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    Usp47 ubiquitin specific peptidase 47 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308896, updated on 27-Nov-2024

    Summary

    Official Symbol
    Usp47provided by RGD
    Official Full Name
    ubiquitin specific peptidase 47provided by RGD
    Primary source
    RGD:1310411
    See related
    EnsemblRapid:ENSRNOG00000026754 AllianceGenome:RGD:1310411
    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 WD40-repeat domain binding activity and cysteine-type deubiquitinase activity. Predicted to be involved in several processes, including monoubiquitinated protein deubiquitination; negative regulation of macromolecule metabolic process; and positive regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage. Predicted to be located in cytoplasm. Predicted to be part of SCF ubiquitin ligase complex. Predicted to be active in cytosol and nucleus. Orthologous to human USP47 (ubiquitin specific peptidase 47). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Muscle (RPKM 466.1), Heart (RPKM 292.0) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Usp47 in Genome Data Viewer
    Location:
    1q33
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (175586758..175669904)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (166152104..166235312)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (176854589..176937763)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134485163 Neighboring gene U6 spliceosomal RNA Neighboring gene dickkopf WNT signaling pathway inhibitor 3 Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 2

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables WD40-repeat domain binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in base-excision repair ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to UV ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of intrinsic apoptotic signaling pathway in response to DNA damage ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in monoubiquitinated protein deubiquitination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of G2/M transition of mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cysteine-type endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cell growth ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of protein stability IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to xenobiotic stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of SCF ubiquitin ligase complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 47
    Names
    ubiquitin specific protease 47
    NP_001101012.2
    XP_006230106.1
    XP_006230107.1
    XP_006230108.1
    XP_038934018.1
    XP_038934024.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001107542.2NP_001101012.2  ubiquitin carboxyl-terminal hydrolase 47

      Status: VALIDATED

      Source sequence(s)
      BC166609, CA512624, CB325126, CF109520, CO571839, CV106232, EV771677
      UniProtKB/TrEMBL
      A0A8I6AAW7, F1MAA1
      Related
      ENSRNOP00000058846.1, ENSRNOT00000065712.4
      Conserved Domains (2) summary
      cd02659
      Location:166546
      peptidase_C19C; 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:167541
      UCH; Ubiquitin carboxyl-terminal hydrolase

    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_086019.1 Reference GRCr8

      Range
      175586758..175669904
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039078096.2XP_038934024.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AAW7
      Conserved Domains (2) summary
      cd02659
      Location:50450
      peptidase_C19C; 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 ...
      NF033609
      Location:712909
      MSCRAMM_ClfA; MSCRAMM family adhesin clumping factor ClfA
    2. XM_006230044.5XP_006230106.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JUX4, A0A8I6A571
      Related
      ENSRNOP00000088486.2, ENSRNOT00000097971.2
      Conserved Domains (2) summary
      cd02659
      Location:186586
      peptidase_C19C; 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:187581
      UCH; Ubiquitin carboxyl-terminal hydrolase
    3. XM_006230046.5XP_006230108.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X3

      UniProtKB/TrEMBL
      A0A8I6A571
      Related
      ENSRNOP00000069266.3, ENSRNOT00000087461.3
      Conserved Domains (2) summary
      cd02659
      Location:186566
      peptidase_C19C; 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:187561
      UCH; Ubiquitin carboxyl-terminal hydrolase
    4. XM_006230045.4XP_006230107.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AAW7
      Conserved Domains (2) summary
      cd02659
      Location:166566
      peptidase_C19C; 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:167561
      UCH; Ubiquitin carboxyl-terminal hydrolase
    5. XM_039078090.2XP_038934018.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AAW7
      Conserved Domains (2) summary
      cd02659
      Location:98498
      peptidase_C19C; 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 ...
      NF033609
      Location:760957
      MSCRAMM_ClfA; MSCRAMM family adhesin clumping factor ClfA