FB2022_02, released March 29, 2022

Gene: Dmel\Vha13

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General Information
Symbol
Dmel\Vha13
Species
D. melanogaster
Name
Vacuolar H+ ATPase 13kD subunit
Annotation Symbol
CG6213
Feature Type
protein_coding_gene
FlyBase ID
FBgn0283536
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Summary
Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (By similarity). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity). In enterocytes, acts as part of a pHCl-2 sensory pathway which mediates Tor-dependent larval growth and metabolism in response to zinc availability (PubMed:32269334). Likely acts in maintaining enterocyte lysosomal acidification which consequently promotes Tor activation at the lysosome membrane (PubMed:32269334). (UniProt, Q9XZH6)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

conjoined, l(3)05113

Key Links
Genomic Location
Cytogenetic map
92A11-92A11
Sequence location
Recombination map
3-66
RefSeq locus
NT_033777 REGION:19643018..19644386
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 (6 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
contributes_to proton-transporting ATPase activity, rotational mechanism
inferred by curator from GO:0033181
(Allan et al., 2005)
enables proton-transporting ATPase activity, rotational mechanism
inferred from electronic annotation with InterPro:IPR005124
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in liquid clearance, open tracheal system
inferred from high throughput mutant phenotype
(Ghabrial et al., 2011)
involved_in terminal branching, open tracheal system
inferred from mutant phenotype
(Francis and Ghabrial, 2015)
inferred from high throughput mutant phenotype
(Ghabrial et al., 2011)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in proton transmembrane transport
inferred from electronic annotation with InterPro:IPR005124
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
inferred by curator from GO:0033181
(Allan et al., 2005)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of plasma membrane proton-transporting V-type ATPase complex
inferred from mutant phenotype
(Allan et al., 2005)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of vacuolar proton-transporting V-type ATPase complex
inferred from biological aspect of ancestor with PANTHER:PTN000295490
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the V-ATPase G subunit family. (Q9XZH6)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
VACUOLAR ATPASE V1 DOMAIN NON-CATALYTIC SUBUNITS -
The V1 domain of V-ATPases is a peripheral membrane domain composed of eight different subunits (A-H) that are expressed as multiple isoforms in a tissue-specific manner. The V1 domain is responsible for ATP hydrolysis. The non-catalytic V1 subunits do not hydrolyze ATP directly but provide regulatory functions and/or interact with the V0 domain. (Adapted from PMID:20450191 and FBrf0188241).
Protein Function (UniProtKB)
Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (By similarity). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity). In enterocytes, acts as part of a pHCl-2 sensory pathway which mediates Tor-dependent larval growth and metabolism in response to zinc availability (PubMed:32269334). Likely acts in maintaining enterocyte lysosomal acidification which consequently promotes Tor activation at the lysosome membrane (PubMed:32269334).
(UniProt, Q9XZH6)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Vha13 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 Q9XZH6)

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 5.56

Gene model reviewed during 5.54

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

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
gene
(Ghabrial et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Vha13-RA
FBtr0083804
NM_058089
703
117
Vha13-RB
FBtr0346100
NM_001300478
943
117
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
Vha13-PA
FBpp0083214
13.6
117
10.24
NP_477437
AAF55686
Vha13-PB
FBpp0311933
13.6
117
10.24
NP_001287407
AHN57406
Polypeptides with Identical Sequences

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

117 aa isoforms: Vha13-PA, Vha13-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (By similarity). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (By similarity). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits VhaAC45 and ATP6AP2 (By similarity).

(UniProt, Q9XZH6)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Vha13 using the Feature Mapper tool.

External Data
Crossreferences
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
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
part_of plasma membrane proton-transporting V-type ATPase complex
inferred from mutant phenotype
(Allan et al., 2005)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Vha13 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
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
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 Vha13
Transgenic constructs containing regulatory region of Vha13
Aberrations (Deficiencies and Duplications) ( 8 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal
lethal (with Df(3R)ED6025)
lethal | embryonic stage | rescuable maternal effect
lethal | recessive
lethal - all die before end of pupal stage, with Scer\GAL4pnr-MD237
lethal - all die during embryonic stage
lethal - all die during larval stage, with Scer\GAL4Mef2.PR
partially lethal, with Df(3R)PR29/Nup58ex1
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
sterile, with Df(3R)PR29/Nup58ex1
Other Phenotypes
Allele
abnormal cell adhesion | somatic clone | third instar larval stage
abnormal cell shape | somatic clone | third instar larval stage
abnormal developmental rate, with Scer\GAL4pHCl-2.PR
decreased feeding behavior | larval stage, with Scer\GAL4pHCl-2.PR
short lived | heat sensitive, with Scer\GAL4tin.CΔ4
some die during embryonic stage
some die during pupal stage, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
apical plasma membrane | third instar larval stage
embryonic/first instar larval cuticle
embryonic/larval tracheal dorsal trunk
embryonic/larval tracheal stalk cell | third instar larval stage
embryonic/larval tracheal system
eye | somatic clone
head
Malpighian tubule
sarcomere, with Scer\GAL4Mef2.PR
terminal tracheal cell
terminal tracheal cell | somatic clone | third instar larval stage
Z disc, with Scer\GAL4Mef2.PR
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (4)
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\ATP6V1G1
13 of 15
Yes
Yes
1  
Hsap\ATP6V1G2
13 of 15
Yes
Yes
1  
Hsap\ATP6V1G3
10 of 15
No
Yes
1  
Hsap\ATP6V1G2-DDX39B
2 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
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\Atp6v1g2
15 of 15
Yes
Yes
Mmus\Atp6v1g1
12 of 15
No
Yes
Mmus\Atp6v1g3
9 of 15
No
Yes
Rattus norvegicus (Norway rat) (3)
Rnor\Atp6v1g2
13 of 13
Yes
Yes
Rnor\Atp6v1g1
11 of 13
No
Yes
Rnor\Atp6v1g3
9 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
Xtro\atp6v1g3
10 of 12
Yes
Yes
Xtro\atp6v1g2
8 of 12
No
Yes
Xtro\atp6v1g1
6 of 12
No
Yes
Danio rerio (Zebrafish) (1)
Drer\atp6v1g1
12 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\vha-10
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
Atha\VAG2
6 of 9
Yes
Yes
Atha\VMA10
6 of 9
Yes
Yes
Atha\VATG3
5 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\VMA10
12 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\vma10
10 of 12
Yes
Yes
Other Organism Orthologs (via OrthoDB)
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?
    ATP6V1G1; ATPase H+ transporting V1 subunit G1
    13 of 15
    607296
         
        ATP6V1G2; ATPase H+ transporting V1 subunit G2
        13 of 15
        606853
             
            ATP6V1G3; ATPase H+ transporting V1 subunit G3
            10 of 15
            618071
                 
                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
                Interactions Browser
                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
                Starting gene(s)
                Interaction type
                Interacting gene(s)
                Reference
                Mitf
                suppressible
                Vha13
                (Zhang et al., 2015)
                External Data
                Subunit Structure (UniProtKB)
                V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (By similarity). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (By similarity). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits VhaAC45 and ATP6AP2 (By similarity).
                (UniProt, Q9XZH6 )
                Linkouts
                BioGRID - A database of protein and genetic interactions.
                MIST (protein-protein) - An integrated Molecular Interaction Database
                Pathways
                Signaling Pathways (FlyBase)
                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)
                3R
                Recombination map
                3-66
                Cytogenetic map
                92A11-92A11
                Sequence location
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                92A11-92A11
                Limits computationally determined from genome sequence between P{EP}EP650 and P{PZ}l(3)1058510585
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                92A11-92B1
                (Dow, 1999.4.14)
                92A13-92A14
                (determined by in situ hybridisation)
                (Spradling et al., 1999, Perrimon et al., 1996)
                92A13-92A14
                (BDGP Project Members, 1994-1999)
                Experimentally Determined Recombination Data
                Location

                3-66

                (FlyBase, 2016)

                3-68.8

                (Comeron et al., 2012)

                3-

                (Ghabrial et al., 2011)
                Left of (cM)
                Right of (cM)
                Notes

                Maps to 3R.

                (Ghabrial et al., 2011)
                Stocks and Reagents
                Stocks (8)
                Genomic Clones (16)
                 

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

                cDNA Clones (251)
                 

                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
                  Antibody Information
                  Laboratory Generated Antibodies
                   
                  Commercially Available Antibodies
                   
                  Other Information
                  Relationship to Other Genes
                  Source for database identify of
                  Source for database merge of

                  Source for merge of: Vha13 l(3)05113

                  (Spradling et al., 1999)

                  Source for merge of: Vha13 BcDNA:AT14009

                  (FlyBase, 1996-)

                  Source for merge of: Vha13 conjoined

                  (Francis and Ghabrial, 2015)
                  Additional comments

                  Source for merge of Vha13 BcDNA:AT14009 was a shared cDNA ( date:030728 ).

                  (FlyBase, 1996-)
                  Other Comments

                  dsRNA made from templates generated with primers directed against Vha13 that is transfected into S2 treated with Listeria monocytogenes reveals Vha13 to be involved in Listeria monocytogenes entry and vacuolar escape, with more bacteria observed as `clumps'.

                  (Cheng et al., 2005)

                  The autosomal "FLP-DFS" technique (using the P{ovoD1-18} P{FRT(whs)} P{hsFLP} chromosomes) has been used to identify the specific maternal effect phenotype for the zygotic lethal mutation.

                  (Perrimon et al., 1996)
                  Origin and Etymology
                  Discoverer
                  Etymology
                  Identification
                  External Crossreferences and Linkouts ( 40 )
                  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.
                  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
                  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
                  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.
                  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 (12)
                  Datasets (8)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  Study result (8)
                  Result
                  Result Type
                  Title
                  scRNAseq_2020_Cattenoz_NI_seq_clustering
                  Clustering analysis of hemocytes from non-infested third instar larvae
                  scRNAseq_2020_Cattenoz_WI_seq_clustering
                  Clustering analysis of hemocytes from wasp-infested third instar larvae
                  scRNAseq_2020_Cho_NI72LG_seq_clustering
                  Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
                  scRNAseq_2020_Cho_NI96LG_seq_clustering
                  Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
                  scRNAseq_2020_Cho_NI120LG_seq_clustering
                  Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
                  scRNAseq_2020_Cho_WI96LG_seq_clustering
                  Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
                  scRNAseq_2020_Cho_NI96HL_seq_clustering
                  Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
                  scRNAseq_2020_Cho_NI120HL_seq_clustering
                  Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
                  References (61)