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General Information
Symbol
Dmel\Ccdc56
Species
D. melanogaster
Name
Coiled-coil domain containing 56
Annotation Symbol
CG42630
Feature Type
FlyBase ID
FBgn0261353
Gene Model Status
Stock Availability
Gene Snapshot
Coiled-coil domain containing 56 (Ccdc56) encodes a small mitochondrial protein required for cytochrome c oxidase assembly and function. [Date last reviewed: 2019-03-07]
Key Links
Genomic Location
Cytogenetic map
Sequence location
3L:11,708,979..11,710,570 [+]
Recombination map

3-36

RefSeq locus
NT_037436 REGION:11708979..11710570
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (4 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001038029
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in mitochondrion
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001038029
(assigned by GO_Central )
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Model and Products
    Number of Transcripts
    1
    Number of Unique Polypeptides
    1

    Please see the JBrowse view of Dmel\Ccdc56 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 5.45

    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Assoc. CDS (aa)
    FBtr0302271
    1529
    87
    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
    RefSeq ID
    GenBank
    FBpp0291477
    9.9
    87
    9.84
    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
    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\Ccdc56 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
    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 mitochondrion
    inferred from direct assay
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\Ccdc56 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
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    Flygut - An atlas of the Drosophila adult midgut
    Images
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 3 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 4 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of Ccdc56
    Transgenic constructs containing regulatory region of Ccdc56
    Aberrations (Deficiencies and Duplications) ( 0 )
    Inferred from experimentation
    Inferred from location
    Phenotypes
    Orthologs
    Human Orthologs (via DIOPT v8.0)
    Homo sapiens (Human) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    8 of 15
    Yes
    Yes
    Model Organism Orthologs (via DIOPT v8.0)
    Mus musculus (laboratory mouse) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    8 of 15
    Yes
    Yes
    Rattus norvegicus (Norway rat) (1)
    7 of 13
    Yes
    Yes
    Xenopus tropicalis (Western clawed frog) (1)
    6 of 12
    Yes
    Yes
    Danio rerio (Zebrafish) (2)
    8 of 15
    Yes
    Yes
    5 of 15
    No
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (1)
    6 of 15
    Yes
    Yes
    Arabidopsis thaliana (thale-cress) (0)
    No records found.
    Saccharomyces cerevisiae (Brewer's yeast) (1)
    1 of 15
    Yes
    Yes
    Schizosaccharomyces pombe (Fission yeast) (1)
    2 of 12
    Yes
    Yes
    Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190JXJ )
    Organism
    Common Name
    Gene
    AAA Syntenic Ortholog
    Multiple Dmel Genes in this Orthologous Group
    Drosophila simulans
    Drosophila erecta
    Drosophila yakuba
    Drosophila ananassae
    Drosophila pseudoobscura pseudoobscura
    Drosophila persimilis
    Drosophila willistoni
    Drosophila virilis
    Drosophila mojavensis
    Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150J8U )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Musca domestica
    House fly
    Mayetiola destructor
    Hessian fly
    Aedes aegypti
    Yellow fever mosquito
    Anopheles darlingi
    American malaria mosquito
    Culex quinquefasciatus
    Southern house mosquito
    Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0Q21 )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Apis florea
    Little honeybee
    Apis mellifera
    Western honey bee
    Bombus impatiens
    Common eastern bumble bee
    Bombus terrestris
    Buff-tailed bumblebee
    Linepithema humile
    Argentine ant
    Dendroctonus ponderosae
    Mountain pine beetle
    Rhodnius prolixus
    Kissing bug
    Zootermopsis nevadensis
    Nevada dampwood termite
    Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0QDF )
    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
    Tetranychus urticae
    Two-spotted spider mite
    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
      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.
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3L
      Recombination map

      3-36

      Cytogenetic map
      Sequence location
      3L:11,708,979..11,710,570 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      68D2-68D2
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (4)
      Genomic Clones (21)
      cDNA Clones (108)
       

      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)
      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: CG42630 Ccdc56

      Source for database merge of
      Additional comments

      One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG42630 and mtTFB1.

      Annotation CG7319 split into CG42630 and CG42631 (mtTFB1) in release 5.22 of the genome annotation.

      Other Comments
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 108 )
      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 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.
      Other crossreferences
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      Flygut - An atlas of the Drosophila adult midgut
      FlyMine - An integrated database for Drosophila genomics
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      Synonyms and Secondary IDs (8)
      Reported As
      Name Synonyms
      Coiled-coil domain containing 56
      Mitochondrial Transcription Factor B1
      coiled-coil domain containing 56
      Secondary FlyBase IDs
      • FBan0007319
      • FBgn0036197
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (13)