U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 55031, updated on 7-Apr-2024

Summary

Go to the top of the page Help
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 thiol-dependent deubiquitinase. Involved in several processes, including monoubiquitinated protein deubiquitination; negative regulation of G2/M transition of mitotic cell cycle; and negative regulation of nitrogen compound metabolic process. Located in cytoplasm. Part of SCF ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 11.7), heart (RPKM 10.2) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See USP47 in Genome Data Viewer
Location:
11p15.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (11841972..11961887)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (11931131..12053770)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Deubiquitinase USP47 attenuates virus-induced type I interferon signaling. Chen HY, et al. Int Immunopharmacol, 2023 May. PMID 37001379
  2. Ubiquitin specific peptidase 47 promotes proliferation of lung squamous cell carcinoma. Yu L, et al. Genes Genomics, 2022 Jun. PMID 35254655
  3. USP47 maintains the stemness of colorectal cancer cells and is inhibited by parthenolide. Zhang S, et al. Biochem Biophys Res Commun, 2021 Jul 12. PMID 34030041
  4. Expression, purification and enzymatic characterization of a recombinant human ubiquitin-specific protease 47. Piao J, et al. J Biochem, 2015 Dec. PMID 26115687
  5. USP47 stabilizes BACH1 to promote the Warburg effect and non-small cell lung cancer development via stimulating Hk2 and Gapdh transcription. Peng J, et al. Am J Cancer Res, 2022. PMID 35141006, Free PMC Article

See all (89) citations in PubMed

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

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 involved in apoptotic process 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
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

Go to the top of the page Help
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)

Go to the top of the page Help

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_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_2023_10

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

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous