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General Information
Symbol
Dmel\bnk
Species
D. melanogaster
Name
bottleneck
Annotation Symbol
CG1480
Feature Type
FlyBase ID
FBgn0004389
Gene Model Status
Stock Availability
Gene Summary
bottleneck (bnk) encodes a protein involved in actin filament bundle organization. It controls the structural organization of the actomyosin network and times basal closure of the cells during cellularization. [Date last reviewed: 2018-09-06] (FlyBase Gene Snapshot)
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:31,193,362..31,194,389 [+]
Recombination map
3-102
RefSeq locus
NT_033777 REGION:31193362..31194389
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (0 terms)
Biological Process (5 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
traceable author statement
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in actin filament
inferred from direct assay
colocalizes_with stress fiber
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in actin filament
non-traceable author statement
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Snapshot
    bottleneck (bnk) encodes a protein involved in actin filament bundle organization. It controls the structural organization of the actomyosin network and times basal closure of the cells during cellularization. [Date last reviewed: 2018-09-06]
    Protein Function (UniProtKB)
    Acts as a regulator of the microfilament network governing cellularization of the embryo. Determines the timing of a key conformational transition in the cortical microfilament network: the proper coordination of membrane invagination and basal closure of the cells. To do this, bnk possibly physically links neighboring contractile units of the early cycle 14 microfilament network in a manner that prevents basal constriction until the proper stage has been reached. Bnk together with nullo and Sry-alpha may provide auxiliary functions, by acting both to stabilize a large and dynamic microfilament structure and regulate its functions.
    (UniProt, P40794)
    Gene Model and Products
    Number of Transcripts
    1
    Number of Unique Polypeptides
    1

    Please see the JBrowse view of Dmel\bnk 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 5.47

    Gene model reviewed during 5.53

    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Assoc. CDS (aa)
    FBtr0085754
    1028
    303
    Additional Transcript Data and Comments
    Reported size (kB)

    1.2 (northern blot)

    Comments
    External Data
    Crossreferences
    Polypeptide Data
    Annotated Polypeptides
    Name
    FlyBase ID
    Predicted MW (kDa)
    Length (aa)
    Theoretical pI
    RefSeq ID
    GenBank
    FBpp0085116
    33.6
    303
    10.68
    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)

    303 (aa); 33.5 (kD)

    Comments
    External Data
    Crossreferences
    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\bnk 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
    Additional Descriptive Data

    nullo and bnk are zygotically transcribed and induced during the slow phase of cellularization. These transcripts rapidly disappear at the transition to the fast phase of cellularization.

    bnk transcripts are first detected during nuclear division cycle 11. They reach a strong peak with the onset of cycle 14 and then levels drop precipitously.

    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    immunolocalization
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    Additional Descriptive Data

    bnk protein is localized to the cellularization front, where it colocalizes with myosin, during cellularization of the embryo.

    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    located_in actin filament
    inferred from direct assay
    colocalizes_with stress fiber
    inferred from direct assay
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\bnk 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
    EMBL-EBI Single Cell Expression Atlas
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    Flygut - An atlas of the Drosophila adult midgut
    Images
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 0 )
    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 bnk
    Transgenic constructs containing regulatory region of bnk
    Aberrations (Deficiencies and Duplications) ( 8 )
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Other Phenotypes
    Allele
    Phenotype manifest in
    Allele
    Orthologs
    Human Orthologs (via DIOPT v8.0)
    Homo sapiens (Human) (0)
    No records found.
    Model Organism Orthologs (via DIOPT v8.0)
    Mus musculus (laboratory mouse) (0)
    No records found.
    Rattus norvegicus (Norway rat) (0)
    No records found.
    Xenopus tropicalis (Western clawed frog) (0)
    No records found.
    Danio rerio (Zebrafish) (0)
    No records found.
    Caenorhabditis elegans (Nematode, roundworm) (0)
    No records found.
    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) ( EOG09190ES4 )
    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 willistoni
    Drosophila virilis
    Drosophila mojavensis
    Drosophila grimshawi
    Drosophila grimshawi
    Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150A5Y )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Musca domestica
    House fly
    Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
    No non-Dipteran orthologies identified
    Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
    No non-Insect Arthropod orthologies identified
    Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
    No non-Arthropod Metazoa orthologies identified
    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?
      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
      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 (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3R
      Recombination map
      3-102
      Cytogenetic map
      Sequence location
      3R:31,193,362..31,194,389 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      100B5-100B5
      Limits computationally determined from genome sequence between P{PZ}Aph-407028&P{PZ}dcorK215 and P{PZ}l(3)rM731rM731
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      100B7-100C1
      (determined by in situ hybridisation)
      Experimentally Determined Recombination Data
      Location
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (2)
      Genomic Clones (29)
      cDNA Clones (7)
       

      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
          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: bnk CG1480

          Source for database merge of
          Additional comments
          Other Comments

          bnk acts as a crosslinker/stabiliser of actin filaments.

          dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

          Area matching Drosophila Bottleneck gene (inverted), Acc. No. U01035.

          Phenotypic analysis is based on deficiency chromosomes.

          The expression pattern and mutant phenotype of bnk suggests a direct role in regulating the dynamic restructuring of the actin-based cytoskeleton of cellularizing embryos.

          Mutant embryos lacking the cellularization locus, bnk, exhibit a variety of defects including premature 'closing off' of the actin/myosin contractile ring.

          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 23 )
          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
          Other crossreferences
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          EMBL-EBI Single Cell Expression Atlas
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          Flygut - An atlas of the Drosophila adult midgut
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL
          modMine - A data warehouse for the modENCODE project
          Linkouts
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          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
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Synonyms and Secondary IDs (5)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (70)