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    ubr3 ubiquitin protein ligase E3 component n-recognin 3 [ Danio rerio (zebrafish) ]

    Gene ID: 553247, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ubr3provided by ZNC
    Official Full Name
    ubiquitin protein ligase E3 component n-recognin 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-1473
    See related
    Ensembl:ENSDARG00000042508 AllianceGenome:ZFIN:ZDB-GENE-030131-1473
    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
    fb72f06; wu:fb72f06
    Summary
    Predicted to enable ubiquitin protein ligase activity. Acts upstream of or within eye morphogenesis. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm. Is expressed in somite. Orthologous to human UBR3 (ubiquitin protein ligase E3 component n-recognin 3). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ubr3 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (3898132..4017933, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (3929146..4049308, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene Sp5 transcription factor a Neighboring gene myosin IIIB Neighboring gene myosin, light chain kinase a Neighboring gene kalirin RhoGEF kinase a

    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. Ubr3, a Novel Modulator of Hh Signaling Affects the Degradation of Costal-2 and Kif7 through Poly-ubiquitination. Li T, et al. PLoS Genet, 2016 May. PMID 27195754, Free PMC Article
    2. Many genes in fish have species-specific asymmetric rates of molecular evolution. Steinke D, et al. BMC Genomics, 2006 Feb 8. PMID 16466575, 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

    What's a GeneRIF?
    1. In zebrafish, loss of Ubr3 causes a decrease in Shh signaling in the developing eyes, somites, and sensory neurons.
      Title: Ubr3, a Novel Modulator of Hh Signaling Affects the Degradation of Costal-2 and Kif7 through Poly-ubiquitination.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within eye morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within ubiquitin-dependent protein catabolic process via the N-end rule pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm 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 ubr3
    Names
    E3 ubiquitin-protein ligase UBR3
    E3 ubiquitin-protein transferase ubr3
    zmp:0000001279
    znf650
    NP_001410687.1
    XP_017213227.1
    XP_021334498.1
    XP_021334499.1

    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_001423758.1 → NP_001410687.1  E3 ubiquitin-protein ligase ubr3

      Status: VALIDATED

      Source sequence(s)
      AI544584, BC124477, CN512516, EB928898, EB941420, GFIL01042617, LO017832
      UniProtKB/TrEMBL
      A0A8M9QJY5

    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_007120.7 Reference GRCz11 Primary Assembly

      Range
      3898132..4017933 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017357738.3 → XP_017213227.1  E3 ubiquitin-protein ligase ubr3 isoform X2

      UniProtKB/Swiss-Prot
      F1QJX5, Q05AJ6, Q1JPS8, Q6AZB6
      Related
      ENSDARP00000156490.1, ENSDART00000181059.1
      Conserved Domains (2) summary
      pfam02207
      Location:82 → 149
      zf-UBR; Putative zinc finger in N-recognin (UBR box)
      cd16483
      Location:1198 → 1336
      RING-H2_UBR3; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins

    2. XM_021478824.2 → XP_021334499.1  E3 ubiquitin-protein ligase ubr3 isoform X3

      UniProtKB/TrEMBL
      A0A8M9QB29
      Conserved Domains (2) summary
      pfam02207
      Location:82 → 149
      zf-UBR; Putative zinc finger in N-recognin (UBR box)
      cd16483
      Location:1209 → 1347
      RING-H2_UBR3; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins

    3. XM_021478823.2 → XP_021334498.1  E3 ubiquitin-protein ligase ubr3 isoform X1

      UniProtKB/TrEMBL
      A0A8M9Q4T2
      Conserved Domains (2) summary
      pfam02207
      Location:82 → 149
      zf-UBR; Putative zinc finger in N-recognin (UBR box)
      cd16483
      Location:1209 → 1347
      RING-H2_UBR3; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F1QJX5.2 GenPept UniProtKB/Swiss-Prot:F1QJX5

    Gene LinkOut

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