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    Ubr3 ubiquitin protein ligase E3 component n-recognin 3 [ Mus musculus (house mouse) ]

    Gene ID: 68795, updated on 8-May-2024

    Summary

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    Official Symbol
    Ubr3provided by MGI
    Official Full Name
    ubiquitin protein ligase E3 component n-recognin 3provided by MGI
    Primary source
    MGI:MGI:1861100
    See related
    Ensembl:ENSMUSG00000044308 AllianceGenome:MGI:1861100
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Zfp650; Znf650; 1110059H15Rik; 4833421P10Rik; A130030D10Rik
    Summary
    Enables ubiquitin protein ligase activity. Involved in embryo development; sensory perception of smell; and ubiquitin-dependent protein catabolic process. Acts upstream of or within in utero embryonic development; olfactory behavior; and suckling behavior. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm. Is expressed in cranial ganglion and dorsal root ganglion. Orthologous to human UBR3 (ubiquitin protein ligase E3 component n-recognin 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in frontal lobe adult (RPKM 12.9), cortex adult (RPKM 10.3) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ubr3 in Genome Data Viewer
    Location:
    2 C2; 2 40.95 cM
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (69727276..69854354)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (69896932..70024010)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr2:69698414-69698714 Neighboring gene STARR-positive B cell enhancer ABC_E4462 Neighboring gene kelch-like 23 Neighboring gene STARR-positive B cell enhancer ABC_E11134 Neighboring gene STARR-seq mESC enhancer starr_04746 Neighboring gene STARR-positive B cell enhancer ABC_E508 Neighboring gene methyltransferase 5, N6-adenosine Neighboring gene STARR-seq mESC enhancer starr_04748 Neighboring gene small RNA binding exonuclease protection factor La Neighboring gene STARR-positive B cell enhancer ABC_E9515 Neighboring gene STARR-seq mESC enhancer starr_04749 Neighboring gene STARR-seq mESC enhancer starr_04750 Neighboring gene STARR-positive B cell enhancer ABC_E4463 Neighboring gene myosin IIIB Neighboring gene STARR-seq mESC enhancer starr_04751 Neighboring gene STARR-seq mESC enhancer starr_04752 Neighboring gene STARR-seq mESC enhancer starr_04756 Neighboring gene STARR-seq mESC enhancer starr_04757 Neighboring gene STARR-seq mESC enhancer starr_04758 Neighboring gene STARR-seq mESC enhancer starr_04760 Neighboring gene ribosomal protein L9, pseudogene 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Tex19.1 inhibits the N-end rule pathway and maintains acetylated SMC3 cohesin and sister chromatid cohesion in oocytes. Reichmann J, et al. J Cell Biol, 2020 May 4. PMID 32232464, Free PMC Article
    2. Ubiquitin ligase UBR3 regulates cellular levels of the essential DNA repair protein APE1 and is required for genome stability. Meisenberg C, et al. Nucleic Acids Res, 2012 Jan. PMID 21933813, Free PMC Article
    3. Altered activity, social behavior, and spatial memory in mice lacking the NTAN1p amidase and the asparagine branch of the N-end rule pathway. Kwon YT, et al. Mol Cell Biol, 2000 Jun. PMID 10805755, Free PMC Article
    4. Biochemical and genetic studies of UBR3, a ubiquitin ligase with a function in olfactory and other sensory systems. Tasaki T, et al. J Biol Chem, 2007 Jun 22. PMID 17462990
    5. 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

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tex19.1 inhibits the N-end rule pathway and maintains acetylated SMC3 cohesin and sister chromatid cohesion in oocytes.
      Title: Tex19.1 inhibits the N-end rule pathway and maintains acetylated SMC3 cohesin and sister chromatid cohesion in oocytes.
    2. Mouse UBR3 poly-ubiquitinates Kif7, the mammalian homologue of Cos2. Finally, loss of UBR3 up-regulates Kif7 protein levels and decreases Hh signaling in cultured cells.
      Title: Ubr3, a Novel Modulator of Hh Signaling Affects the Degradation of Costal-2 and Kif7 through Poly-ubiquitination.
    3. Knockout of the Ubr3 gene in mouse embryonic fibroblasts leads to an up-regulation of the cellular levels of APE1 protein and subsequent genomic instability.
      Title: Ubiquitin ligase UBR3 regulates cellular levels of the essential DNA repair protein APE1 and is required for genome stability.
    4. the UBR box of UBR3 may recognize small compounds that modulate the targeting, by this E3, of its currently unknown substrates
      Title: Biochemical and genetic studies of UBR3, a ubiquitin ligase with a function in olfactory and other sensory systems.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (1)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in embryo development ending in birth or egg hatching IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within olfactory behavior IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sensory perception of smell IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within suckling behavior IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    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
    N-recognin-3
    RING-type E3 ubiquitin transferase UBR3
    ubiquitin-protein ligase E3-alpha-3
    ubiquitin-protein ligase E3-alpha-III
    zinc finger protein 650
    NP_001289962.1
    NP_808451.2
    XP_006500183.2
    XP_036018419.1
    XP_036018420.1
    XP_036018421.1

    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_001303033.1 → NP_001289962.1  E3 ubiquitin-protein ligase UBR3 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
      Source sequence(s)
      AK037622, AK050359, AL929249, BQ571759, CO042454
      UniProtKB/TrEMBL
      F6QC57
      Conserved Domains (1) summary
      pfam02207
      Location:120 → 187
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    2. NM_177783.6 → NP_808451.2  E3 ubiquitin-protein ligase UBR3 isoform 2

      See identical proteins and their annotated locations for NP_808451.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 3. This results in isoform (2) which is shorter than isoform 3.
      Source sequence(s)
      AK037622, AK050359, AL929249, BQ571759, CO042454
      Consensus CDS
      CCDS16104.2
      UniProtKB/Swiss-Prot
      A2AV04, A6MFP4, Q5U430, Q69Z32
      UniProtKB/TrEMBL
      F6QC57
      Related
      ENSMUSP00000060159.10, ENSMUST00000055758.16
      Conserved Domains (1) summary
      pfam02207
      Location:120 → 187
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      69727276..69854354
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036162526.1 → XP_036018419.1  E3 ubiquitin-protein ligase UBR3 isoform X1

      UniProtKB/TrEMBL
      F6QC57
      Conserved Domains (3) summary
      cd16483
      Location:1245 → 1383
      RING-H2_UBR3; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins
      pfam02207
      Location:120 → 187
      zf-UBR; Putative zinc finger in N-recognin (UBR box)
      pfam18995
      Location:1441 → 1887
      PRT6_C; Proteolysis_6 C-terminal

    2. XM_036162527.1 → XP_036018420.1  E3 ubiquitin-protein ligase UBR3 isoform X2

      UniProtKB/TrEMBL
      F6QC57
      Conserved Domains (3) summary
      cd16483
      Location:1244 → 1382
      RING-H2_UBR3; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins
      pfam02207
      Location:120 → 187
      zf-UBR; Putative zinc finger in N-recognin (UBR box)
      pfam18995
      Location:1440 → 1886
      PRT6_C; Proteolysis_6 C-terminal

    3. XM_036162528.1 → XP_036018421.1  E3 ubiquitin-protein ligase UBR3 isoform X3

      UniProtKB/TrEMBL
      F6QC57
      Conserved Domains (3) summary
      cd16483
      Location:1245 → 1383
      RING-H2_UBR3; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins
      pfam02207
      Location:120 → 187
      zf-UBR; Putative zinc finger in N-recognin (UBR box)
      pfam18995
      Location:1437 → 1883
      PRT6_C; Proteolysis_6 C-terminal

    4. XM_006500120.3 → XP_006500183.2  E3 ubiquitin-protein ligase UBR3 isoform X4

      Conserved Domains (2) summary
      cd16483
      Location:1245 → 1383
      RING-H2_UBR3; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins
      pfam02207
      Location:120 → 187
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    RNA

    1. XR_004940720.1 RNA Sequence

    2. XR_004940722.1 RNA Sequence

    3. XR_004940719.1 RNA Sequence

    4. XR_004940721.1 RNA Sequence

    5. XR_004940723.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001081548.2: Suppressed sequence

      Description
      NM_001081548.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5U430.3 GenPept UniProtKB/Swiss-Prot:Q5U430

    Gene LinkOut

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