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General Information
Symbol
Dmel\Usp47
Species
D. melanogaster
Name
Ubiquitin specific protease 47
Annotation Symbol
CG5486
Feature Type
FlyBase ID
FBgn0016756
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As
Ubp64E, Ubp64, E(var)3-64E, D-UBP-64E
Key Links
Genomic Location
Cytogenetic map
Sequence location
3L:5,752,973..5,761,886 [+]
Recombination map
3-15
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the peptidase C19 family. (Q24574)
Summaries
Gene Group (FlyBase)
UBIQUITIN SPECIFIC PROTEASES (DEUBIQUITINASES) -
The Ubiquitin Specific Proteases (USP) is the largest sub-family of deubiquitinases. They are cysteine proteases and catalyze the removal of ubiquitin from ubiquitin chains and ubiquitinated proteins. (Adapted from PMID:19626045).
Pathway (FlyBase)
Positive Regulators of Wnt-TCF Signaling Pathway -
Positive regulators of canonical Wnt signaling up-regulate the pathway, resulting in the enhancement of transcriptional regulation mediated by β-catenin (arm).
Protein Function (UniProtKB)
Ubiquitin-specific protease that deubiquitinates target proteins to regulate different cellular and developmental pathways (PubMed:10949024, PubMed:18160715, PubMed:26169834, PubMed:27552662). Functions downstream of Dsor1/MEK to positively regulate the Ras/MAPK signaling pathway (PubMed:27552662). Likely to modulate the pathway during various cellular and developmental processes including rl/MAPK activation by the receptors InR, Egfr and sevenless/sev (PubMed:27552662). Functions in the post-translational stabilization of rl/MAPK levels in a mechanism that is independent of rl activity and opposes the activity of the E2 enzyme Unc6 and the putative E3 ligases poe, Ufd4 and Kcmf1, which mediate the ubiquitination and proteasomal degradation of rl (PubMed:27552662). During eye development it may also act downstream of rl/MAPK to negatively regulate the Ras/MAPK signaling pathway by stabilizing the transcriptional repressor ttk and consequently inhibiting photoreceptor cell development (PubMed:18160715). This suggests that at least during eye development, it may act in both the positive and negative regulation of the Ras/MAPK signaling pathway to mediate the development of different cell types (PubMed:18160715, PubMed:27552662). Positively regulates border follicle cell migration during oogenesis by mediating the deubiquitination and stabilization of slbo (PubMed:10949024). In the wing disks it positively regulates wg signaling by stabilizing arm (PubMed:26169834). Has an effect on position-effect variegation (PubMed:8816485).
(UniProt, Q24574)
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Usp47 or the JBrowse view of Dmel\Usp47 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.44
Gene model reviewed during 5.45
Gene model reviewed during 5.56
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0077095
5475
1556
FBtr0077096
4835
1556
FBtr0306259
5493
1538
Additional Transcript Data and Comments
Reported size (kB)
5.0 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0076802
173.8
1556
5.35
FBpp0076803
173.8
1556
5.35
FBpp0297369
171.9
1538
5.43
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1556 aa isoforms: Usp47-PA, Usp47-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)
Interacts with ttk.
(UniProt, Q24574)
Crossreferences
MEROPS - An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Usp47 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (10 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002541993
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN002541993
(assigned by GO_Central )
Biological Process (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002541993
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Usp47 transcripts are detected throughout development on northern blots. The transcripts were observed to be ubiquitous and strongly expressed in embryos by in situ hybridization. The central nervous system is strongly stained in stages 14-16.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Usp47 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 16 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Usp47
Transgenic constructs containing regulatory region of Usp47
Deletions and Duplications ( 1 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (8)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
1 of 15
No
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
1 of 15
No
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
No
Yes
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (6)
9 of 13
Yes
Yes
1 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
10 of 12
Yes
Yes
1 of 12
No
Yes
1 of 12
No
Yes
Danio rerio (Zebrafish) (6)
5 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (4)
11 of 15
Yes
Yes
2 of 15
No
Yes
1 of 15
No
No
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (3)
2 of 9
Yes
No
2 of 9
Yes
No
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
2 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
1 of 12
Yes
No
1 of 12
Yes
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900JI )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500T3 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00CQ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00RB )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Stegodyphus mimosarum
African social velvet spider
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0173 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (10)
2 of 10
2 of 10
2 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Interacts with ttk.
    (UniProt, Q24574 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    Positive Regulators of Wnt-TCF Signaling Pathway -
    Positive regulators of canonical Wnt signaling up-regulate the pathway, resulting in the enhancement of transcriptional regulation mediated by β-catenin (arm).
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-15
    Cytogenetic map
    Sequence location
    3L:5,752,973..5,761,886 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    64E5-64E6
    Limits computationally determined from genome sequence between P{PZ}sinu06524 and P{PZ}Bre101640
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    64E-64E
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (8)
    Genomic Clones (23)
    cDNA Clones (185)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    BDGP DGC clones
    Other clones
      Drosophila Genomics Resource Center cDNA clones

      For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

      cDNA Clones, End Sequenced (ESTs)
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
       
      polyclonal
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of
      Source for identity of: Ubp64E CG5486
      Source for identity of: Usp47 Ubp64E
      Source for database merge of
      Source for merge of: Ubp64E BcDNA:LD12764
      Additional comments
      Changed symbol from 'Ubp64E' to 'Usp47' to make it consistent with all other 'Usp' genes in D. melanogaster named for their molecular function/orthology (that have a 'Usp' prefix and reflect the HGNC nomenclature of their human orthologs), and to avoid referring to D. melanogaster-specific cytological location. (Orthology call to human USP47 is consistent with the OrthoDB orthology shown in FlyBase, and that given in FBrf0219256 and FBrf0225968.)
      Source for merge of Ubp64E BcDNA:LD12764 was a shared cDNA ( date:030728 ).
      Other Comments
      Area matching Drosophila EST AA440949 (inverted).
      Previously localised to the second chromosome using of aneuploid segregants of T(2;3)apXa but is relocalised on the third chromosome by in situ hybridisation.
      Reduced dose of Ubp64E acts as a general enhancer of position effect variegation (PEV). Ubp64E is not a regulator of homeotic genes.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 59 )
      Sequence Crossreferences
      NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
      GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
      RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
      UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MEROPS - An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
      modMine - A data warehouse for the modENCODE project
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyMine - An integrated database for Drosophila genomics
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (21)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (77)