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General Information
Symbol
Dmel\Rpt4R
Species
D. melanogaster
Name
Regulatory particle triple-A ATPase 4-related
Annotation Symbol
CG7257
Feature Type
FlyBase ID
FBgn0036224
Gene Model Status
Stock Availability
Enzyme Name (EC)
Proteasome ATPase (5.6.1.5)
Gene Summary
Contribute a Gene Snapshot for this gene.
Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-37
RefSeq locus
NT_037436 REGION:11941912..11943485
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables ATP binding
inferred from electronic annotation with InterPro:IPR003959, InterPro:IPR003960
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR003959, InterPro:IPR003960, InterPro:IPR035263
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000553037
(assigned by GO_Central )
inferred from sequence model
Biological Process (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000553116
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000553037
(assigned by GO_Central )
inferred from sequence or structural similarity with FLYBASE:Rpt4; FB:FBgn0028685
inferred from biological aspect of ancestor with PANTHER:PTN000553116
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000553116
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000553037
(assigned by GO_Central )
inferred from sequence or structural similarity with SGD:S000005785
Protein Family (UniProt)
-
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
ATP + H(2)O + polypeptide = ADP + phosphate + unfolded polypeptide (5.6.1.5)
Summaries
Gene Group (FlyBase)
PROTEASOME REGULATORY PARTICLE ATPASES -
The 26S proteasome degrades polyubiquitinated proteins in the cytoplasm and nucleus. It is formed from a cylindrical catalytic core 20S proteasome capped at each end by a regulatory 19S particle. The 19S regulatory particle recognizes, unfolds, and translocates ubiquitinated proteins into the catalytic core particle in an ATP-dependent manner. Within the regulatory particle base, six paralogous AAA-ATPases, termed Rpt1-Rpt6, associate in three pairs (Rpt1-Rpt2, Rpt3-Rpt6, Rpt4-Rpt5), which arrange into a ring to form a trimer of dimers. (Adapted from FBrf0215459 and PMID:28583440.)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Rpt4R 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
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VTQ9)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

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)
FBtr0076040
1391
398
FBtr0346545
1502
398
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
FBpp0075772
45.0
398
7.41
Polypeptides with Identical Sequences

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

398 aa isoforms: Rpt4R-PA, Rpt4R-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rpt4R using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. 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

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Rpt4R 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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 0 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Rpt4R
Transgenic constructs containing regulatory region of Rpt4R
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (7)
9 of 13
Yes
No
2 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (6)
6 of 12
Yes
No
2 of 12
No
No
2 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (7)
9 of 15
Yes
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (8)
12 of 15
Yes
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (11)
7 of 9
Yes
No
7 of 9
Yes
No
1 of 9
No
No
1 of 9
No
No
1 of 9
No
No
1 of 9
No
No
1 of 9
No
No
1 of 9
No
No
1 of 9
No
No
1 of 9
No
No
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (3)
12 of 15
Yes
No
1 of 15
No
No
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
9 of 12
Yes
No
Other Organism Orthologs (via OrthoDB)
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (8)
8 of 10
4 of 10
4 of 10
4 of 10
3 of 10
3 of 10
3 of 10
3 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 ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 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
    Interactions Browser
    Summary of Genetic Interactions
    esyN Network Diagram
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-37
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    68E3-68E3
    Limits computationally determined from genome sequence between P{PZ}CycA02461&P{PZ}CycA03946 and P{PZ}rols08232&P{lacW}l(3)j2D3j2D3
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (5)
    Genomic Clones (29)
    cDNA Clones (7)
     

    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 sequenced
    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)
    BDGP DGC clones
    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
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of

    Source for identity of: Rpt4R CG7257

    Source for database merge of
    Additional comments

    The nomenclature of genes encoding subunits of the 26S proteasome of D. melanogaster have been standardized according to FBrf0215459. These symbols/names largely follow those used already in FlyBase, and largely mirror fly community usage. HOWEVER, note that at least one other nomenclature system exists that is followed by the HUGO Gene Nomenclature Committee (HGNC), for example, with the unfortunate result that several D. melanogaster genes have shared synonyms.

    Other Comments
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 81 )
    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 Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
    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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
    UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
    EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
    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
    KEGG Genes - Molecular building blocks of life in the genomic space.
    MARRVEL_MODEL - MARRVEL (model organism gene)
    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
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (6)
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    Study result (0)
    Result
    Result Type
    Title
    References (37)