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Aliases for USP47 Gene

Aliases for USP47 Gene

  • Ubiquitin Specific Peptidase 47 2 3 5
  • 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 Metabolism of proteins and Ubiquitin-Proteasome Dependent Proteolysis. 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 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 , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP47 Gene

Genomics for USP47 Gene

Regulatory Elements for USP47 Gene

Enhancers for USP47 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F011812 1.2 Ensembl ENCODE 28 -27.4 -27419 2.6 PKNOX1 ARID4B SIN3A DMAP1 YY1 GATA2 FOS DEK MIER2 KAT8 USP47 PIR62366 MIR8070
GH11F011798 1 Ensembl ENCODE 29.2 -42.4 -42388 0.4 ZNF263 GTF2F1 CTCF CEBPB REST ZIC2 DNMT3B RAD21 RFX5 JUND USP47 MIR8070 PIR62366
GH11F011840 1.5 FANTOM5 ENCODE 17 +2.0 2032 5.3 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 DEK ZBED5 USP47 PARVA ENSG00000255492
GH11F011871 0.8 Ensembl ENCODE 26.5 +30.4 30378 1.6 SMARCA4 ZBTB48 ZNF530 ZBTB33 KDM1A ZIC2 USP47 ENSG00000255492 PIR48629
GH11F011848 1.1 Ensembl ENCODE 16.5 +8.3 8278 3.0 HDAC1 TBL1XR1 WRNIP1 RAD21 RFX5 CHAMP1 YY1 SCRT2 ZNF143 RCOR1 USP47 ZBED5 ENSG00000255492
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP47 on UCSC Golden Path with GeneCards custom track

Promoters for USP47 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000317664 1377 3601 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 FOS

Genomic Location for USP47 Gene

Chromosome:
11
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

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:
    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

Post-translational modifications for USP47 Gene

  • Ubiquitination at Lys 122, Lys 660, and Lys 1274
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for USP47 Gene

Domains & Families for USP47 Gene

Gene Families for USP47 Gene

Protein Domains for USP47 Gene

Graphical View of Domain Structure for InterPro Entry

Q96K76

UniProtKB/Swiss-Prot:

UBP47_HUMAN :
  • Contains 1 USP domain.
  • Belongs to the peptidase C19 family.
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 regulate 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:0004843 thiol-dependent ubiquitin-specific protease activity IDA 21362556
GO:0005515 protein binding IPI 21362556
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase 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:

Animal Model Products

  • Taconic Biosciences Mouse Models for USP47

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP47

Flow Cytometry Products

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

Cytoplasm.

Subcellular locations from

COMPARTMENTS
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
cytoskeleton 3
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 IEA,IDA 21362556
GO:0019005 SCF ubiquitin ligase complex IDA 19966869
genes like me logo Genes that share ontologies with USP47: view

Pathways & Interactions for USP47 Gene

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

Pathways by source for USP47 Gene

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

(3) 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
USP7-USP47 inhibitor Pharma USP7/USP47 inhibitor 0

(2) ApexBio Compounds for USP47 Gene

Compound Action Cas Number
P 22077 USP7/(DUB)USP47 inhibitor 1247819-59-5
USP7-USP47 inhibitor USP7/USP47 inhibitor 1247825-37-1
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:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids 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 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, PaxDb, MaxQB, and MOPED for USP47 Gene



Protein tissue co-expression partners for USP47 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of USP47 Gene:

USP47

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 expression patterns with USP47: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and 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 34 35
  • 99.73 (n)
dog
(Canis familiaris)
Mammalia USP47 34 35
  • 94.76 (n)
cow
(Bos Taurus)
Mammalia USP47 34 35
  • 94.32 (n)
oppossum
(Monodelphis domestica)
Mammalia USP47 35
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Usp47 34 16 35
  • 89.54 (n)
rat
(Rattus norvegicus)
Mammalia Usp47 34
  • 89.3 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia USP47 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP47 34 35
  • 83.22 (n)
lizard
(Anolis carolinensis)
Reptilia USP47 35
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp47 34
  • 73.69 (n)
zebrafish
(Danio rerio)
Actinopterygii usp47 35
  • 65 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Ubp64E 34 35
  • 49.66 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007106 34
  • 47.65 (n)
worm
(Caenorhabditis elegans)
Secernentea T05H10.1 35
  • 30 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP15 35
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 42 (a)
OneToMany
Species where no ortholog for USP47 was found in the sources mined by GeneCards:
  • 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

(2) 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
rs10219228 -- 11,958,704(+) TTCTA(A/G)GGCGG utr-variant-3-prime
rs10577564 -- 11,877,850(+) GTGTG(-/TGTGTGTGTG)CGCGC intron-variant
rs10578253 -- 11,946,757(+) AACAA(-/ATTAA)GAGAA intron-variant
rs10590881 -- 11,877,867(+) CGCGC(A/G)CAGAT intron-variant
rs10652918 -- 11,876,264(+) AACTC(-/TT)TTGAC intron-variant

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

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

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)

Relevant External Links for USP47 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP47

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 beta. (PMID: 21362556) Parsons J.L. … Dianov G.L. (Mol. Cell 2011) 3 4 64
  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 64
  3. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil S.A. … Gygi S.P. (Nat. Biotechnol. 2006) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. 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 64

Products for USP47 Gene

Sources for USP47 Gene

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