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    otud4 OTU deubiquitinase 4 [ Danio rerio (zebrafish) ]

    Gene ID: 327127, updated on 9-Dec-2024

    Summary

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    Official Symbol
    otud4provided by ZNC
    Official Full Name
    OTU deubiquitinase 4provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-5338
    See related
    Ensembl:ENSDARG00000077810 AllianceGenome:ZFIN:ZDB-GENE-030131-5338
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    wu:fd14a11; wu:fe11h08; zgc:165536
    Summary
    Predicted to enable K63-linked deubiquitinase activity and cysteine-type deubiquitinase activity. Acts upstream of or within camera-type eye development; cerebellum development; and dorsal/ventral pattern formation. Orthologous to human OTUD4 (OTU deubiquitinase 4). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See otud4 in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (43668710..43692121)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (43868070..43890608)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100537734 Neighboring gene solute carrier family 10 member 7 Neighboring gene ATP-binding cassette, sub-family E (OABP), member 1 Neighboring gene anaphase promoting complex subunit 10

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Ataxia, dementia, and hypogonadotropism caused by disordered ubiquitination. Margolin DH, et al. N Engl J Med, 2013 May 23. PMID 23656588, Free PMC Article
    2. Zebrafish transforming growth factor-β-stimulated clone 22 domain 3 (TSC22D3) plays critical roles in Bmp-dependent dorsoventral patterning via two deubiquitylating enzymes Usp15 and Otud4. Tse WK, et al. Biochim Biophys Acta, 2013 Oct. PMID 23665588
    3. Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. Tse WK, et al. BMC Genomics, 2009 Dec 30. PMID 20040115, Free PMC Article
    4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. interruption of Bmp4 signaling by double knockdown of usp15 and otud4 reduced the ventralized effects in tsc22d3-overexpressing embryos
      Title: Zebrafish transforming growth factor-β-stimulated clone 22 domain 3 (TSC22D3) plays critical roles in Bmp-dependent dorsoventral patterning via two deubiquitylating enzymes Usp15 and Otud4.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within camera-type eye development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within camera-type eye development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cerebellum development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within cerebellum development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal/ventral pattern formation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    OTU domain-containing protein 4
    Names
    OTU domain containing 4 protein
    parp11
    NP_001299588.3
    XP_005174208.2
    XP_068072783.1

    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_001312659.3 → NP_001299588.3  OTU domain-containing protein 4

      Status: VALIDATED

      Source sequence(s)
      CABZ01058306, CU681840, FO704781
      UniProtKB/TrEMBL
      A0A8M1QHT8, A0A8M9PSY0
      Related
      ENSDARP00000098303.4, ENSDART00000112598.4
      Conserved Domains (4) summary
      cd04508
      Location:293 → 340
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      pfam15320
      Location:1306 → 1350
      RAM; mRNA cap methylation, RNMT-activating mini protein
      cl19932
      Location:41 → 120
      OTU; OTU-like cysteine protease
      cl26464
      Location:521 → 936
      Atrophin-1; Atrophin-1 family

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      43668710..43692121
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068216682.1 → XP_068072783.1  OTU domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A8M1P7L2

    2. XM_005174151.5 → XP_005174208.2  OTU domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8M1P7L2, A0A8M2BLE4
      Conserved Domains (4) summary
      cd04508
      Location:293 → 340
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      pfam15320
      Location:1311 → 1355
      RAM; mRNA cap methylation, RNMT-activating mini protein
      cl19932
      Location:41 → 120
      OTU; OTU-like cysteine protease
      cl26464
      Location:526 → 941
      Atrophin-1; Atrophin-1 family
    Nucleotide Protein Strain
    Heading Accession and Version

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