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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

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