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General Information
Symbol
Dmel\Chc
Species
D. melanogaster
Name
Clathrin heavy chain
Annotation Symbol
CG9012
Feature Type
FlyBase ID
FBgn0000319
Gene Model Status
Stock Availability
Gene Summary
Clathrin heavy chain (Chc) encodes a protein that forms part of the clathrin complex, which is the major component of coated vesicles. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
Also Known As

clathrin, l(1)G0438

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-52
RefSeq locus
NC_004354 REGION:15827986..15835490
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (34 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:BicD; FB:FBgn0000183
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000033442
(assigned by GO_Central )
inferred from sequence or structural similarity with HGNC:2090
inferred from electronic annotation with InterPro:IPR001473, InterPro:IPR015348, InterPro:IPR016025
(assigned by InterPro )
Biological Process (19 terms)
Terms Based on Experimental Evidence (17 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
involved_in dsRNA transport
inferred from mutant phenotype
involved_in endocytosis
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:AP-2α; FB:FBgn0264855
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000033442
(assigned by GO_Central )
Cellular Component (12 terms)
Terms Based on Experimental Evidence (8 terms)
CV Term
Evidence
References
located_in cell cortex
inferred from direct assay
inferred from direct assay
inferred from direct assay
inferred from direct assay
inferred from direct assay
located_in plasma membrane
inferred from direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
is_active_in cell cortex
inferred from biological aspect of ancestor with PANTHER:PTN002568829
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001473, InterPro:IPR015348, InterPro:IPR016025
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000033442
(assigned by GO_Central )
inferred from sequence or structural similarity with HGNC:2090
inferred from biological aspect of ancestor with PANTHER:PTN000816063
(assigned by GO_Central )
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the clathrin heavy chain family. (P29742)
Summaries
Gene Snapshot
Clathrin heavy chain (Chc) encodes a protein that forms part of the clathrin complex, which is the major component of coated vesicles. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
CLATHRIN COMPLEX -
Clathrin is the major component of coated vesicles. It is a heterohexamer formed from three clathrin light chains and three heavy chains adopting a three-legged triskelion structure. To form coated vesicles, clathrin assembles into a polygonal lattice around the invaginating membrane, interacting with adaptors proteins which in-turn interact with the membrane. After membrane scission, the clatherin cage is disassembled from the vesicle. (Adapted from PMID:17702618).
Protein Function (UniProtKB)
Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.
(UniProt, P29742)
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
7
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Chc 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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry P29742)

If you don't see the viewer to the right, 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.

Comments on Gene Model

Gene model reviewed during 5.49

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

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

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0074179
5696
1678
FBtr0074180
5653
1678
FBtr0074181
5734
1678
FBtr0074182
5793
1678
FBtr0112797
5683
1678
FBtr0112798
5577
1678
FBtr0339445
5788
1678
Additional Transcript Data and Comments
Reported size (kB)

5.4 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
FBpp0073966
191.2
1678
5.46
FBpp0073967
191.2
1678
5.46
FBpp0089397
191.2
1678
5.46
FBpp0089398
191.2
1678
5.46
FBpp0111709
191.2
1678
5.46
FBpp0111710
191.2
1678
5.46
FBpp0308531
191.2
1678
5.46
Polypeptides with Identical Sequences

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

1678 aa isoforms: Chc-PA, Chc-PB, Chc-PC, Chc-PD, Chc-PE, Chc-PF, Chc-PG
Additional Polypeptide Data and Comments
Reported size (kDa)

1678 (aa); 191 (kD predicted)

Comments
External Data
Subunit Structure (UniProtKB)

Clathrin triskelions, composed of 3 heavy chains and 3 light chains, are the basic subunits of the clathrin coat (By similarity). Interacts with sau (PubMed:24786584).

(UniProt, P29742)
Domain

The C-terminal third of the heavy chains forms the hub of the triskelion. This region contains the trimerization domain and the light-chain binding domain involved in the assembly of the clathrin lattice.

The N-terminal seven-bladed beta-propeller is formed by WD40-like repeats, and projects inward from the polyhedral outer clathrin coat. It constitutes a major protein-protein interaction node (By similarity).

(UniProt, P29742)
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Chc 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 the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. 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
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

Chc transcripts are found in all cells during embryogenesis but are upregulated in gut, salivary gland, the tracheal system, and epidermis in the second half of embryogenesis. In late embryogenesis, strong expression is observed in CNS, leading edge cells, and garland cells. In third instar larvae, Chc is highly expressed in imaginal discs (including wing and eye discs), garland cells, fat body, ring gland, and salivary glands.

Chc transcripts have been detected in adult RNA.

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

Chc protein localization in developing oocytes is dynamic; a fraction of Chc protein dynamically colocalizes with BicD protein.

Chc vesicles are apically enriched in cells of tubular organs in embryos, such as the gut and trachea.

Chc protein is found in all cells during embryogenesis but are upregulated in gut, salivary gland, the tracheal system, and epidermis in the second half of embryogenesis. In late embryogenesis, strong expression is observed in CNS, leading edge cells, and garland cells. In third instar larvae, Chc is highly expressed in imaginal discs (including wing and eye discs), garland cells, fat body, ring gland, and salivary glands.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cell cortex
inferred from direct assay
inferred from direct assay
inferred from direct assay
inferred from direct assay
inferred from direct assay
located_in plasma membrane
inferred from direct assay
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Chc 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
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 ( 14 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 28 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Chc
Transgenic constructs containing regulatory region of Chc
Aberrations (Deficiencies and Duplications) ( 9 )
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
spermatid & nucleus
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
12 of 15
No
Yes
2 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
2 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
11 of 13
Yes
Yes
2 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
9 of 12
Yes
Yes
2 of 12
No
Yes
Danio rerio (Zebrafish) (3)
14 of 15
Yes
Yes
9 of 15
No
Yes
6 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
9 of 9
Yes
Yes
9 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
13 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
11 of 12
Yes
Yes
Other Organism Orthologs (via OrthoDB)
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 ( 1 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 4 )
    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.
    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:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    RNA-protein
    Physical Interaction
    Assay
    References
    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
    Subunit Structure (UniProtKB)
    Clathrin triskelions, composed of 3 heavy chains and 3 light chains, are the basic subunits of the clathrin coat (By similarity). Interacts with sau (PubMed:24786584).
    (UniProt, P29742 )
    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
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
    External Data
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-52
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    13F5-13F7
    Limits computationally determined from genome sequence between P{EP}BEST:RE35685EP1581&P{EP}sdEP1088 and P{EP}Gβ13FEP1071
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    13F1-13F4
    (determined by in situ hybridisation)
    13F2-13F2
    (determined by in situ hybridisation)
    Determined by comparing Celera genomic sequence with sequence from BDGP BAC and P1 clones.
    Experimentally Determined Recombination Data
    Location
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (20)
    Genomic Clones (20)
    cDNA Clones (263)
     

    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)
    Other 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: Chc CG9012

    Source for database merge of

    Source for merge of: Chc l(1)G0438

    Additional comments

    FlyBase curator comment: the insertion in the "e03916" Exelixis line (PBac{RB}CG32582e03916) was originally assigned to the Chc gene in FBrf0179797, resulting in the "Chce03916" (FBal0160701) allele. However, FBrf0184340 shows that the insertion is actually within CG32582.

    Other Comments

    dsRNA made from templates generated with primers directed against Chc that is transfected into S2 treated with Listeria monocytogenes reveals Chc to be involved in Listeria monocytogenes entry and intracellular growth.

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

    Candidate gene for cyst presence/absence quantitative trait locus.

    Maternally derived Chc allows the survival of Chc mutants through most of embryonic development, but is insufficient for hatching to larval stages.

    Chc has been cloned and homologies found with rat clathrin heavy chains.

    Chc gene has been cloned and characterized.

    One of 16 complementation groups identified in a screen for mutations that fail to complement Df(1)sd72b for viability.

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 81 )
    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.
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    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
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    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
    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    KEGG Genes - Molecular building blocks of life in the genomic space.
    MARRVEL_MODEL - MARRVEL (model organism gene)
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (19)
    Reported As
    Symbol Synonym
    Chc
    (van de Leemput et al., 2022, Atienza-Manuel et al., 2021, Bouska and Bai, 2021, Evans et al., 2021, Wang et al., 2021, Maurer et al., 2020, Nakamura et al., 2020, Zheng et al., 2020, Kim et al., 2019, Laffafian and Tepass, 2019, Myat et al., 2019, Ogi et al., 2019, Weiss et al., 2019, Camuglia et al., 2018, Zong et al., 2018, Kamalesh et al., 2017, Laflamme et al., 2017, Transgenic RNAi Project members, 2017-, Vazquez-Pianzola et al., 2017, Fang et al., 2016, Iwanami et al., 2016, Dent et al., 2015, Johnson et al., 2015, Liu et al., 2015, Zang et al., 2015, Zirin et al., 2015, Ashwal-Fluss et al., 2014, Borner et al., 2014, de Vreede et al., 2014, Haelterman et al., 2014, Kasprowicz et al., 2014, Luck et al., 2014, Merlo et al., 2014, Sechi et al., 2014, Vazquez-Pianzola et al., 2014, Abdallah et al., 2013, Beckett et al., 2013, Kwon et al., 2013, Kwon et al., 2013, Yamamoto et al., 2013-, Zhang et al., 2013, Zhu et al., 2013, Tokusumi et al., 2012, Vazquez-Pianzola and Suter, 2012, Xie et al., 2012, Banks et al., 2011, Burgess et al., 2011, Friedman et al., 2011, Yang et al., 2011, Zhou et al., 2011, Kallappagoudar et al., 2010, Li et al., 2010, Windler and Bilder, 2010, Zhang and Ten Hagen, 2010, Christensen et al., 2009.2.28, Jiang et al., 2009, Parks and Muskavitch, 2009.3.2, Peng et al., 2009, Peralta et al., 2009, Venken et al., 2009, Wingen et al., 2009, Yan et al., 2009, Eun et al., 2008, Guo et al., 2008, Devergne et al., 2007, Kaltenbach et al., 2007, Korolchuk et al., 2007, Stuart et al., 2007, Beller et al., 2006, Otsuna and Ito, 2006, Saleh et al., 2006, Ulvila et al., 2006)
    l(1)13Fb
    l(1)VI
    Secondary FlyBase IDs
    • FBgn0014972
    • FBgn0028268
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    Study result (0)
    Result
    Result Type
    Title
    References (233)