General Information
Symbol
Dmel\Dark
Species
D. melanogaster
Name
Death-associated APAF1-related killer
Annotation Symbol
CG6829
Feature Type
FlyBase ID
FBgn0263864
Gene Model Status
Stock Availability
Gene Snapshot
Death-associated APAF1-related killer (Dark) is an essential component of the apoptosome. Dark and the caspase Dronc form a pivotal holoenzyme required for apoptotic cell death with Dark acting as an adaptor of the multimeric complex. [Date last reviewed: 2017-03-02]
Also Known As
ark, hac-1, Apaf-1, dapaf-1, Hac1
Genomic Location
Cytogenetic map
Sequence location
2R:17,020,027..17,026,703 [+]
Recombination map
2-81
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Summaries
Gene Group Membership
APOPTOSOME -
The apoptosome is a ring-like multisubunit complex assembled upon receiving a pro-apoptotic signal. In Drosophila, Dark assembles into two stacked rings of eight subunits each. This scaffold binds ADP and an initiator caspase (Dronc in D.mel) which cleaves effector caspase(s). (Adapted from FBrf0212736).
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Dark or the JBrowse view of Dmel\Dark 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
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.50
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0086967
4883
531
FBtr0086968
4824
1440
Additional Transcript Data and Comments
Reported size (kB)
7.0 (northern blot)
5 (northern blot)
5.5 (unknown)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0086121
62.3
531
8.15
FBpp0086122
165.6
1440
6.08
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
Distinct caspases are activated by the long and short isoforms of Dark protein.
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\Dark 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 (31 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR002182
(assigned by InterPro )
inferred from sequence model
inferred from biological aspect of ancestor with PANTHER:PTN001108738
(assigned by GO_Central )
inferred from sequence or structural similarity with HGNC:576
Biological Process (24 terms)
Terms Based on Experimental Evidence (22 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from direct assay
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
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001108738
(assigned by GO_Central )
Expression Data
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
The short form of Dark transcript appears to be the minor form which is detected in embryos.
The longer form of Dark transcript appears to be the predominantly expressed form. It is detected in embyros, larvae, pupae, and S2 cells on northern blots. It is expressed ubiquitously in embryos and in larval eye and wing discs.
Dark transcripts are detected at all stages assayed on northern blots. Levels are elevated in times associated with histolysis of larval tissues (third instar larvae and early pupae). Levels are lowest in embryos and adults.
Dark transcripts are broadly distributed in preblastoderm embryos. By stage 7, transcripts are predominantly located in the ventral neurogenic region and around several invagination furrows. In stages 10-11, the highest Dark transcript levels are found in the ectoderm and mesoderm of the procephalic region. Later, expression is observed in a segmentally repeated pattern. Dark expression is induced by X-ray or UV irradiation.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Dark 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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 46 )
For All Classical and Insertion Alleles Show
 
Allele of Dark
Class
Mutagen
Associated Insertion
Stocks
Known lesion
Other relevant insertions
miscellaneous insertions
Name
Expression Data
Transgenic Constructs ( 16 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Dark
Allele of Dark
Mutagen
Associated Transgenic Construct
Stocks
Transgenic constructs containing regulatory region of Dark
Deletions and Duplications ( 4 )
Summary of Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
5 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?
5 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
5 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
3 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
4 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
1 of 15
Yes
Yes
 
Arabidopsis thaliana (thale-cress) (0)
No orthologs reported.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No orthologs reported.
Schizosaccharomyces pombe (Fission yeast) (0)
No orthologs reported.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900JR )
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) ( EOG091502J6 )
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) ( EOG090W026J )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch 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
Tribolium castaneum
Red flour beetle
Rhodnius prolixus
Kissing bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X023U )
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
Stegodyphus mimosarum
African social velvet spider
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G03E3 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 1 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    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
    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
    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
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    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)
    2R
    Recombination map
    2-81
    Cytogenetic map
    Sequence location
    2R:17,020,027..17,026,703 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    53E4-54A2
    Limits computationally determined from genome sequence between P{lacW}l(2)k09837k09837 and P{lacW}l(2)k11405k11405&P{EP}EP641; Left limit from in situ hybridisation (FBrf0157097) Right limit from in situ hybridisation (FBrf0157097)
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    54A2-54A2
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (13)
    Genomic Clones (22)
    cDNA Clones (26)
     

    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
      RNAi and Array Information
      Linkouts
      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: Dark Ark
      Source for database merge of
      Source for merge of: Ark anon-53Fa
      Source for merge of: Ark Hac1
      Source for merge of: l(2)SH0173 Ark
      Additional comments
      Changed from 'Ark' to 'Dark' to reflect common usage in the literature.
      Source for merge of Ark Hac1 was sequence comparison ( date:991227 ).
      Other Comments
      Gene expression is increased in response to the presence of two copies of Scer\GAL4hs.PB.
      Ark mutant hemocytes are completely resistant to a Smac mimetic (which antagonises inhibitor of apoptosis proteins) or cycloheximide.
      Expression of Ark in the post-embryonic central nervous system is necessary to reverse organismal lethality and to produce a viable adult.
      Ark is required for programmed cell death.
      Removal of Ark results in profound developmental defects and lethality.
      dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.
      1 allele of l(2)SH0173 recovered in a P-insertion screen.
      Loss of Ark function results in pronounced inhibition of stress-induced apoptosis, but not rpr or grim induced apoptosis.
      Loss of function mutations of Ark show reduced cell death and caspase activities in embryos.
      Loss of function mutations in Ark attenuate programmed cell deaths during development, resulting in hyperplasia of the central nervous system and other abnormalities including melanotic tumours and defective wings.
      Ark is required for normal cell death during embryonic development.
      Loss of Ark function causes reduced cell death.
      Transcription unit identified during molecular analysis of the RhoGEF2 region.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 41 )
      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
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      Linkouts
      ApoDroso - Functional genomic database for photoreceptor development, survival and function
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
      DroID - A comprehensive database of gene and protein interactions.
      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
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      KEGG Genes - Molecular building blocks of life in the genomic space.
      Synonyms and Secondary IDs (51)
      Reported As
      Symbol Synonym
      Dapaf-1/HAC-1
      Dark/Apaf-I
      Dark/Dapaf-1/HAC1
      Dark/Hac-1/dApaf-1
      Dark/Hac-1/dApaf1
      Hac-1/Dark
      anon-53Fa
      dApaf-1/DARK/HAC-1
      dark/dapaf-1/hac-1
      dark/hac-1/dapaf-1
      l(2)SH0173
      Name Synonyms
      Apaf-1 related
      Apaf-1-Related Killer
      Apaf-1-related-killer
      Death-associated APAF1-related killer
      Drosophila Apaf-1-related killer
      Transcription unit 1
      apaf1-related killer
      lethal (2) SH0173
      Secondary FlyBase IDs
      • FBgn0065914
      • FBgn0024252
      • FBgn0028733
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (252)