FlyBase Gene Report: Dmel\bnk

General Information

Symbol

Dmel\bnk

Species

D. melanogaster

Name

bottleneck

Annotation Symbol

CG1480

Feature Type

protein_coding_gene

FlyBase ID

FBgn0004389

Gene Model Status

Current

Stock Availability

3 publicly available

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)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

100B5-100B5

Sequence location

3R:31,193,362..31,194,389 [+]

Recombination map

3-102

RefSeq locus

NT_033777 REGION:31193362..31194389

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (10 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables actin filament binding

inferred from direct assay

(Krueger et al., 2019)

enables phosphatidylinositol-3,4,5-trisphosphate binding

inferred from direct assay

(Reversi et al., 2014)

enables phosphatidylinositol-4,5-bisphosphate binding

inferred from direct assay

(Reversi et al., 2014)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (5 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in actin filament bundle assembly

inferred from direct assay

(Krueger et al., 2019)

involved_in actin filament bundle organization

inferred from direct assay

(Reversi et al., 2014)

involved_in regulation of embryonic cell shape

inferred from mutant phenotype

(Reversi et al., 2014)

involved_in syncytial embryo cellularization

inferred from mutant phenotype

(Krueger et al., 2019)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in actin filament organization

traceable author statement

(Mazumdar and Mazumdar, 2002)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in actin filament

inferred from direct assay

(Schejter and Wieschaus, 1993)

colocalizes_with stress fiber

inferred from direct assay

(Reversi et al., 2014)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in actin filament

non-traceable author statement

(Tepass et al., 2001)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

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

Number of Unique Polypeptides

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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry P40794)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.47

Gene model reviewed during 5.53

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

bnk-RA

FBtr0085754

NM_079865

1028

303

Additional Transcript Data and Comments

Reported size (kB)

1.2 (northern blot)

(Schejter and Wieschaus, 1993)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

bnk-PA

FBpp0085116

33.6

303

10.68

P40794

NP_524604

AAF57125

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)

(Schejter and Wieschaus, 1993)

Comments

External Data

Crossreferences

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

P40794

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.

bnk_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.19

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 5 -- 9

Comment: 2-4 hr AEL

(Schejter and Wieschaus, 1993)

embryonic cycle 14

organism

(Lecuit et al., 2002)

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.

(Lecuit et al., 2002)

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.

(Schejter and Wieschaus, 1993)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 5

furrow canal | restricted

(Thomas and Wieschaus, 2004)

Additional Descriptive Data

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

(Thomas and Wieschaus, 2004, Schejter and Wieschaus, 1993)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in actin filament

inferred from direct assay

(Schejter and Wieschaus, 1993)

colocalizes_with stress fiber

inferred from direct assay

(Reversi et al., 2014)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\bnk in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\bnk

View exonic expression by tissue for Dmel\bnk

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

43687/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004389

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004389

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004389

Flygut - An atlas of the Drosophila adult midgut

FBgn0004389

Images

FlyBase Wiki

Image Based Resources

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 )

Inferred from experimentation ( 8 )

Gene disrupted in

Df(3R)A113

(Schejter and Wieschaus, 1993)

Df(3R)chp^J1

(Schejter and Wieschaus, 1993)

Df(3R)Exel6218

(Ryder, 2004.4.26)

Df(3R)Exel7379

(Ryder, 2004.4.26)

Df(3R)tll-e

(Schejter and Wieschaus, 1993)

Ts(YLt;3Lt)P60

(Muller et al., 1999)

Gene duplicated in

Dp(3;1)48

(Schejter and Wieschaus, 1993)

Gene not disrupted in

Df(3R)tll-g

(Schejter and Wieschaus, 1993)

Inferred from location ( 5 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Other Phenotypes

Allele

wild-type

bnk^+t2.8

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:bnk. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (0)

Human Disease Associations

FlyBase Human Disease Model Reports

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 v9.1 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

Interaction Browsers

Summary of Genetic Interactions

Interaction Browsers

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.

FBgn0004389

MIST (protein-protein) - An integrated Molecular Interaction Database

43687

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-102

Cytogenetic map

100B5-100B5

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}dco^rK215 and P{PZ}l(3)rM731^rM731

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

100B7-100C1

(determined by in situ hybridisation)

(Schejter and Wieschaus, 1992)

Experimentally Determined Recombination Data

Location

3-102

(FlyBase, 2016)

3-99.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

67354

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06459}attP40

1480R-1

v102160

Genomic Clones (29)

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

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

RT02911

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.

FBgn0004389

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004389

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Reversi et al., 2014, Thomas and Wieschaus, 2004, Schejter and Wieschaus, 1993)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

bnk acts as a crosslinker/stabiliser of actin filaments.

(Reversi et al., 2014)

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

(Kiger et al., 2003)

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

(Davies, 2001.3.15)

Phenotypic analysis is based on deficiency chromosomes.

(Schejter and Wieschaus, 1993)

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.

(Schejter and Wieschaus, 1993)

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

(Schejter and Wieschaus, 1991)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: bnk CG1480

(Yao, 1999.11)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Name Synonyms

Bottleneck

(Schmidt and Grosshans, 2018)

bottleneck

(Reversi et al., 2014, Abdu et al., 2006, Pilot et al., 2006, ten Bosch et al., 2006, Schejter et al., 1997)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 24 )

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.

43687

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.

P40794

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

P40794

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.

P40794

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

43687/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004389

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004389

FlyMine - An integrated database for Drosophila genomics

FBgn0004389

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG1480

MARRVEL_MODEL - MARRVEL (model organism gene)

43687

Linkouts

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0004389

DroID - A comprehensive database of gene and protein interactions.

FBgn0004389

DRSC - Results frm RNAi screens

FBgn0004389

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

bnk_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004389

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004389

Flygut - An atlas of the Drosophila adult midgut

FBgn0004389

MIST (protein-protein) - An integrated Molecular Interaction Database

43687

References (76)

The following external sites may use different assemblies or annotations than FlyBase.

-0.19

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