Aliases for USP47 Gene

Aliases for USP47 Gene

  • Ubiquitin Specific Peptidase 47 2 3 5
  • Ubiquitin-Specific-Processing Protease 47 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 47 3 4
  • Deubiquitinating Enzyme 47 3 4
  • Ubiquitin Thioesterase 47 3 4
  • Trf (TATA Binding Protein-Related Factor)-Proximal Homolog (Drosophila) 2
  • Trf (TATA Binding Protein-Related Factor)-Proximal Homolog 3
  • Ubiquitin Specific Protease 47 2
  • Ubiquitin Thiolesterase 47 3
  • EC 4
  • USP47 5
  • TRFP 3

External Ids for USP47 Gene

Previous GeneCards Identifiers for USP47 Gene

  • GC11P011902
  • GC11P011827
  • GC11P011538

Summaries for USP47 Gene

GeneCards Summary for USP47 Gene

USP47 (Ubiquitin Specific Peptidase 47) is a Protein Coding gene. Among its related pathways are Deubiquitination and Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include cysteine-type endopeptidase activity and thiol-dependent ubiquitinyl hydrolase activity. An important paralog of this gene is USP40.

UniProtKB/Swiss-Prot Summary for USP47 Gene

  • Ubiquitin-specific protease that specifically deubiquitinates monoubiquitinated DNA polymerase beta (POLB), stabilizing POLB thereby playing a role in base-excision repair (BER). Acts as a regulator of cell growth and genome integrity. May also indirectly regulate CDC25A expression at a transcriptional level.

Gene Wiki entry for USP47 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP47 Gene

Genomics for USP47 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP47 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP47 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP47

Top Transcription factor binding sites by QIAGEN in the USP47 gene promoter:
  • Egr-2
  • FOXD3
  • GATA-1
  • GATA-6
  • HNF-1
  • HNF-1A
  • HNF-3beta
  • Lmo2
  • Sox9
  • TGIF

Genomic Locations for USP47 Gene

Latest Assembly
120,465 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
119,916 bases
Plus strand

(GRCh37/hg19 by Ensembl)
117,901 bases
Plus strand

Genomic View for USP47 Gene

Genes around USP47 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP47 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP47 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP47 Gene

Proteins for USP47 Gene

  • Protein details for USP47 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 47
    Protein Accession:
    Secondary Accessions:
    • B3KXF5
    • E9PM46
    • Q658U0
    • Q86Y73
    • Q8TEP6
    • Q9BWI0
    • Q9NWN1

    Protein attributes for USP47 Gene

    1375 amino acids
    Molecular mass:
    157311 Da
    Quaternary structure:
    • Interacts with BTRC and FBXW11. Interacts with POLB.
    • Sequence=BAA91348.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BC071559; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for USP47 Gene


neXtProt entry for USP47 Gene

Post-translational modifications for USP47 Gene

  • Ubiquitination at Lys122, Lys1274, and Lys660
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for USP47 Gene

Domains & Families for USP47 Gene

Gene Families for USP47 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for USP47 Gene

  • Ubiquitin thiolesterase, family 2

Suggested Antigen Peptide Sequences for USP47 Gene

GenScript: Design optimal peptide antigens:
  • USP47 protein (A0PJ80_HUMAN)
  • Ubiquitin carboxyl-terminal hydrolase (E9PM46_HUMAN)
  • Ubiquitin carboxyl-terminal hydrolase (F5H2J6_HUMAN)
  • Ubiquitin-specific-processing protease 47 (UBP47_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C19 family.
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP47: view

Function for USP47 Gene

Molecular function for USP47 Gene

UniProtKB/Swiss-Prot Function:
Ubiquitin-specific protease that specifically deubiquitinates monoubiquitinated DNA polymerase beta (POLB), stabilizing POLB thereby playing a role in base-excision repair (BER). Acts as a regulator of cell growth and genome integrity. May also indirectly regulate CDC25A expression at a transcriptional level.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).; EC=; Evidence={ECO:0000269|PubMed:21362556};.

Enzyme Numbers (IUBMB) for USP47 Gene

Phenotypes From GWAS Catalog for USP47 Gene

Gene Ontology (GO) - Molecular Function for USP47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IBA 21873635
GO:0004843 thiol-dependent ubiquitin-specific protease activity IBA,IDA 21362556
GO:0005515 protein binding IPI 21362556
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
genes like me logo Genes that share ontologies with USP47: view
genes like me logo Genes that share phenotypes with USP47: view

Animal Models for USP47 Gene

MGI Knock Outs for USP47:
  • Usp47 Usp47<tm1b(EUCOMM)Wtsi>

Animal Models for research

  • Taconic Biosciences Mouse Models for USP47

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP47

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USP47 Gene

Localization for USP47 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP47 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP47 gene
Compartment Confidence
nucleus 5
cytosol 4
cytoskeleton 3
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Intermediate filaments (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for USP47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 21362556
GO:0005829 cytosol IBA 21873635
GO:0019005 SCF ubiquitin ligase complex IDA 19966869
genes like me logo Genes that share ontologies with USP47: view

Pathways & Interactions for USP47 Gene

PathCards logo

SuperPathways for USP47 Gene

genes like me logo Genes that share pathways with USP47: view

Pathways by source for USP47 Gene

1 Qiagen pathway for USP47 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

Gene Ontology (GO) - Biological Process for USP47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006284 base-excision repair IMP 21362556
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0006974 cellular response to DNA damage stimulus IMP 21362556
genes like me logo Genes that share ontologies with USP47: view

No data available for SIGNOR curated interactions for USP47 Gene

Drugs & Compounds for USP47 Gene

(2) Drugs for USP47 Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
P 22077 Pharma USP7/(DUB)USP47 inhibitor 0

(1) ApexBio Compounds for USP47 Gene

Compound Action Cas Number
P 22077 USP7/(DUB)USP47 inhibitor 1247819-59-5
genes like me logo Genes that share compounds with USP47: view

Drug products for research

Transcripts for USP47 Gene

mRNA/cDNA for USP47 Gene

24 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP47

Alternative Splicing Database (ASD) splice patterns (SP) for USP47 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b ·
SP1: - - - -
SP2: -
SP4: - -

ExUns: 21c ^ 22 ^ 23a · 23b · 23c ^ 24a · 24b ^ 25a · 25b ^ 26a · 26b ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31
SP1: - - - - -
SP3: -
SP5: - -
SP6: -
SP7: - -

Relevant External Links for USP47 Gene

GeneLoc Exon Structure for

Expression for USP47 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP47 Gene

Protein differential expression in normal tissues from HIPED for USP47 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (17.7), Lymph node (9.5), and Lavage (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for USP47 Gene

Protein tissue co-expression partners for USP47 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP47

SOURCE GeneReport for Unigene cluster for USP47 Gene:


mRNA Expression by UniProt/SwissProt for USP47 Gene:

Tissue specificity: Expressed in skeletal muscle, heart and testis.

Evidence on tissue expression from TISSUES for USP47 Gene

  • Liver(4.4)
  • Spleen(4.3)
  • Eye(4.3)
  • Stomach(4.3)
  • Nervous system(3.8)
  • Intestine(2.4)
  • Kidney(2.3)
  • Heart(2.2)
  • Muscle(2.2)
  • Lung(2.2)
  • Blood(2)
  • Skin(2)
genes like me logo Genes that share expression patterns with USP47: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP47 Gene

Orthologs for USP47 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for USP47 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia USP47 29 30
  • 99.73 (n)
(Canis familiaris)
Mammalia USP47 29 30
  • 94.76 (n)
(Bos Taurus)
Mammalia USP47 29 30
  • 94.32 (n)
(Monodelphis domestica)
Mammalia USP47 30
  • 90 (a)
(Mus musculus)
Mammalia Usp47 29 16 30
  • 89.54 (n)
(Rattus norvegicus)
Mammalia Usp47 29
  • 89.3 (n)
(Ornithorhynchus anatinus)
Mammalia USP47 30
  • 84 (a)
(Gallus gallus)
Aves USP47 29 30
  • 83.22 (n)
(Anolis carolinensis)
Reptilia USP47 30
  • 83 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia usp47 29
  • 73.69 (n)
(Danio rerio)
Actinopterygii usp47 30
  • 65 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta Ubp64E 29 30
  • 49.66 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007106 29
  • 47.65 (n)
(Caenorhabditis elegans)
Secernentea T05H10.1 30
  • 30 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP15 30
  • 16 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 42 (a)
Species where no ortholog for USP47 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for USP47 Gene

Gene Tree for USP47 (if available)
Gene Tree for USP47 (if available)
Evolutionary constrained regions (ECRs) for USP47: view image
Alliance of Genome Resources:
Additional Orthologs for USP47

Paralogs for USP47 Gene

(2) SIMAP similar genes for USP47 Gene using alignment to 3 proteins:

  • A0PJ80_HUMAN
  • E9PM46_HUMAN
genes like me logo Genes that share paralogs with USP47: view

Variants for USP47 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP47 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs182726093 Benign: not provided 11,948,540(+) T/G
NM_001282659.2(USP47):c.3330T>G (p.Leu1110=)
rs11022079 -- p.Gly163Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for USP47 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for USP47 Gene

Variant ID Type Subtype PubMed ID
dgv1058n100 CNV loss 25217958
dgv1655n54 CNV loss 21841781
dgv1656n54 CNV loss 21841781
dgv52e215 CNV deletion 23714750
esv2668480 CNV deletion 23128226
esv2744114 CNV deletion 23290073
esv28059 CNV gain+loss 19812545
esv3547330 CNV deletion 23714750
esv3579369 CNV loss 25503493
esv3625382 CNV loss 21293372
esv3625384 CNV gain 21293372
esv3625386 CNV gain 21293372
nsv1040757 CNV gain 25217958
nsv1054113 CNV loss 25217958
nsv483000 CNV loss 15286789
nsv511478 CNV loss 21212237
nsv512212 CNV loss 21212237
nsv524777 CNV loss 19592680
nsv553532 CNV loss 21841781
nsv553537 CNV loss 21841781
nsv553538 CNV loss 21841781
nsv553539 CNV loss 21841781
nsv553540 CNV loss 21841781
nsv553543 CNV loss 21841781
nsv553544 CNV gain 21841781
nsv7681 CNV deletion 18451855
nsv821457 CNV deletion 20802225
nsv832066 CNV gain 17160897
nsv832067 CNV gain 17160897
nsv8792 CNV gain+loss 18304495

Variation tolerance for USP47 Gene

Residual Variation Intolerance Score: 2.71% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.28; 40.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP47 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP47 Gene

Disorders for USP47 Gene

Additional Disease Information for USP47

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for USP47 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP47 Gene

Publications for USP47 Gene

  1. USP47 is a deubiquitylating enzyme that regulates base excision repair by controlling steady-state levels of DNA polymerase β. (PMID: 21362556) Parsons JL … Dianov GL (Molecular cell 2011) 3 4
  2. The ubiquitin-specific protease USP47 is a novel beta-TRCP interactor regulating cell survival. (PMID: 19966869) Peschiaroli A … Melino G (Oncogene 2010) 3 4
  3. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for USP47 Gene

Sources for USP47 Gene