Oral Keratinocytes by Enhancing TGF-β3 Signaling.
    8. Mechanistically, YOD1 deubiquitinates ITCH, an E3 ligase of LATS, and enhances the stability of ITCH, which leads to reduced levels of LATS and a subsequent increase in the YAP/TAZ level.
      Title: Deubiquitinase YOD1 potentiates YAP/TAZ activities through enhancing ITCH stability.
    9. Data suggest that YOD1 is a novel regulator of the Hippo pathway, and thereby a potential therapeutic target for liver cancer.
      Title: Deubiquitinase YOD1: the potent activator of YAP in hepatomegaly and liver cancer.
    10. These data define that YOD1 antagonizes TRAF6/p62-dependent IL-1 signaling to NF-kappaB.
      Title: YOD1/TRAF6 association balances p62-dependent IL-1 signaling to NF-κB.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    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

    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

    • DKFZp451J1719

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K48-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables K63-linked deubiquitinase activity TAS
    Traceable Author Statement
    more info
    		 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 deubiquitinase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in macroautophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein K11-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K11-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein K27-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K29-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K33-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 K48-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein K63-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K63-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin thioesterase OTU1
    Names
    DUBA-8
    HIN-7
    HIV-1-induced protease 7
    OTU domain containing 2
    OTU domain-containing protein 2
    YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)
    hsHIN7
    NP_001263249.1
    NP_061036.3
    XP_047280403.1
    XP_054193502.1

    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_001276320.2 → NP_001263249.1  ubiquitin thioesterase OTU1 isoform 2

      See identical proteins and their annotated locations for NP_001263249.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AL445493
      Consensus CDS
      CCDS60402.1
      UniProtKB/Swiss-Prot
      Q5VVQ6
      Related
      ENSP00000356051.1, ENST00000367084.1
      Conserved Domains (1) summary
      COG5539
      Location:47 → 303
      COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]

    2. NM_018566.4 → NP_061036.3  ubiquitin thioesterase OTU1 isoform 1

      See identical proteins and their annotated locations for NP_061036.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL445493
      Consensus CDS
      CCDS31002.1
      UniProtKB/Swiss-Prot
      B2RNX3, Q5VVQ5, Q5VVQ6, Q6ZRS6, Q86T63, Q9P1L8
      Related
      ENSP00000326813.4, ENST00000315927.9
      Conserved Domains (1) summary
      COG5539
      Location:91 → 347
      COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]

    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
      207043849..207053116 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424447.1 → XP_047280403.1  ubiquitin thioesterase OTU1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      206309040..206318351 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337527.1 → XP_054193502.1  ubiquitin thioesterase OTU1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VVQ6.1 GenPept UniProtKB/Swiss-Prot:Q5VVQ6

    Gene LinkOut

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

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