FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Vps60
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General Information
Symbol
Dmel\Vps60
Species
D. melanogaster
Name
Vacuolar protein sorting 60
Annotation Symbol
CG6259
Feature Type
protein_coding_gene
FlyBase ID
FBgn0036740
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Summary
Vacuolar protein sorting 60 (Vps60) encodes a member of the Vps4 complex. It contributes to the formation of intraluminal vesicles and multi-vesicular bodies by supporting the dissociation of the ESCRT complex from the invaginating membranes on endosomes. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
74E2-74E2
Sequence location
Recombination map
3-45
RefSeq locus
NT_037436 REGION:17620123..17621625
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (9 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (6 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in symbiont entry into host cell
inferred from high throughput mutant phenotype
(Hodgson et al., 2019)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
involved_in endosome transport via multivesicular body sorting pathway
inferred from sequence or structural similarity with SGD:S000002894
(Gene Ontology Curators, 2002-)
involved_in late endosome to vacuole transport via multivesicular body sorting pathway
inferred from biological aspect of ancestor with PANTHER:PTN000509386
(GO Reference Genome Project, 2011-)
involved_in nuclear membrane reassembly
inferred from biological aspect of ancestor with PANTHER:PTN000509386
(GO Reference Genome Project, 2011-)
involved_in vacuolar transport
inferred from electronic annotation with InterPro:IPR005024
(InterPro Project Members, 2004-)
involved_in vesicle budding from membrane
inferred from biological aspect of ancestor with PANTHER:PTN000509386
(GO Reference Genome Project, 2011-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of ESCRT III complex
inferred from biological aspect of ancestor with PANTHER:PTN000509386
(GO Reference Genome Project, 2011-)
non-traceable author statement
(Capalbo et al., 2012)
is_active_in multivesicular body
inferred from biological aspect of ancestor with PANTHER:PTN000509386
(GO Reference Genome Project, 2011-)
is_active_in nuclear envelope
inferred from biological aspect of ancestor with PANTHER:PTN000509386
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the SNF7 family. (Q9VVI9)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Vacuolar protein sorting 60 (Vps60) encodes a member of the Vps4 complex. It contributes to the formation of intraluminal vesicles and multi-vesicular bodies by supporting the dissociation of the ESCRT complex from the invaginating membranes on endosomes. [Date last reviewed: 2019-03-21]
Gene Group (FlyBase)
ESCRT-III 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. ESCRT-III is a dynamic complex, that assembles on endosomes. The components of the complex are less well defined, but it has four core subunits. It assembles into a filament around the neck of the budding vesicle. ESCRT-III mediates the recruitment of deubiquitinases and, together with the Vps4-Vta1 complex, which it recruits, mediates membrane scission. (Adapted from PMID:22361144 and FBrf0209668).
Protein Function (UniProtKB)
Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and are delivered to lysosomes enabling degradation of membrane proteins (By similarity). Specifically down-regulates Notch signaling activity in the germarium, probably by facilitating Notch endocytosis (PubMed:24762813).
(UniProt, Q9VVI9)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Vps60 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
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VVI9)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.46

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Vps60-RA
FBtr0075201
NM_140740
980
226
Vps60-RB
FBtr0333123
NM_001275065
1100
226
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
Vps60-PA
FBpp0074964
25.2
226
4.35
Q9VVI9
NP_648997
AAF49322
Vps60-PB
FBpp0305334
25.2
226
4.35
Q9VVI9
NP_001261994
AGB94687
Polypeptides with Identical Sequences

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

226 aa isoforms: Vps60-PA, Vps60-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III).

(UniProt, Q9VVI9)
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\Vps60 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
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

2.44

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Vps60 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Vps60
Transgenic constructs containing regulatory region of Vps60
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3L)Exel9005
(Ryder, 2004.4.26)
Inferred from location ( 6 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (7)
Hsap\CHMP5
14 of 14
Yes
Yes
Hsap\CHMP4A
2 of 14
No
No
2  
Hsap\CHMP4B
2 of 14
No
No
6  
Hsap\CHMP4BP1
2 of 14
No
No
Hsap\CHMP4C
2 of 14
No
No
3  
Hsap\CHMP6
1 of 14
No
No
Hsap\CHMP7
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (7)
Rnor\Chmp5
14 of 14
Yes
Yes
Rnor\Chmp4bl1
2 of 14
No
No
Rnor\Chmp4b
2 of 14
No
No
Rnor\Chmp4c
2 of 14
No
No
Rnor\Chmp6
1 of 14
No
No
Rnor\Chmp7
1 of 14
No
No
Rnor\Odf2l
1 of 14
No
No
Mus musculus (laboratory mouse) (7)
Mmus\Chmp5
13 of 14
Yes
Yes
Mmus\Chmp4b
2 of 14
No
No
2  
Mmus\Chmp4c
2 of 14
No
No
1  
Mmus\Chmp6
1 of 14
No
No
Mmus\Chmp7
1 of 14
No
No
Mmus\Lama4
1 of 14
No
No
Mmus\Odf2l
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\chmp5
11 of 13
Yes
Yes
Xtro\sema4g
10 of 13
No
Yes
Xtro\chmp4b
2 of 13
No
No
Xtro\chmp7
1 of 13
No
No
Danio rerio (Zebrafish) (8)
Drer\chmp5a
13 of 14
Yes
Yes
Drer\chmp5b
13 of 14
Yes
Yes
Drer\chmp4ba
2 of 14
No
No
Drer\chmp4c
2 of 14
No
No
Drer\chmp4bb
1 of 14
No
No
Drer\chmp6a
1 of 14
No
No
Drer\chmp6b
1 of 14
No
No
Drer\chmp7
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (5)
Cele\vps-60
14 of 14
Yes
Yes
Cele\R12C12.5
2 of 14
No
No
Cele\vps-32.1
2 of 14
No
No
Cele\chmp-7
1 of 14
No
No
Cele\vps-20
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (4)
Agam\AgaP_AGAP005100
12 of 12
Yes
Yes
Agam\AgaP_AGAP005316
2 of 12
No
No
Agam\AgaP_AGAP006229
1 of 12
No
No
Agam\AgaP_AGAP012459
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (9)
Atha\VPS60.1
13 of 13
Yes
Yes
Atha\VPS60.2
13 of 13
Yes
Yes
Atha\SNF7.1
2 of 13
No
No
Atha\SNF7.2
2 of 13
No
No
Atha\AT3G62080
1 of 13
No
No
Atha\VPS2.1
1 of 13
No
No
Atha\VPS2.3
1 of 13
No
No
Atha\VPS20.1
1 of 13
No
No
Atha\VPS20.2
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (4)
Scer\VPS60
12 of 13
Yes
Yes
Scer\SNF7
2 of 13
No
No
Scer\CHM7
1 of 13
No
No
Scer\VPS20
1 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\SPCC162.06c
11 of 12
Yes
Yes
Spom\vps32
2 of 12
No
No
Spom\vps20
1 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Vps60. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (3)
shrb
3 of 13
CG5498
2 of 13
Vps20
2 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    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 v9.1 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?
    CHMP5; charged multivesicular body protein 5
    14 of 14
    610900
        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
        Summary of Genetic Interactions
        Interaction Browsers
        View in FlyBase Interactions Browser   View in MIST tool (external link)
        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Vps60
        enhanceable
        Ist1
        (Bäumers et al., 2019)
        Vps60
        suppressible
        N
        (Berns et al., 2014)
        Vps60|Ist1
        suppressible
        shrb
        (Bäumers et al., 2019)
        Vps60
        suppressible
        shrb
        (Bäumers et al., 2019)
        Vps60
        suppressible
        Vps20
        (Bäumers et al., 2019)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III).
        (UniProt, Q9VVI9 )
        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
        FlyBase
        External Links
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-45
        Cytogenetic map
        74E2-74E2
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        74E2-74E2
        Limits computationally determined from genome sequence between P{lacW}l(3)j11B2j11B2 and P{PZ}W05014
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-45

        (FlyBase, 2016)

        3-41.1

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (6)
        Genomic Clones (12)
         

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

        cDNA Clones (42)
         

        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 JBrowse 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
          Other clones
          RNAi and Array Information
          Linkouts
          DRSC - Results frm RNAi screens
          Antibody Information
          Laboratory Generated Antibodies
           
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments

              Identification: 1.2kb transcript identified during molecular analysis of the Eip74EF genomic region.

              (Burtis et al., 1990)
              Relationship to Other Genes
              Source for database merge of

              Source for merge of: CG6259 anon-74EFb

              (FlyBase, 1996-)
              Additional comments
              Nomenclature History
              Source for database identify of

              Source for identity of: Vps60 CG6259

              (Berns et al., 2014)
              Nomenclature comments
              Etymology

              Named 'Vps60' after the yeast ortholog.

              (Berns et al., 2014)
              Synonyms and Secondary IDs (8)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 38 )
              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/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
              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
              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
              FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
              FlyMine - An integrated database for Drosophila genomics
              InterPro - A database of protein families, domains and functional sites
              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.
              Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
              DroID - A comprehensive database of gene and protein interactions.
              DRSC - Results frm RNAi screens
              Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
              FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
              Flygut - An atlas of the Drosophila adult midgut
              iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
              KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
              MIST (protein-protein) - An integrated Molecular Interaction Database
              Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
              References (46)