FB2024_04 , released June 25, 2024
Gene: Dmel\CkIIβ
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General Information
Symbol
Dmel\CkIIβ
Species
D. melanogaster
Name
Casein kinase II β subunit
Annotation Symbol
CG15224
Feature Type
FlyBase ID
FBgn0000259
Gene Model Status
Stock Availability
Gene Summary
Casein kinase II β subunit (CkIIβ) encodes the regulatory subunit of the CKII holoenzyme, a protein serine/threonine kinase composed of a and b subunits. Interactions have been reported with other kinases (e.g., the products of PIP4K and S6kII), the RNA-binding protein encoded by orb , the Hedgehog signaling pathway and clock proteins such as the products of tim and per. The product of CkIIβ functions in oogenesis, neurogenesis, development (brain and other tissues) as well as circadian behavior. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
Also Known As

CK2, CKII, CK2β, And, Andante

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-36
RefSeq locus
NC_004354 REGION:11792533..11801587
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (15 terms)
Molecular Function (1 term)
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
Biological Process (8 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
involved_in circadian rhythm
inferred from mutant phenotype
involved_in locomotor rhythm
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:orb; FB:FBgn0004882
inferred from mutant phenotype
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in eclosion rhythm
traceable author statement
involved_in rhythmic behavior
traceable author statement
Cellular Component (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
located_in nucleus
inferred from direct assay
is_active_in presynaptic cytosol
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000201362
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the casein kinase 2 subunit beta family. (P08182)
Summaries
Gene Snapshot
Casein kinase II β subunit (CkIIβ) encodes the regulatory subunit of the CKII holoenzyme, a protein serine/threonine kinase composed of a and b subunits. Interactions have been reported with other kinases (e.g., the products of PIP4K and S6kII), the RNA-binding protein encoded by orb , the Hedgehog signaling pathway and clock proteins such as the products of tim and per. The product of CkIIβ functions in oogenesis, neurogenesis, development (brain and other tissues) as well as circadian behavior. [Date last reviewed: 2019-03-07]
Protein Function (UniProtKB)
Participates in Wnt signaling (By similarity). Plays a complex role in regulating the basal catalytic activity of the alpha subunit.
(UniProt, P08182)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
And: Andante (J.C. Hall)
The normal free-running 24 hr periods of the circadian rhythms of eclosion and adult locomotor activity (in constant conditions) are lengthened by 1.5-2 hr/cycle; And/+ heterozygotes have a period phenotype intermediate between wild-type and mutant homozygotes (Konopka, R. Smith and Orr). The phase-response curves (PRCs) for eclosion and activity rhythms, indicating light-induced phase shifts, show a similar degree of lengthening as seen in free-running periodicities. And rhythms are highly temperature-compensated, as are those of wild-type (Konopka et al.). And males are defective in after effects on courtship behavior that are usually induced by prior exposure to mated females or very young males (Jackson et al., 1983).
CkII β: Casein kinase II, β subunit
The structural gene for the autophosphorylated, regulatory β subunit of casein kinase II (CKII).
Summary (Interactive Fly)

CkII catalytic and regulatory subunits - modulates Antennapedia's properties, restricting its activity to an appropriate level - a regulator of the active zone protein Bruchpilot - stabilizes Clock and represses its activity in circadian oscillator - promotes Hedgehog signaling by regulating both smoothened and Cubitus interrupt Myc and Casein kinase 2 target mushroom body miniature, which is required for ribosome biogenesis and cell growth of central brain neuroblasts

Gene Model and Products
Number of Transcripts
10
Number of Unique Polypeptides
5

Please see the JBrowse view of Dmel\CkIIβ 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 P08182)

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

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0073558
3121
215
FBtr0073560
1331
215
FBtr0073561
966
215
FBtr0073562
2392
235
FBtr0100540
1043
215
FBtr0299569
997
215
FBtr0307896
2376
215
FBtr0308084
1600
233
FBtr0308085
934
233
FBtr0333204
2006
234
Additional Transcript Data and Comments
Reported size (kB)

0.946 (longest cDNA)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
FBpp0073403
24.8
215
5.29
FBpp0073405
24.8
215
5.29
FBpp0073406
24.8
215
5.29
FBpp0089135
27.1
235
4.99
FBpp0288844
24.8
215
5.29
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

Additional Polypeptide Data and Comments
Reported size (kDa)

215 (aa); 24.7 (kD predicted)

28.2 (kD observed)

Comments

Two CkIIα polypeptides plus two CkIIβ polypeptides form a 130 kD tetramer.

External Data
Subunit Structure (UniProtKB)

Tetramer of two alpha and two beta subunits.

(UniProt, P08182)
Post Translational Modification

Phosphorylated by alpha subunit.

(UniProt, P08182)
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\CkIIβ 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).

-0.96

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
located_in nucleus
inferred from direct assay
is_active_in presynaptic cytosol
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\CkIIβ in JBrowse
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
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
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 22 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 34 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of CkIIβ
Transgenic constructs containing regulatory region of CkIIβ
Aberrations (Deficiencies and Duplications) ( 0 )
Variants
Variant Molecular Consequences
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 v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
14 of 14
Yes
Yes
3  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
11 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
13 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
11 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (4)
13 of 13
Yes
Yes
13 of 13
Yes
Yes
12 of 13
No
Yes
12 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
12 of 13
Yes
Yes
5 of 13
No
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
12 of 12
Yes
Yes
5 of 12
No
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:CkIIβ. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Drosophila melanogaster (Fruit fly) (17)
11 of 13
6 of 13
5 of 13
5 of 13
4 of 13
4 of 13
4 of 13
4 of 13
4 of 13
4 of 13
4 of 13
4 of 13
4 of 13
4 of 13
3 of 13
2 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 ( 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
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement
    Other Interaction Browsers

    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
    Subunit Structure (UniProtKB)
    Tetramer of two alpha and two beta subunits.
    (UniProt, P08182 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    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
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-36
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    10E3-10E3
    Limits computationally determined from genome sequence between P{EP}EP345&P{EP}EP1409 and P{EP}ATP7EP308
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    10E1-10E2
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (32)
    Genomic Clones (11)
     

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

    cDNA Clones (100)
     

    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)
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments

        Splice isoforms CkIIβ-VIIc and -VIId are dispensable for viability and for formation of normal mushroom bodies.

        CkIIβ dependant phosphorylation has a role in the circadian rhythm.

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

        The number of neurons forming the adult mushroom body is greatly reduced in CkIIβ hypomorphs.

        Mutations in CkIIβ reduce the number of mushroom body neurons (Kenyon cells).

        Stimulation of CkIIβ activity by a polyamine molecule and its binding efficiency toward CkIIβ rely not only on its number of positive charges but also on the length of its aliphatic chain.

        Casein kinase II specifically phosphorylates a set of serine residues within the cact PEST domain.

        Casein kinase II phosphorylates Ser468 (a residue in the PEST domain) of cact in vitro.

        Casein kinase II (encoded by CkIIα and CkIIβ) phosphorylates dsh in vitro. This phosphorylation is regulated by fz2, implicating a role for Casein kinase II in wg signalling.

        Genetic mosaic analysis identifies the tissues that require the CkIIβ product.

        Serine 2 and Serine 4 residues are major sites of autophosphorylation of the β subunit of casein kinase (as shown by the construction of A2 and A4 mutants in vitro). Autophosphorylation of this subunit reduces the phosphorylation of some substrate proteins in vitro (calmodulin, elongation factor 1, glycogen synthase) but not of others (casein).

        Recombinant CkII in vitro binds to spermine and this interaction is concomitant with a striking effect on the structural polymeric organisation on the kinase which in the presence of the polyamine exhibits a ring-like structure.

        Chimeric β subunits of human and Drosophila cDNA reveal that the N terminal region of the CkIIβ subunit is responsible for the requirement for the redox state during renaturation, and is also responsible for solubility and electrophoretic mobility. of S.cerevisiae deleted for both genes.

        Recombinant Casein kinase reconstituted from human and Drosophila, α and β subunits demonstrate that CkIIβ is responsible for renaturation and reconstitution of Casein kinase II dependent on the redox conditions.

        CkIIβ is primarily an inhibitor of the catalytic activity of CkIIα in the absence of salt.

        Casein kinase II-mediated phosphorylation of Top2 stimulates its activity by enhancing the ability of the enzyme to hydrolyse its high energy ATP cofactor.

        Relationship to Other Genes
        Source for database merge of

        Source for merge of: CkIIβ mbu

        Additional comments

        The 'Andante' mutant chromosome carries two independent EMS-induced mutations, one in dy (dyQ189stop) and one in CkIIβ (CkIIβAnd). The dyQ189stop mutation has no effect on rhythmicity, rather the CkIIβAnd allele is responsible for the circadian long-period phenotype of the mutant chromosome.

        Drosophila Casein kinase II α and β subunits can rescue the lethality of S.cerevisiae deleted for both genes.

        Nomenclature History
        Source for database identify of
        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (47)
        Reported As
        Symbol Synonym
        CKII-beta1
        Cask-II-b
        Ds cas kin
        dCKII beta
        Secondary FlyBase IDs
        • FBgn0027953
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 106 )
        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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        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.
        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
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        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)
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (221)