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General Information
Symbol
Dmel\g
Species
D. melanogaster
Name
garnet
Annotation Symbol
CG10986
Feature Type
FlyBase ID
FBgn0001087
Gene Model Status
Stock Availability
Gene Snapshot
garnet (g) encodes a protein that forms the Adaptor protein 3 (AP-3) complex together with the other subunits encoded by or, rb and cm. These complexes select cargo for inclusion into vesicles for transport within the cell. AP-3 delivers protein cargo to a number of specialized organelles including pigment granules, late endosomes, lysosomes and synaptic vesicles. AP-3 genes were first found through defects in pigment granules that alter eye color. [Date last reviewed: 2019-03-07]
Also Known As
AP-3δ, apl5
Key Links
Genomic Location
Cytogenetic map
Sequence location
X:13,727,204..13,736,278 [-]
Recombination map
1-45
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the adaptor complexes large subunit family. (P54362)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
Summaries
Gene Group (FlyBase)
ADAPTOR PROTEIN COMPLEX 3 -
Adaptor protein (AP) complexes select cargo for inclusion into coated vesicles in the late secretory and endocytic pathways. AP complexes are heterotetramers. AP-3 is associated with endosomes and, to a less extent, the trans-Golgi network and appears to function independently of clathrin. Drosophila AP-3 genes were first linked to defects in the biogenesis of visual pigment granules. (Adapted from FBrf0129983 and PMID:15066634).
Protein Function (UniProtKB)
Part of the AP-3 complex, an adapter-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes (By similarity). May be a coat protein involved in the formation of specialized structures like pigment granules.
(UniProt, P54362)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
g: garnet
Eye color brownish, darkening with age; both pteridine and ommochrome pigments variably reduced in different alleles, giving rise to such descriptions as deep purplish ruby, pinkish, brownish, yellowish ruby, orange, etc. Nolte (1959, Heredity 13: 233-41) measured both pigments spectroscopically for g alleles (g1,g2,g3,g4) and detected subtle differences. Hexter (1963, Proc. Nat. Acad. Sci. USA 50: 372-79) claims g1,g2,g3, and g4 indistinguishable phenotypically but g53d to be orange eyed and easily separable. Earlier authors claims g2 lighter than g1. Pigmentation of Malpighian tubules also reduced (Brehme and Demerec, 1942, Growth 6: 351-56). Eye color (g2) autonomous in transplants into wild type host (Beadle and Ephrussi, 1936, Genetics 21: 225-47).
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
3

Please see the GBrowse view of Dmel\g or the JBrowse view of Dmel\g 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 5.39
Low-frequency RNA-Seq exon junction(s) not annotated.
Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.
Gene model reviewed during 5.45
Gene model reviewed during 5.54
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0073842
3853
1034
FBtr0331709
4147
1033
FBtr0331710
3993
967
Additional Transcript Data and Comments
Reported size (kB)
4.0, 3.8 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0073673
114.8
1034
7.31
FBpp0304098
114.7
1033
7.16
FBpp0304099
107.0
967
6.89
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
1034 (aa); 115 (kD predicted)
Comments
External Data
Subunit Structure (UniProtKB)
Adaptor protein complex 3 (AP-3) is a heterotetramer composed of two large chains (delta and beta3), a medium chain (mu3) and a small chain (sigma3).
(UniProt, P54362)
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\g 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 (29 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from sequence or structural similarity with FLYBASE:AP-2α; FB:FBgn0264855
Biological Process (20 terms)
Terms Based on Experimental Evidence (10 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from expression pattern
(assigned by UniProt )
inferred from direct assay
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (10 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000513028
(assigned by GO_Central )
non-traceable author statement
(assigned by UniProt )
inferred from biological aspect of ancestor with PANTHER:PTN000513025
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000513025
(assigned by GO_Central )
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN000513028
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000513025
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000513028
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000513028
(assigned by GO_Central )
Cellular Component (8 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000513025
(assigned by GO_Central )
non-traceable author statement
(assigned by UniProt )
inferred from biological aspect of ancestor with PANTHER:PTN000513025
(assigned by GO_Central )
non-traceable author statement
(assigned by UniProt )
inferred from biological aspect of ancestor with PANTHER:PTN000513028
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000513028
(assigned by GO_Central )
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
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\g in GBrowse 2
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
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
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 64 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of g
Transgenic constructs containing regulatory region of g
Deletions and Duplications ( 54 )
Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 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
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
10 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
7 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
13 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
8 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
12 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
10 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091902VD )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915015M )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W031H )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X02YC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G04IL )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
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 ( 4 )
    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?
    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

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    suppressible
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Adaptor protein complex 3 (AP-3) is a heterotetramer composed of two large chains (delta and beta3), a medium chain (mu3) and a small chain (sigma3).
    (UniProt, P54362 )
    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 (genetic) - An integrated Molecular Interaction Database
    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.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-45
    Cytogenetic map
    Sequence location
    X:13,727,204..13,736,278 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    12B4-12B4
    Limits computationally determined from genome sequence between P{EP}NFATEP1390&P{EP}CG11164EP1396 and P{EP}gEP514
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    12B6-12B7
    Determined by comparing Celera genomic sequence with sequence from BDGP BAC and P1 clones.
    Experimentally Determined Recombination Data
    Location
    Notes
    Stocks and Reagents
    Stocks (86)
    Genomic Clones (21)
    cDNA Clones (47)
     

    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)
    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 database merge of
    Source for merge of: g CG11197
    Source for merge of: g CG10986
    Additional comments
    Other Comments
    Shows genomic imprinting on Dp(1;f)LJ9. These variegating phenotypes persist for one generation only, i.e. is reset by passage through the germ line. The imprint is a response to the physiological sex of the parent, and does not depend on the particular allele of g opposite Dp(1;f)LJ9. Factors that affect position effect variegation influence the somatic expression but not the establishment of the imprinting.
    The eye pigmentation defect of g mutants suggests the protein is required for proper biogenesis of eye pigment granules.
    Eye color brownish, darkening with age; both pteridine and ommochrome pigments variably reduced in different alleles, giving rise to such descriptions as deep purplish ruby, pinkish, brownish, yellowish ruby, orange, etc.
    Lesions in g reduce or eliminate pigmentation in the eyes and ocelli and block pigmentation of the fat body and tubules: g is required for normal pigmentation of all four tissues.
    Pteridines (neodrosopterin, drosopterin, isodrosopterin, aurodrosopterin, 6-acetyl-dihydrohomopterin, sepiapterin, dihydrobiopterin, biopterin, pterin and isoxanthopterin) have been quantified in single and double mutants.
    It is likely that this gene is required for the normal transport of eye-pigment precursors.
    Pigmentation of Malpighian tubules also reduced.
    Origin and Etymology
    Discoverer
    Bridges, 19th Feb. 1915.
    Etymology
    Identification
    External Crossreferences and Linkouts ( 50 )
    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)
    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
    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 (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (15)
    Reported As
    Secondary FlyBase IDs
    • FBgn0001800
    • FBgn0030516
    • FBgn0030517
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (210)