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    ube3d ubiquitin protein ligase E3D [ Danio rerio (zebrafish) ]

    Gene ID: 553294, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ube3dprovided by ZNC
    Official Full Name
    ubiquitin protein ligase E3Dprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-091218-3
    See related
    Ensembl:ENSDARG00000026178 AllianceGenome:ZFIN:ZDB-GENE-091218-3
    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
    ube2cbp
    Summary
    Predicted to enable cyclin binding activity; ubiquitin conjugating enzyme binding activity; and ubiquitin protein ligase activity. Acts upstream of or within regulation of angiogenesis; regulation of melanosome transport; and regulation of neural retina development. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytosol and nucleus. Is expressed in eye. Orthologous to human UBE3D (ubiquitin protein ligase E3D). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ube3d in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (4770268..4796565)
    105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (4940979..4967276)

    Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene sphingomyelin phosphodiesterase acid like 3B Neighboring gene thymocyte selection associated family member 2 Neighboring gene replication protein A2 Neighboring gene trophoblast glycoprotein Neighboring gene inhibitor of Bruton agammaglobulinemia tyrosine kinase

    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 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. ube3d, a New Gene Associated with Age-Related Macular Degeneration, Induces Functional Changes in Both In Vivo and In Vitro Studies. Xia H, et al. Mol Ther Nucleic Acids, 2020 Jun 5. PMID 32200270, Free PMC Article
    2. Genetic landscape of T cells identifies synthetic lethality for T-ALL. O'Meara CP, et al. Commun Biol, 2021 Oct 20. PMID 34671088, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. 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
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables cyclin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin conjugating enzyme binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein autoubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein monoubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of melanosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of neural retina development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase E3D
    Names
    ubiquitin-conjugating enzyme E2C binding protein
    NP_001313339.1
    XP_005157915.1

    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_001326410.1 → NP_001313339.1  E3 ubiquitin-protein ligase E3D

      Status: VALIDATED

      Source sequence(s)
      CU929362, EH554838, EH575949
      UniProtKB/TrEMBL
      A0A8M1P8Z2, F1Q7U1
      Related
      ENSDARP00000030264.7, ENSDART00000038036.8
      Conserved Domains (1) summary
      pfam09814
      Location:13 → 378
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

    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_007127.7 Reference GRCz11 Primary Assembly

      Range
      4770268..4796565
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005157858.4 → XP_005157915.1  E3 ubiquitin-protein ligase E3D isoform X1

      UniProtKB/TrEMBL
      A0A8M2B479
      Conserved Domains (1) summary
      pfam09814
      Location:13 → 377
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    Nucleotide Protein Strain
    Heading Accession and Version

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