FB2021_01, released Feb 18, 2021

Gene: Dmel\Vps52

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General Information
Symbol
Dmel\Vps52
Species
D. melanogaster
Name
Vacuolar protein sorting 52
Annotation Symbol
CG7371
Feature Type
protein_coding_gene
FlyBase ID
FBgn0031710
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
Key Links
Genomic Location
Cytogenetic map
25E5-25E5
Sequence location
2L:5,521,281..5,523,898 [-]
Recombination map

2-17

RefSeq locus
NT_033779 REGION:5521281..5523898
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 Ontology (GO) Annotations (10 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables small GTPase binding
inferred from physical interaction with FLYBASE:Rab4; FB:FBgn0016701
(Gillingham et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables syntaxin binding
inferred from biological aspect of ancestor with PANTHER:PTN000367098
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with HGNC:10518
(FlyBase Curators, 2008--)
Biological Process (4 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in endocytic recycling
inferred from direct assay
(Rosa-Ferreira et al., 2015)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
involved_in endocytic recycling
inferred from biological aspect of ancestor with PANTHER:PTN000367098
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with HGNC:10518
(FlyBase Curators, 2008--)
involved_in Golgi to vacuole transport
inferred from biological aspect of ancestor with PANTHER:PTN000367098
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in lysosomal transport
inferred from biological aspect of ancestor with PANTHER:PTN001021633
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in retrograde transport, endosome to Golgi
inferred from biological aspect of ancestor with PANTHER:PTN000367098
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of GARP complex
inferred from direct assay
(Rosa-Ferreira et al., 2015)
located_in trans-Golgi network
inferred from direct assay
(Rosa-Ferreira et al., 2015)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of GARP complex
inferred from biological aspect of ancestor with PANTHER:PTN000367098
(assigned by GO_Central )
(Gaudet et al., 2011)
located_in Golgi apparatus
inferred from sequence or structural similarity with HGNC:10518
(FlyBase Curators, 2008--)
located_in recycling endosome
inferred from sequence or structural similarity with HGNC:10518
(FlyBase Curators, 2008--)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
GOLGI-ASSOCIATED RETROGRADE PROTEIN COMPLEX I -
GARP is a tethering complex, which is found on the Golgi and involved in retrograde traffic from endosomes. GARP complex has been shown to exist in two versions, called GARPI and GARPII, that differ in their composition. (Adapted from FBrf0226902).
GOLGI-ASSOCIATED RETROGRADE PROTEIN COMPLEX II -
GARP is a tethering complex, which is found on the Golgi and involved in retrograde traffic from endosomes. GARP complex has been shown to exist in two versions, called GARPI and GARPII, that differ in their composition. GARPII can interact with Rab4. (Adapted from FBrf0226902).
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Vps52 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 5.44

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Vps52-RA
FBtr0079129
NM_135087
2168
662
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
Vps52-PA
FBpp0078760
77.4
662
6.61
NP_608931
AAF52254
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
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\Vps52 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 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
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of GARP complex
inferred from direct assay
(Rosa-Ferreira et al., 2015)
located_in trans-Golgi network
inferred from direct assay
(Rosa-Ferreira et al., 2015)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Vps52 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, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
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 Vps52
Transgenic constructs containing regulatory region of Vps52
Aberrations (Deficiencies and Duplications) ( 3 )
Inferred from experimentation
Gene partially disrupted in
Df(2L)cl9d1.Δ6
(Giordano et al., 2003)
Df(2L)cl9d1.Δ76
(Giordano et al., 2003)
Gene disrupted in
Df(2L)Exel6012
(Ryder, 2004.4.26)
Inferred from location
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
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\VPS52
14 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
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\Vps52
14 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Vps52
13 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\vps52
9 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\vps52
13 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\vps-52
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\POK
9 of 9
Yes
Yes
Atha\AT1G71300
7 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\VPS52
10 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\vps52
9 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091903U1 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00001081
Drosophila simulans
Dsim\GD22649
Drosophila sechellia
Dsec\GM18019
Drosophila erecta
Dere\GG24302
Drosophila yakuba
Dyak\GE18997
Drosophila ananassae
Dana\GF14751
Drosophila pseudoobscura pseudoobscura
Dpse\GA20303
Drosophila persimilis
Dper\GL25904
Drosophila willistoni
Dwil\GK15054
Drosophila virilis
Dvir\GJ17821
Drosophila mojavensis
Dmoj\GI21912
Drosophila grimshawi
Dgri\GH11452
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091502T3 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17012929
Glossina morsitans
Tsetse fly
Gmor\GMOY005846
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_05813
Mayetiola destructor
Hessian fly
Mdes\Mdes012557
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL014070
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL012115
Anopheles darlingi
American malaria mosquito
Adar\ADAC005726
Anopheles gambiae
Malaria mosquito
Agam\AGAP009739
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ005833
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02C1 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA002965
Danaus plexippus
Monarch butterfly
Dple\DPOGS211085-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL012491
Apis florea
Little honeybee
Aflo\3306192100
Apis mellifera
Western honey bee
Amel\LOC412346
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP24121
Bombus terrestris
Buff-tailed bumblebee
Bter\15206941
Linepithema humile
Argentine ant
Lhum\LH20492
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:001d07
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG000202
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_06103
Tribolium castaneum
Red flour beetle
Tcas\TC013395
Pediculus humanus
Human body louse
Phum\PHUM164360
Rhodnius prolixus
Kissing bug
Rpro\RPRC011973
Cimex lectularius
Bed bug
Clec\CLEC007152
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI009728
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_11279
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X025C )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR011923
Ixodes scapularis
Black-legged tick
Isca\ISCW015564
Stegodyphus mimosarum
African social velvet spider
Smim\KFM74812.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM74811.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur49g00060
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_204587
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G02UM )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Vps52L
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_000869gn
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000003665
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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?
    VPS52; VPS52 subunit of GARP complex
    14 of 15
    603443
        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
        View in Interactions Browser
        Please see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        Vps52 - Arl5
        pull down, peptide massfingerprinting
        (Rosa-Ferreira et al., 2015)
        Vps52 - Rab4
        pull down, peptide massfingerprinting, anti tag western blot
        (Gillingham et al., 2014, Gillingham et al., 2014, Gillingham et al., 2014)
        Vps52 - Vps50
        anti tag coimmunoprecipitation, anti tag western blot
        (Gillingham et al., 2014)
        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.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2L
        Recombination map

        2-17

        Cytogenetic map
        25E5-25E5
        Sequence location
        2L:5,521,281..5,523,898 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        25E5-25E5
        Limits computationally determined from genome sequence between P{lacW}vrik05901&P{PZ}cype03771 and P{lacW}Hel25Ek11511
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-17

        (FlyBase, 2016)

        2-18.5

        (Comeron et al., 2012)
        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 (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 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
        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: Vps52 CG7371

        (Rosa-Ferreira et al., 2015)
        Source for database merge of
        Additional comments

        FlyBase curator comment: the insertion in the "d06812" Exelixis line (P{XP}CG6907d06812) was originally assigned to the CG7371 gene in FBrf0179797, resulting in the "CG7371d06812" (FBal0161041) allele. However, FBrf0184340 shows that the insertion is actually within CG6907.

        (Bloomington Drosophila Stock Center, 2004.11.6)
        Other Comments
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 29 )
        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/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
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        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
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        FlyMine - An integrated database for Drosophila genomics
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        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 (3)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (29)