FB2025_02 , released April 17, 2025
Gene: Dmel\Vps16A
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General Information
Symbol
Dmel\Vps16A
Species
D. melanogaster
Name
Vacuolar protein sorting 16A
Annotation Symbol
CG8454
Feature Type
FlyBase ID
FBgn0285911
Gene Model Status
Stock Availability
Gene Summary
Vacuolar protein sorting 16A (Vps16A) encodes a subunit of a heterohexameric tethering complex known as homotypic fusion and protein sorting (HOPS). HOPS roles include promoting the fusion of late endosomes, autophagosomes, biosynthetic vesicles, and lysosomes, and the biogenesis of lysosome-related eye pigment granules. The product of Vps16A is also part of miniCORVET (class C core vacuole/endosome tethering), a tethering complex involved in endosome maturation in nephrocytes and blood cells. [Date last reviewed: 2019-03-28] (FlyBase Gene Snapshot)
Also Known As

Vps16, dVps16A, DmVps16, ma, maroon

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-48
RefSeq locus
NT_033777 REGION:9267019..9270224
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (22 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
contributes_to syntaxin binding
inferred from physical interaction with FLYBASE:Syx17; FB:FBgn0035540
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000301724
Biological Process (12 terms)
Terms Based on Experimental Evidence (8 terms)
CV Term
Evidence
References
inferred from mutant phenotype
involved_in crinophagy
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:ema; FB:FBgn0038427
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000301724
inferred from sequence or structural similarity with SGD:S000005966
inferred from sequence or structural similarity with SGD:S000005966
inferred from biological aspect of ancestor with PANTHER:PTN000301724
inferred from electronic annotation with InterPro:IPR016534
Cellular Component (7 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
located_in autophagosome
inferred from direct assay
inferred from direct assay
located_in cytosol
inferred from direct assay
located_in endosome
inferred from direct assay
part_of HOPS complex
inferred from direct assay
inferred from mutant phenotype
inferred from physical interaction with UniProtKB:Q24314, UniProtKB:Q5KU39, UniProtKB:Q9Y1I2
located_in lysosome
inferred from direct assay
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with SGD:S000005966
located_in cytoplasm
inferred from electronic annotation with InterPro:IPR006925, InterPro:IPR006926
is_active_in endosome
inferred from biological aspect of ancestor with PANTHER:PTN000301724
part_of HOPS complex
inferred from biological aspect of ancestor with PANTHER:PTN000301724
inferred from sequence or structural similarity with SGD:S000005966
Gene Group (FlyBase)
Protein Family (UniProt)
-
Summaries
Gene Snapshot
Vacuolar protein sorting 16A (Vps16A) encodes a subunit of a heterohexameric tethering complex known as homotypic fusion and protein sorting (HOPS). HOPS roles include promoting the fusion of late endosomes, autophagosomes, biosynthetic vesicles, and lysosomes, and the biogenesis of lysosome-related eye pigment granules. The product of Vps16A is also part of miniCORVET (class C core vacuole/endosome tethering), a tethering complex involved in endosome maturation in nephrocytes and blood cells. [Date last reviewed: 2019-03-28]
Gene Group (FlyBase)
VPS-C COMPLEXES: HOPS AND CORVET -
The heterohexameric VPS-C complexes, HOPS and CORVET have been extensively characterised in yeast. They interact with SNAREs and Rabs to promote vesicle tethering. The CORVET complex is involved in early endosome fusion, interacting with Rab5-GTP. The HOPS complex interacts with Rab7-GTP on late endosomes (multivesicular bodies) to promote fusion with the lysosomal compartment (and vacuoles) and also autophagosome-lysosome fusion. The VPS-C complexes share common subunits and CORVET to HOPS conversion intermediates (i-CORVET and i-HOPS) have been proposed to accompany early to late endosome maturation. (Adapted from PMID:19575650 and FBrf0223135).
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
ma: maroon
Eye color dull ruby, approaching wild type with age; classification slow. Larval Malpighian tubes pale yellow (Beadle, 1937, Genetics 22: 587-611). Eye color autonomous in transplant into wild-type host (Beadle and Ephrussi, 1936, Genetics 21: 230). Wild-type levels of aldehyde oxidase and xanthine dehydrogenase activity (Hickey and Singh, 1982, DIS 58: 74.)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Vps16A 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 Q9VHG1)

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 5.49

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0081979
2741
833
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
FBpp0081459
96.0
833
6.99
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

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\Vps16A using the Feature Mapper tool.

External Data
Crossreferences
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).

-0.37

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
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in autophagosome
inferred from direct assay
inferred from direct assay
located_in cytosol
inferred from direct assay
located_in endosome
inferred from direct assay
part_of HOPS complex
inferred from direct assay
inferred from mutant phenotype
inferred from physical interaction with UniProtKB:Q24314, UniProtKB:Q5KU39, UniProtKB:Q9Y1I2
located_in lysosome
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Vps16A in JBrowse
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 ( 5 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Vps16A
Transgenic constructs containing regulatory region of Vps16A
Aberrations (Deficiencies and Duplications) ( 4 )
Variants
Variant Molecular Consequences
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 v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
14 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
7 of 13
Yes
Yes
5 of 13
No
Yes
Danio rerio (Zebrafish) (1)
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
13 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
13 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
12 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
12 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Vps16A. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 1 )
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?
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

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
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.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3R
Recombination map
3-48
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
85D7-85D7
Limits computationally determined from genome sequence between P{PZ}Aats-trp03559 and P{lacW}l(3)L4092L4092
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (6)
Genomic Clones (17)
 

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

cDNA Clones (9)
 

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
      RNAi and Array Information
      Linkouts
      Antibody Information
      Laboratory Generated Antibodies
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: Vps16A Vps16

          Source for merge of: Vps16A ma

          Additional comments

          FlyBase curator comment: source for merge of Vps16 with Vps16A was comparison of the description of "Vps16" as being next to "Aats-trp" in FBrf0126862 with the region of the genome surrounding Aats-trp.

          "ma49" may be allelic with "je1" (mutation stated to be lost), which appeared in the same stock several years earlier.

          Nomenclature History
          Source for database identify of

          Source for identity of: Vps16A CG8454

          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (12)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 25 )
          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
          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.
          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
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          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
          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.
          References (78)