FB2026_02 , released June 18, 2026
Gene: Dmel\knk
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General Information
Symbol
Dmel\knk
Species
D. melanogaster
Name
knickkopf
Annotation Symbol
CG6217
Feature Type
protein_coding_gene
FlyBase ID
FBgn0001321
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
knickkopf (knk) encodes a GPI-anchorded protein, needed for chitin organisation in the cuticle and the tracheal system (tracheal cuticle, tube diameter regulation & gas filling). [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

gnar

Key Links
Genomic Location
Cytogenetic map
85F13-85F13
Sequence location
Recombination map
3-49
RefSeq locus
NT_033777 REGION:10122365..10125664
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (12 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (10 terms)
Terms Based on Experimental Evidence (10 terms)
CV Term
Evidence
References
involved_in adult chitin-based cuticle development
inferred from mutant phenotype
(Li et al., 2017)
involved_in chitin-based cuticle development
inferred from mutant phenotype
(Shaik et al., 2014, Devine et al., 2005)
involved_in embryonic epithelial tube formation
inferred from mutant phenotype
(Devine et al., 2005)
involved_in larval chitin-based cuticle development
inferred from mutant phenotype
(Pesch et al., 2015)
involved_in liquid clearance, open tracheal system
inferred from high throughput mutant phenotype
(Ghabrial et al., 2011)
involved_in lumen formation, open tracheal system
inferred from high throughput mutant phenotype
(Ghabrial et al., 2011)
involved_in open tracheal system development
inferred from mutant phenotype
(Moussian et al., 2006, Beitel and Krasnow, 2000)
involved_in regulation of tube architecture, open tracheal system
inferred from mutant phenotype
(Moussian et al., 2006)
involved_in regulation of tube diameter, open tracheal system
inferred from mutant phenotype
(Moussian et al., 2006)
involved_in regulation of tube size, open tracheal system
inferred from mutant phenotype
(Beitel and Krasnow, 2000)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in chitin-based extracellular matrix
inferred from direct assay
(Pesch et al., 2015, Petkau et al., 2012, Moussian et al., 2006)
located_in external side of plasma membrane
inferred from direct assay
(Moussian et al., 2006)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
knickkopf (knk) encodes a GPI-anchorded protein, needed for chitin organisation in the cuticle and the tracheal system (tracheal cuticle, tube diameter regulation & gas filling). [Date last reviewed: 2019-03-14]
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
knk: knickkopf
Homozygous lethal; head skeleton defective; denticle bands narrowed; embryo rarely inverted in egg case.
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\knk 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 Q9VH23)

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 5.46

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
knk-RA
FBtr0082194
NM_141724
2674
689
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
knk-PA
FBpp0081672
77.7
689
5.89
Q9VH23
NP_649981
AAF54497
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)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\knk 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
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).

-0.63

Transcript Expression
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 15 -- 17
epithelial cell of tracheal section
(Moussian et al., 2006)
embryonic stage 16 -- 17
epidermal cell
(Moussian et al., 2006)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
pupal stage -- adult stage
organism
(Li et al., 2017)
Additional Descriptive Data

knk protein is anchored to the apical cell surface of cells in the developing tracheae and epidermis. knk protein is observed to localize to the apical and apical-lateral surface of epithelial cells in the developing trachea from embryonic stage 15, and at the apical surface of epidermal cells from embryonic stage 16.

(Moussian et al., 2006)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in chitin-based extracellular matrix
inferred from direct assay
(Pesch et al., 2015, Petkau et al., 2012, Moussian et al., 2006)
located_in external side of plasma membrane
inferred from direct assay
(Moussian et al., 2006)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\knk in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 11-12
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 14 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 15 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of knk
Transgenic constructs containing regulatory region of knk
Aberrations (Deficiencies and Duplications) ( 7 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\THBD
2 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Thbd
2 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Thbd
2 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (0)
Danio rerio (Zebrafish) (0)
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\W01C8.5
10 of 14
Yes
No
Cele\H06A10.1
6 of 14
No
Yes
Anopheles gambiae (African malaria mosquito) (4)
Agam\AgaP_AGAP004500
12 of 12
Yes
Yes
Agam\AgaP_AGAP012575
5 of 12
No
Yes
Agam\AgaP_AGAP003513
4 of 12
No
No
Agam\AgaP_AGAP003887
4 of 12
No
No
Arabidopsis thaliana (thale-cress) (3)
Atha\AT5G54830
9 of 13
Yes
Yes
Atha\AT3G07570
1 of 13
No
No
Atha\AT3G61750
1 of 13
No
No
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:knk. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
CG34355
11 of 13
Skel
9 of 13
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 ( 1 )
    Human Ortholog
    Disease
    Evidence
    References
    THBD; thrombomodulin
    model of  thrombophilia due to thrombomodulin defect
    IEA
    (FlyBase, 2019-)
    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
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    knk - obst-A
    pull down, western blot
    (Petkau et al., 2012)
    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.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    External Data
    Linkouts
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-49
    Cytogenetic map
    85F13-85F13
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    85F13-85F13
    Limits computationally determined from genome sequence between P{EP}Fmr1EP3517&P{PZ}tws02414 and P{PZ}jumu06439&P{lacW}l(3)j8B6j8B6
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-49

    (FlyBase, 2016, Tearle and Nusslein-Volhard, 1987)

    3-46.6

    (Comeron et al., 2012)

    3-49.1

    Left of (cM)
    (Ostrowski et al., 2002)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (10)
    Genomic Clones (11)
     

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

    cDNA Clones (19)
     

    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
    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
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
     

    polyclonal

    (Moussian et al., 2006)
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments

        knk is an apical GPI-linked protein that acts at the plasma membrane. knk is required for chitin filament assembly in the tracheal lumen and cuticle.

        (Moussian et al., 2006)

        Mutation in knk alters tracheal tube size in embryos without affecting other aspects of tracheal development including primary branch budding and outgrowth or branch fusion.

        (Beitel and Krasnow, 2000)

        Zygotically active locus involved in the terminal developmental program in the embryo.

        (Strecker et al., 1991)

        knk mutants display a defective head skeleton, narrow denticle bands and the embryo is rarely inverted in the egg case.

        (Jurgens et al., 1984)
        Relationship to Other Genes
        Source for database merge of

        Source for merge of: knk CG6217

        (Ostrowski et al., 2002)

        Source for merge of: knk gnar

        (Devine et al., 2005)
        Additional comments

        One allele is temperature-sensitive.

        Nomenclature History
        Source for database identify of
        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (10)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 34 )
        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/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.
        UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        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.
        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
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        FlyMine - An integrated database for Drosophila genomics
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Linkouts
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (78)