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    Usp39 ubiquitin specific peptidase 39 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 297336, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Usp39provided by RGD
    Official Full Name
    ubiquitin specific peptidase 39provided by RGD
    Primary source
    RGD:1308103
    See related
    Ensembl:ENSRNOG00000010930 AllianceGenome:RGD:1308103
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable zinc ion binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to be located in nucleoplasm. Predicted to be part of U4/U6 x U5 tri-snRNP complex. Orthologous to human USP39 (ubiquitin specific peptidase 39). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 95.5), Muscle (RPKM 83.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Usp39 in Genome Data Viewer
    Location:
    4q32
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (105932140..105964551, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (104373948..104406359, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (100181408..100211425, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene atonal bHLH transcription factor 8 Neighboring gene uncharacterized LOC120102308 Neighboring gene surfactant protein B Neighboring gene similar to human chromosome 2 open reading frame 68 Neighboring gene transmembrane protein 150A Neighboring gene ring finger protein 181 Neighboring gene vesicle-associated membrane protein 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. 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
    2. Molecular architecture of the human U4/U6.U5 tri-snRNP. Agafonov DE, et al. Science, 2016 Mar 25. PMID 26912367
    3. Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics. Yang W, et al. J Proteome Res, 2012 Feb 3. PMID 22082260, 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

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    NOT enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    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 IEA
    Inferred from Electronic Annotation
    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
    U4/U6.U5 tri-snRNP-associated protein 2
    ubiquitin specific protease 39
    NP_001100067.1
    NP_001385670.1
    XP_063141848.1

    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_001106597.2 → NP_001100067.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 1

      See identical proteins and their annotated locations for NP_001100067.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A6IAA2
      Conserved Domains (4) summary
      cd02669
      Location:105 → 549
      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 → 548
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam08648
      Location:6 → 88
      DUF1777; Protein of unknown function (DUF1777)
      pfam12300
      Location:3 → 93
      DUF3628; Protein of unknown function (DUF3628)

    2. NM_001398741.1 → NP_001385670.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A9K3Y7X0, B2GV41, F7F1N8
      Related
      ENSRNOP00000015563.5, ENSRNOT00000015562.7
      Conserved Domains (1) 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 ...

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      105932140..105964551 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063285778.1 → XP_063141848.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X1

      UniProtKB/TrEMBL
      A0A9K3Y7X0, B2GV41, F7F1N8
    Nucleotide Protein Strain
    Heading Accession and Version

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