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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 Summary
Death-associated APAF1-related killer (Dark) encodes an essential component of the apoptosome. The products of Dark and Dronc form a pivotal holoenzyme required for apoptotic cell death with the products of Dark acting as an adaptor of the multimeric complex. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
Also Known As

ark, hac-1, Apaf-1, dapaf-1, Apaf-1 related killer

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-81
RefSeq locus
NT_033778 REGION:17020027..17026703
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (25 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables ADP binding
inferred from electronic annotation with InterPro:IPR002182
(assigned by InterPro )
inferred from sequence model
Biological Process (20 terms)
Terms Based on Experimental Evidence (20 terms)
CV Term
Evidence
References
inferred from mutant phenotype
involved_in chaeta development
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:Ank2; FB:FBgn0261788
inferred from direct assay
inferred from direct assay
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of apoptosome
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Summaries
Gene Snapshot
Death-associated APAF1-related killer (Dark) encodes an essential component of the apoptosome. The products of Dark and Dronc form a pivotal holoenzyme required for apoptotic cell death with the products of Dark acting as an adaptor of the multimeric complex. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
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).
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see 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
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
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
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

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.

The short form of Dark transcript appears to be the minor form which is detected in embryos.

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
part_of apoptosome
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
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 ( 46 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 17 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Dark
Transgenic constructs containing regulatory region of Dark
Aberrations (Deficiencies and Duplications) ( 4 )
Alleles Representing Disease-Implicated Variants
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 v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
7 of 15
Yes
Yes
0  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
6 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
7 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
5 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
5 of 15
Yes
Yes
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
2 of 15
Yes
Yes
2  
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091900JR )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
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
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 ( 2 )
    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?
    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.
    MIST (genetic) - An integrated Molecular Interaction Database
    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.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-81
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    53E4-53E4
    Limits computationally determined from genome sequence between P{lacW}l(2)k09837k09837 and P{lacW}l(2)k11405k11405&P{EP}EP641
    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 (11)
    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 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
      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 ( 49 )
      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
      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
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      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
      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.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      Linkouts
      ApoDroso - Functional genomic database for photoreceptor development, survival and function
      DroID - A comprehensive database of gene and protein interactions.
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      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 (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 (276)