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    Usp39 ubiquitin specific peptidase 39 [ Mus musculus (house mouse) ]

    Gene ID: 28035, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Usp39provided by MGI
    Official Full Name
    ubiquitin specific peptidase 39provided by MGI
    Primary source
    MGI:MGI:107622
    See related
    Ensembl:ENSMUSG00000056305 AllianceGenome:MGI:107622
    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
    SAD1; CGI-21; D6Wsu157e
    Summary
    Predicted to enable thiol-dependent deubiquitinase and zinc ion binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to act upstream of or within RNA splicing and cell division. Predicted to be located in nucleoplasm. Predicted to be part of U4/U6 x U5 tri-snRNP complex. Is expressed in cerebral cortex; early conceptus; and genitourinary system. Orthologous to human USP39 (ubiquitin specific peptidase 39). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in placenta adult (RPKM 20.2), liver E14 (RPKM 19.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    6 C1; 6 32.27 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (72295749..72322190, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (72318676..72345208, complement)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 30782 Neighboring gene surfactant associated protein B Neighboring gene STARR-seq mESC enhancer starr_16282 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:72295216-72295399 Neighboring gene RIKEN cDNA 0610030E20 gene Neighboring gene transmembrane protein 150A Neighboring gene ring finger protein 181

    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. High expression of ubiquitin-specific peptidase 39 is associated with the development of vascular remodeling. He S, et al. Mol Med Rep, 2017 May. PMID 28447728, Free PMC Article
    2. USP39 Regulates NF-κB-Mediated Inflammatory Responses through Deubiquitinating K48-Linked IκBα. Quan J, et al. J Immunol, 2023 Mar 1. PMID 36651806
    3. The spliceosome component Usp39 controls B cell development by regulating immunoglobulin gene rearrangement. Ruan GX, et al. Cell Rep, 2022 Feb 8. PMID 35139388
    4. The 65 and 110 kDa SR-related proteins of the U4/U6.U5 tri-snRNP are essential for the assembly of mature spliceosomes. Makarova OV, et al. EMBO J, 2001 May 15. PMID 11350945, Free PMC Article
    5. The unfolded protein response contributes to preimplantation mouse embryo death in the DDK syndrome. Hao L, et al. Biol Reprod, 2009 May. PMID 19129515, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy.
      Title: Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy.
    2. USP39 Regulates NF-kappaB-Mediated Inflammatory Responses through Deubiquitinating K48-Linked IkappaBalpha.
      Title: USP39 Regulates NF-κB-Mediated Inflammatory Responses through Deubiquitinating K48-Linked IκBα.
    3. High expression of ubiquitin-specific peptidase 39 is associated with the development of vascular remodeling.
      Title: High expression of ubiquitin-specific peptidase 39 is associated with the development of vascular remodeling.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 
    • Endonuclease-mediated (3)  1 citation

    Pathways from PubChem

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    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 cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding 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 RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cell cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spliceosomal complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of U4/U6 x U5 tri-snRNP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 39
    Names
    SnRNP assembly defective 1 homolog
    U4/U6.U5 tri-snRNP-associated 65 kDa protein
    U4/U6.U5 tri-snRNP-associated protein 2
    inactive ubiquitin-specific peptidase 39
    ubiquitin specific protease 39
    NP_001397563.1
    NP_613058.1
    XP_006506279.1

    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_001410634.1 → NP_001397563.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC116115

    2. NM_138592.5 → NP_613058.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 1

      See identical proteins and their annotated locations for NP_613058.1

      Status: VALIDATED

      Source sequence(s)
      AC116115
      Consensus CDS
      CCDS20238.1
      UniProtKB/Swiss-Prot
      Q3TI55, Q3TIX9, Q8BLI5, Q8BZZ5, Q9CQR1
      Related
      ENSMUSP00000064515.4, ENSMUST00000070345.5
      Conserved Domains (3) summary
      cd02669
      Location:105 → 552
      Peptidase_C19M; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      pfam00443
      Location:223 → 551
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam12300
      Location:3 → 93
      DUF3628; Protein of unknown function (DUF3628)

    RNA

    1. NR_177101.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC116115

    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_000072.7 Reference GRCm39 C57BL/6J

      Range
      72295749..72322190 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006506216.5 → XP_006506279.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X2

      See identical proteins and their annotated locations for XP_006506279.1

      Conserved Domains (2) summary
      PRK04537
      Location:3 → 93
      PRK04537; ATP-dependent RNA helicase RhlB; Provisional
      cd02669
      Location:105 → 550
      Peptidase_C19M; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3TIX9.2 GenPept UniProtKB/Swiss-Prot:Q3TIX9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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