FB2019_05, released Oct 15, 2019

Gene: Dmel\Vps60

Open Close
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
3 publicly available
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]
Other Summaries
Key Links
Genomic Location
Cytogenetic map
74E2-74E2
Sequence location
3L:17,620,123..17,621,625 [-]
Recombination map
3-45
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
GO Summary Ribbons
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the SNF7 family. (Q9VVI9)
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
-
Summaries
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 GBrowse view of Dmel\Vps60 or 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
Comments on Gene Model
Gene model reviewed during 5.46
Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
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
RefSeq ID
GenBank
Vps60-PA
FBpp0074964
25.2
226
4.35
NP_648997
AAF49322
Vps60-PB
FBpp0305334
25.2
226
4.35
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
Gene Ontology (3 terms)
Molecular Function (0 terms)
There is no information supporting a Molecular Function term for this gene. (Based on a review of available data on: 2013-10-07 )
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
endosome transport via multivesicular body sorting pathway
inferred from sequence or structural similarity with SGD:S000002894
(FlyBase Curators, 2008--)
vacuolar transport
inferred from electronic annotation with InterPro:IPR005024
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
ESCRT III complex
non-traceable author statement
(Capalbo et al., 2012)
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
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
• membrane
(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

GBrowse - Visual display of RNA-Seq signals

View Dmel\Vps60 in GBrowse 2
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
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Vps60
Transgenic constructs containing regulatory region of Vps60
Deletions and Duplications ( 1 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\CHMP5
14 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Chmp5
13 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Chmp5
13 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\chmp5
11 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
Drer\chmp5b
14 of 15
Yes
Yes
Drer\chmp5a
11 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\vps-60
14 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\VPS60.1
9 of 9
Yes
Yes
Atha\VPS60.2
9 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\VPS60
14 of 15
Yes
Yes
Scer\SNF7
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPCC162.06c
12 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190G1V )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\Vps60
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00010432
Drosophila simulans
Dsim\GD12393
Drosophila sechellia
Dsec\GM24320
Drosophila erecta
Dere\GG15798
Drosophila yakuba
Dyak\GE22134
Drosophila ananassae
Dana\GF23900
Drosophila pseudoobscura pseudoobscura
Dpse\GA19474
Drosophila persimilis
Dper\GL25031
Drosophila willistoni
Dwil\GK10800
Drosophila virilis
Dvir\GJ13097
Drosophila mojavensis
Dmoj\GI12953
Drosophila grimshawi
Dgri\GH15350
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150B6T )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17005403
Musca domestica
House fly
Mdoa\17004426
Glossina morsitans
Tsetse fly
Gmor\GMOY003170
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_12874
Mayetiola destructor
Hessian fly
Mdes\Mdes010856
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL012313
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL005797
Anopheles darlingi
American malaria mosquito
Adar\ADAC001477
Anopheles gambiae
Malaria mosquito
Agam\AGAP005100
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015382
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ016047
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0EB8 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA002470
Danaus plexippus
Monarch butterfly
Dple\DPOGS208897-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL015774
Apis florea
Little honeybee
Aflo\2168833060
Apis mellifera
Western honey bee
Amel\LOC408939
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP21634
Bombus terrestris
Buff-tailed bumblebee
Bter\15207159
Linepithema humile
Argentine ant
Lhum\LH10690
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:001499
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG008710
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_07747
Tribolium castaneum
Red flour beetle
Tcas\TC004434
Pediculus humanus
Human body louse
Phum\PHUM125160
Rhodnius prolixus
Kissing bug
Rpro\RPRC002491
Cimex lectularius
Bed bug
Clec\CLEC003792
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI001352
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_09623
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0EA1 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR015661
Ixodes scapularis
Black-legged tick
Isca\ISCW023077
Stegodyphus mimosarum
African social velvet spider
Smim\KFM78962.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur11g03300
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_307757
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0LIN )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Chmp5
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000004764
Gallus gallus
Domestic chicken
Ggal\CHMP5
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (3)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG5498
1 of 10
shrb
1 of 10
Vps20
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 ( 0 )
    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?
    CHMP5; charged multivesicular body protein 5
    14 of 15
    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
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement
        View in Interactions Browser
        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Vps60
        suppressible
        N
        (Berns et al., 2014)
        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.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Gene Group - Pathway Membership (FlyBase)
        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
        3-45
        Cytogenetic map
        74E2-74E2
        Sequence location
        3L:17,620,123..17,621,625 [-]
        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 (3)
        Genomic Clones (12)
         

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

        cDNA Clones (45)
         

        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)
          BDGP DGC clones
          Other 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: Vps60 CG6259
          (Berns et al., 2014)
          Source for database merge of
          Source for merge of: CG6259 anon-74EFb
          (FlyBase, 1996-)
          Additional comments
          Other Comments
          Identification: 1.2kb transcript identified during molecular analysis of the Eip74EF genomic region.
          (Burtis et al., 1990)
          Origin and Etymology
          Discoverer
          Etymology
          Named 'Vps60' after the yeast ortholog.
          (Berns et al., 2014)
          Identification
          External Crossreferences and Linkouts ( 37 )
          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/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)
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
          modMine - A data warehouse for the modENCODE project
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          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.
          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 (7)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (38)