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Aliases for USP47 Gene

Aliases for USP47 Gene

  • Ubiquitin Specific Peptidase 47 2 3
  • Ubiquitin-Specific-Processing Protease 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 Carboxyl-Terminal Hydrolase 47 3
  • Ubiquitin Specific Protease 47 2
  • Ubiquitin Thiolesterase 47 3
  • EC 3.4.19.12 4
  • 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 Ubiquitin-Proteasome Dependent Proteolysis. GO annotations related to this gene include ubiquitin thiolesterase activity and WD40-repeat domain binding. An important paralog of this gene is USP41.

UniProtKB/Swiss-Prot 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 regulates CDC25A expression at a transcriptional level.

Gene Wiki entry for USP47 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP47 Gene

Genomics for USP47 Gene

Regulatory Elements for USP47 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for USP47 Gene

Start:
11,841,423 bp from pter
End:
11,959,325 bp from pter
Size:
117,903 bases
Orientation:
Plus strand

Genomic View for USP47 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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:
    Q96K76-UBP47_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 47
    Protein Accession:
    Q96K76
    Secondary Accessions:
    • B3KXF5
    • E9PM46
    • Q658U0
    • Q86Y73
    • Q8TEP6
    • Q9BWI0
    • Q9NWN1

    Protein attributes for USP47 Gene

    Size:
    1375 amino acids
    Molecular mass:
    157311 Da
    Quaternary structure:
    • Interacts with BTRC and FBXW11. Interacts with POLB.
    SequenceCaution:
    • Sequence=BAA91348.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BC071559; Type=Frameshift; Positions=707; Evidence={ECO:0000305};

    Alternative splice isoforms for USP47 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP47 Gene

Proteomics data for USP47 Gene at MOPED

Post-translational modifications for USP47 Gene

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

Other Protein References for USP47 Gene

No data available for DME Specific Peptides for USP47 Gene

Domains for USP47 Gene

Gene Families for USP47 Gene

HGNC:
  • USP :Ubiquitin-specific peptidases

Protein Domains for USP47 Gene

Graphical View of Domain Structure for InterPro Entry

Q96K76

UniProtKB/Swiss-Prot:

UBP47_HUMAN :
  • Q96K76
Domain:
  • Contains 1 USP domain.
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 CatalyticActivity: 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).
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 regulates CDC25A expression at a transcriptional level.

Enzyme Numbers (IUBMB) 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 --
GO:0004843 ubiquitin-specific protease activity IDA 21362556
GO:0005515 protein binding IPI 21362556
GO:0036459 ubiquitinyl hydrolase activity --
GO:0071987 WD40-repeat domain binding IPI 19966869
genes like me logo Genes that share ontologies with USP47: view

Phenotypes for USP47 Gene

MGI mutant phenotypes for USP47:
inferred from 1 alleles
genes like me logo Genes that share phenotypes with USP47: view

Animal Model Products

CRISPR Products

miRNA for USP47 Gene

miRTarBase miRNAs that target USP47

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for USP47

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for USP47 Gene

Localization for USP47 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP47 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for USP47 Gene COMPARTMENTS Subcellular localization image for USP47 gene
Compartment Confidence
nucleus 3
cytoskeleton 2
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for USP47 Gene

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

Pathways 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

Gene Ontology (GO) - Biological Process for USP47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006284 base-excision repair IMP 21362556
GO:0006511 ubiquitin-dependent protein catabolic process --
GO:0006974 cellular response to DNA damage stimulus IMP 21362556
GO:0010972 negative regulation of G2/M transition of mitotic cell cycle IMP 19966869
GO:0030307 positive regulation of cell growth IMP 19966869
genes like me logo Genes that share ontologies with USP47: view

Compounds for USP47 Gene

(1) HMDB Compounds for USP47 Gene

Compound Synonyms Cas Number PubMed IDs
Water
  • Dihydrogen oxide
7732-18-5
genes like me logo Genes that share compounds with USP47: view

Transcripts for USP47 Gene

Unigene Clusters for USP47 Gene

Ubiquitin specific peptidase 47:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for USP47

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for USP47

Flow Cytometry Products

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: -
SP3:
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:

ExUns: 21c ^ 22 ^ 23a · 23b · 23c ^ 24a · 24b ^ 25a · 25b ^ 26a · 26b ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31
SP1: - - - - -
SP2:
SP3: -
SP4:
SP5: - -
SP6: -
SP7: - -
SP8:
SP9:

Relevant External Links for USP47 Gene

GeneLoc Exon Structure for
USP47
ECgene alternative splicing isoforms for
USP47

Expression for USP47 Gene

mRNA expression in normal human tissues for USP47 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for USP47 Gene

SOURCE GeneReport for Unigene cluster for USP47 Gene Hs.577256

mRNA Expression by UniProt/SwissProt for USP47 Gene

Q96K76-UBP47_HUMAN
Tissue specificity: Expressed in skeletal muscle, heart and testis.
genes like me logo Genes that share expressions with USP47: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues 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
chimpanzee
(Pan troglodytes)
Mammalia USP47 35
  • 99.73 (n)
  • 99.7 (a)
USP47 36
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia USP47 35
  • 94.32 (n)
  • 97.49 (a)
USP47 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia USP47 35
  • 94.76 (n)
  • 98.36 (a)
USP47 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Usp47 35
  • 89.54 (n)
  • 95.06 (a)
Usp47 16
Usp47 36
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia USP47 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP47 36
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp47 35
  • 89.3 (n)
  • 95.65 (a)
chicken
(Gallus gallus)
Aves USP47 35
  • 83.22 (n)
  • 90.7 (a)
USP47 36
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP47 36
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp47 35
  • 73.69 (n)
  • 82.7 (a)
zebrafish
(Danio rerio)
Actinopterygii usp47 36
  • 65 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007106 35
  • 47.65 (n)
  • 43.33 (a)
fruit fly
(Drosophila melanogaster)
Insecta Ubp64E 35
  • 49.66 (n)
  • 46.14 (a)
Ubp64E 36
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T05H10.1 36
  • 30 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP15 36
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 42 (a)
OneToMany
Species with no ortholog for USP47:
  • A. gosspyii yeast (Ashbya 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 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

ENSEMBL:
Gene Tree for USP47 (if available)
TreeFam:
Gene Tree for USP47 (if available)

Paralogs for USP47 Gene

Paralogs for USP47 Gene

Selected SIMAP similar genes for USP47 Gene using alignment to 3 proteins:

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

Variants for USP47 Gene

Sequence variations from dbSNP and Humsavar for USP47 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs11255 -- 11,958,045(+) CAGCT(A/G)TTTGG utr-variant-3-prime
rs13903 -- 11,958,850(+) CAGCC(C/T)TCACA utr-variant-3-prime
rs1979687 -- 11,958,127(+) CTATC(A/G)CACAA utr-variant-3-prime
rs2279566 -- 11,958,902(+) TTTAA(A/G)ATTCT utr-variant-3-prime
rs2307073 -- 11,956,026(+) TGGAA(C/T)TGACA synonymous-codon, reference

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

Variant ID Type Subtype PubMed ID
nsv832066 CNV Gain 17160897
nsv483000 CNV Loss 15286789
nsv832067 CNV Gain 17160897
nsv896993 CNV Loss 21882294
nsv511478 CNV Loss 21212237
nsv8792 CNV Gain+Loss 18304495
nsv512212 CNV Loss 21212237
esv2744114 CNV Deletion 23290073
esv2668480 CNV Deletion 23128226
esv28059 CNV Gain+Loss 19812545
nsv821457 CNV Deletion 20802225
nsv7681 CNV Loss 18451855
nsv524777 CNV Loss 19592680

Relevant External Links for USP47 Gene

HapMap Linkage Disequilibrium report
USP47

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

Disorders for USP47 Gene

Relevant External Links for USP47

Genetic Association Database (GAD)
USP47
Human Genome Epidemiology (HuGE) Navigator
USP47
genes like me logo Genes that share disorders with USP47: view

No data available for UniProtKB/Swiss-Prot 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 beta. (PMID: 21362556) Parsons J.L. … Dianov G.L. (Mol. Cell 2011) 3 4
  2. Human and mouse proteases: a comparative genomic approach. (PMID: 12838346) Puente X.S. … Lopez-Otin C. (Nat. Rev. Genet. 2003) 2 3
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. (PMID: 14715245) Quesada V. … Lopez-Otin C. (Biochem. Biophys. Res. Commun. 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4

Products for USP47 Gene

Sources for USP47 Gene

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