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    USP47 ubiquitin specific peptidase 47 [ Homo sapiens (human) ]

    Gene ID: 55031, updated on 14-Nov-2024

    Summary

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    Official Symbol
    USP47provided by HGNC
    Official Full Name
    ubiquitin specific peptidase 47provided by HGNC
    Primary source
    HGNC:HGNC:20076
    See related
    Ensembl:ENSG00000170242 MIM:614460; AllianceGenome:HGNC:20076
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TRFP
    Summary
    Enables WD40-repeat domain binding activity and cysteine-type deubiquitinase activity. Involved in several processes, including monoubiquitinated protein deubiquitination; negative regulation of macromolecule metabolic process; and positive regulation of canonical Wnt signaling pathway. Located in cytoplasm. Part of SCF ubiquitin ligase complex. Is active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 11.7), heart (RPKM 10.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See USP47 in Genome Data Viewer
    Location:
    11p15.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (11841972..11961887)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (11931131..12053770)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (11863519..11983434)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene microRNA 8070 Neighboring gene uncharacterized LOC107984311 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:11862595-11863460 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:11863461-11864324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:11892436-11893242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:11893243-11894047 Neighboring gene H3 histone pseudogene 33 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3160 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:11989412-11990036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:11990037-11990660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:11990661-11991284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:11991285-11991908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:11997959-11998520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:11998521-11999082 Neighboring gene dickkopf WNT signaling pathway inhibitor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12028425-12029360 Neighboring gene long intergenic non-protein coding RNA 2547

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. USP47 stabilizes YBX1 to promote the progression of acute myeloid leukemia.
      Title: USP47 stabilizes YBX1 to promote the progression of acute myeloid leukemia.
    2. USP47 inhibits m6A-dependent c-Myc translation to maintain regulatory T cell metabolic and functional homeostasis.
      Title: USP47 inhibits m6A-dependent c-Myc translation to maintain regulatory T cell metabolic and functional homeostasis.
    3. Structural and functional characterization of USP47 reveals a hot spot for inhibitor design.
      Title: Structural and functional characterization of USP47 reveals a hot spot for inhibitor design.
    4. Deubiquitinase USP47 attenuates virus-induced type I interferon signaling.
      Title: Deubiquitinase USP47 attenuates virus-induced type I interferon signaling.
    5. USP47 deubiquitylates Groucho/TLE to promote Wnt-beta-catenin signaling.
      Title: USP47 deubiquitylates Groucho/TLE to promote Wnt-β-catenin signaling.
    6. Ubiquitin specific peptidase 47 promotes proliferation of lung squamous cell carcinoma.
      Title: Ubiquitin specific peptidase 47 promotes proliferation of lung squamous cell carcinoma.
    7. USP47 maintains the stemness of colorectal cancer cells and is inhibited by parthenolide.
      Title: USP47 maintains the stemness of colorectal cancer cells and is inhibited by parthenolide.
    8. Spatial transcriptomics identifies spatially dysregulated expression of GRM3 and USP47 in amyotrophic lateral sclerosis.
      Title: Spatial transcriptomics identifies spatially dysregulated expression of GRM3 and USP47 in amyotrophic lateral sclerosis.
    9. Proteomics analysis reveals the role of ubiquitin specific protease (USP47) in Epithelial to Mesenchymal Transition (EMT) induced by TGFbeta2 in breast cells.
      Title: Proteomics analysis reveals the role of ubiquitin specific protease (USP47) in Epithelial to Mesenchymal Transition (EMT) induced by TGFβ2 in breast cells.
    10. Long non-coding RNA DSCAM-AS1 upregulates USP47 expression through sponging miR-101-3p to accelerate osteosarcoma progression.
      Title: Long non-coding RNA DSCAM-AS1 upregulates USP47 expression through sponging miR-101-3p to accelerate osteosarcoma progression.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • FLJ20727, DKFZp686C13257

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables WD40-repeat domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in base-excision repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to UV ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in intrinsic apoptotic signaling pathway in response to DNA damage IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoubiquitinated protein deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of G2/M transition of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cysteine-type endopeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein deubiquitination TAS
    Traceable Author Statement
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of SCF ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 47
    Names
    Trf (TATA binding protein-related factor)-proximal homolog
    deubiquitinating enzyme 47
    ubiquitin thioesterase 47
    ubiquitin thiolesterase 47
    ubiquitin-specific-processing protease 47
    NP_001269588.1
    NP_001317137.1
    NP_001359020.1
    NP_001359021.1
    NP_001359022.1
    NP_001359023.1
    NP_001359024.1
    NP_001359025.1
    NP_001359026.1
    NP_001359027.1
    NP_001359028.1
    NP_001359029.1
    NP_001359030.1
    NP_001359031.1
    NP_001359032.1
    NP_060414.3
    XP_011518498.1
    XP_016873443.1
    XP_054225196.1
    XP_054225197.1

    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_001282659.2 → NP_001269588.1  ubiquitin carboxyl-terminal hydrolase 47 isoform a

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Consensus CDS
      CCDS60725.1
      UniProtKB/Swiss-Prot
      Q96K76
      UniProtKB/TrEMBL
      Q68D97
      Related
      ENSP00000433146.2, ENST00000527733.7
      Conserved Domains (2) summary
      cd02659
      Location:166 → 546
      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:167 → 541
      UCH; Ubiquitin carboxyl-terminal hydrolase

    2. NM_001330208.2 → NP_001317137.1  ubiquitin carboxyl-terminal hydrolase 47 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Consensus CDS
      CCDS81554.1
      UniProtKB/Swiss-Prot
      B3KXF5, E9PM46, Q658U0, Q86Y73, Q8TEP6, Q96K76, Q9BWI0, Q9NWN1
      Related
      ENSP00000382382.2, ENST00000399455.2

    3. NM_001372091.1 → NP_001359020.1  ubiquitin carboxyl-terminal hydrolase 47 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:166 → 546
      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 ...

    4. NM_001372092.1 → NP_001359021.1  ubiquitin carboxyl-terminal hydrolase 47 isoform e

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:166 → 542
      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 ...

    5. NM_001372093.1 → NP_001359022.1  ubiquitin carboxyl-terminal hydrolase 47 isoform f

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:160 → 540
      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 ...

    6. NM_001372094.1 → NP_001359023.1  ubiquitin carboxyl-terminal hydrolase 47 isoform f

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:160 → 540
      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 ...

    7. NM_001372095.1 → NP_001359024.1  ubiquitin carboxyl-terminal hydrolase 47 isoform g

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:160 → 540
      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 ...

    8. NM_001372096.1 → NP_001359025.1  ubiquitin carboxyl-terminal hydrolase 47 isoform h

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:186 → 566
      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 ...

    9. NM_001372097.1 → NP_001359026.1  ubiquitin carboxyl-terminal hydrolase 47 isoform i

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:166 → 502
      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 ...

    10. NM_001372098.1 → NP_001359027.1  ubiquitin carboxyl-terminal hydrolase 47 isoform j

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:166 → 496
      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 ...

    11. NM_001372099.1 → NP_001359028.1  ubiquitin carboxyl-terminal hydrolase 47 isoform k

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:98 → 478
      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 ...

    12. NM_001372100.1 → NP_001359029.1  ubiquitin carboxyl-terminal hydrolase 47 isoform l

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:86 → 466
      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 ...

    13. NM_001372101.1 → NP_001359030.1  ubiquitin carboxyl-terminal hydrolase 47 isoform n

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:98 → 478
      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 ...

    14. NM_001372102.1 → NP_001359031.1  ubiquitin carboxyl-terminal hydrolase 47 isoform o

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:1 → 372
      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 ...

    15. NM_001372103.1 → NP_001359032.1  ubiquitin carboxyl-terminal hydrolase 47 isoform m

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Conserved Domains (1) summary
      cd02659
      Location:86 → 466
      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 ...

    16. NM_017944.4 → NP_060414.3  ubiquitin carboxyl-terminal hydrolase 47 isoform b

      See identical proteins and their annotated locations for NP_060414.3

      Status: VALIDATED

      Source sequence(s)
      AC104383, AC124276
      Consensus CDS
      CCDS41619.1
      UniProtKB/Swiss-Prot
      Q96K76
      Related
      ENSP00000339957.5, ENST00000339865.9
      Conserved Domains (2) summary
      cd02659
      Location:98 → 478
      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:99 → 473
      UCH; Ubiquitin carboxyl-terminal hydrolase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      11841972..11961887
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520196.2 → XP_011518498.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X1

      Conserved Domains (1) summary
      cl02553
      Location:1 → 167
      Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

    2. XM_017017954.2 → XP_016873443.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X1

      Conserved Domains (1) summary
      cl02553
      Location:1 → 167
      Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      11931131..12053770
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369222.1 → XP_054225197.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X1

    2. XM_054369221.1 → XP_054225196.1  ubiquitin carboxyl-terminal hydrolase 47 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96K76.3 GenPept UniProtKB/Swiss-Prot:Q96K76

    Gene LinkOut

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