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General Information
Symbol
Dmel\Vps4
Species
D. melanogaster
Name
Vacuolar protein sorting 4
Annotation Symbol
CG6842
Feature Type
FlyBase ID
FBgn0283469
Gene Model Status
Stock Availability
Gene Summary
Vacuolar protein sorting 4 (Vps4) encodes an AAA family ATPase. It catalyzes the ATP-dependent dissociation of class E VPS proteins from endosomal membranes. It functions in endosomal sorting of cargo into the multivesicular body for lysosomal degradation, abscission during cell division, virus release and nuclear envelope membrane sealing after cell division. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)
Also Known As

BcDNA:GH02678 , dvps4

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-59
RefSeq locus
NC_004354 REGION:17907692..17911097
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (15 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables ATP binding
inferred from electronic annotation with InterPro:IPR003959, InterPro:IPR003960
(assigned by InterPro )
inferred from sequence or structural similarity with UniProtKB:O75351
inferred from sequence or structural similarity with SGD:S000006377
Biological Process (11 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
involved_in neuron remodeling
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:Ras85D; FB:FBgn0003205
inferred from genetic interaction with FLYBASE:Egfr; FB:FBgn0003731
inferred from genetic interaction with FLYBASE:rho; FB:FBgn0004635
inferred from genetic interaction with FLYBASE:spi; FB:FBgn0005672
inferred from mutant phenotype
inferred from mutant phenotype
inferred from high throughput mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000553912
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000553912
(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
located_in endosome
inferred from sequence or structural similarity with UniProtKB:P52917
inferred from sequence or structural similarity with UniProtKB:P52917
Gene Group (FlyBase)
Protein Family (UniProt)
-
Summaries
Gene Snapshot
Vacuolar protein sorting 4 (Vps4) encodes an AAA family ATPase. It catalyzes the ATP-dependent dissociation of class E VPS proteins from endosomal membranes. It functions in endosomal sorting of cargo into the multivesicular body for lysosomal degradation, abscission during cell division, virus release and nuclear envelope membrane sealing after cell division. [Date last reviewed: 2019-03-21]
Gene Group (FlyBase)
VPS4-VTA1 COMPLEX -
The ESCRT (Endosomal Sorting Complexes Required for Transport) machinery is made up of five complexes, ESCRT-0 to -III and the Vps4-Vta1 ATPase complex, which are sequentially recruited to the cytosolic face of the membrane, and mediate cargo recognition, membrane budding and fission. The Vps4-Vta1 complex catalyzes disassembly of the ESCRT-III filament around the neck of the budding vesicle in an ATP-driven reaction, resulting in membrane scission and recycling of the ESCRT-III components back to the cytosol. (Adapted from PMID:22361144 and FBrf0209668).
OTHER ATPASES -
The 'other ATPases group comprises ATPases that do not fit into any of the other major ATPase groups.
Pathway (FlyBase)
Positive Regulators of EGFR Signaling Pathway -
Positive regulators of Epidermal Growth Factor Receptor signaling up-regulate the pathway, enhancing the activation of ERK kinase (rl) or acting on downstream effectors.
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Vps4 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 Q9Y162)

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 5.50

Low-frequency RNA-Seq exon junction(s) not annotated.

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.51

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0074504
2031
442
FBtr0342787
2411
442
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
FBpp0074278
49.6
442
6.96
FBpp0309628
49.6
442
6.96
Polypeptides with Identical Sequences

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

442 aa isoforms: Vps4-PA, Vps4-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\Vps4 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
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
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\Vps4 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
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
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Vps4
Transgenic constructs containing regulatory region of Vps4
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
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
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
actin filament & dorsal mesothoracic disc, with Scer\GAL4Bx-MS1096-KE
actin filament & egg chamber, with Scer\GAL4hs.PB
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
13 of 15
Yes
Yes
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
12 of 15
No
Yes
1 of 15
No
No
Rattus norvegicus (Norway rat) (3)
12 of 13
Yes
Yes
11 of 13
No
Yes
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (3)
12 of 12
Yes
Yes
7 of 12
No
Yes
1 of 12
No
No
Danio rerio (Zebrafish) (3)
11 of 15
Yes
Yes
8 of 15
No
Yes
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
8 of 9
Yes
Yes
1 of 9
No
Yes
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
13 of 15
Yes
Yes
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
10 of 12
Yes
Yes
Other Organism Orthologs (via OrthoDB)
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (7)
3 of 10
2 of 10
2 of 10
2 of 10
2 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 ( 1 )
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
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
Linkouts
BioGRID - A database of protein and genetic interactions.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Positive Regulators of EGFR Signaling Pathway -
Positive regulators of Epidermal Growth Factor Receptor signaling up-regulate the pathway, enhancing the activation of ERK kinase (rl) or acting on downstream effectors.
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)
X
Recombination map
1-59
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
16F1-16F2
Limits computationally determined from genome sequence between P{EP}EP1464 and P{EP}EP970
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (7)
Genomic Clones (4)
 

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (46)
 

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)
RNAi and Array Information
Linkouts
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: Vps4 CG6842

Source for database merge of

Source for merge of: Vps4 3B1

Additional comments
Other Comments

Vps4 is required cell autonomously for dendrite pruning in sensory neurons.

S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.

dsRNA made from templates generated with primers directed against CG6842 that is transfected into S2 treated with Listeria monocytogenes reveals CG6842 to be involved in Listeria monocytogenes entry, intracellular growth and vacuolar escape.

Origin and Etymology
Discoverer
Etymology
Identification
External Crossreferences and Linkouts ( 39 )
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.
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
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)
Linkouts
BioGRID - A database of protein and genetic interactions.
KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
MIST (genetic) - An integrated Molecular Interaction Database
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 (12)
Reported As
Name Synonyms
CG6842
Vacuolar protein sorting 4
vacuolar protein sorting 4
Secondary FlyBase IDs
  • FBgn0264354
  • FBgn0027605
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
Study result (0)
Result
Result Type
Title
References (91)