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

Gene ID: 68795, updated on 28-Oct-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 several processes, including sensory perception of smell; suckling behavior; and ubiquitin-dependent protein catabolic process. Acts upstream of or within in utero embryonic development and olfactory behavior. Predicted to be located in 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, Oct 2024]
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 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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
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 protein ubiquitination IEA
Inferred from Electronic Annotation
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 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
  
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
  
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
    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
    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

    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

    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

    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

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