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    CLTC clathrin heavy chain [ Homo sapiens (human) ]

    Gene ID: 1213, updated on 5-Sep-2021

    Summary

    Official Symbol
    CLTCprovided by HGNC
    Official Full Name
    clathrin heavy chainprovided by HGNC
    Primary source
    HGNC:HGNC:2092
    See related
    Ensembl:ENSG00000141367 MIM:118955
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Hc; CHC; CHC17; MRD56; CLH-17; CLTCL2
    Summary
    Clathrin is a major protein component of the cytoplasmic face of intracellular organelles, called coated vesicles and coated pits. These specialized organelles are involved in the intracellular trafficking of receptors and endocytosis of a variety of macromolecules. The basic subunit of the clathrin coat is composed of three heavy chains and three light chains. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 67.0), thyroid (RPKM 49.4) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CLTC in Genome Data Viewer
    Location:
    17q23.1
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (59619895..59696956)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57697256..57774317)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371847 Neighboring gene RNA, U4 small nuclear 13, pseudogene Neighboring gene DEAH-box helicase 40 Neighboring gene Sharpr-MPRA regulatory region 22 Neighboring gene peptidyl-tRNA hydrolase 2 Neighboring gene vacuole membrane protein 1 Neighboring gene VMP1 intron CAGE-defined low expression enhancer

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    env HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    gag-pol HIV-1 particles incorporate the clathrin heavy chain together with associated light chains through HIV-1 Gag-Pol in an IN-dependent manner PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    nef The leucine-based motif of Nef is required for targeting into clathrin-associated AP complexes and the Nef-mediated alterations of trafficking of CD4 receptor PubMed
    nef Knocking down either AP-1 gamma, AP-1 mu1, or clathrin strongly inhibits Nef-induced downregulation of HLA-A2 PubMed
    nef HIV-1 Nef induces the formation of clathrin-coated pits in the presence of CD4 in human lymphocytes by interacting with components of the clathrin-coated surface domain PubMed
    Pol gag-pol Clathrin stabilizes HIV-1 Pol proteins in HIV-1 infected cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of clathrin, heavy chain (CLTC) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    vpr HIV-1 Vpr C-terminus (residues 52-96) entry into cells is mediated through clathrin- and caveolae/raft-dependent endocytosis PubMed
    integrase gag-pol Deletion of the HIV-1 IN C-terminal domain and the IN N184L/F185K mutation abolish clathrin incorporation into virions PubMed
    gag-pol HIV-1 particles incorporate the clathrin heavy chain together with associated light chains through HIV-1 Gag-Pol in an IN-dependent manner PubMed
    matrix gag HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes PubMed
    reverse transcriptase gag-pol Mutations in HIV-1 RT, including L234A, that inhibit RT dimerization abolish clathrin incorporation into virions PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0034

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables clathrin light chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables clathrin light chain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables disordered domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables double-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables low-density lipoprotein particle receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables structural molecule activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables ubiquitin-specific protease binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in amyloid-beta clearance by transcytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in clathrin coat assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in clathrin coat assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in clathrin-dependent endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mitotic cell cycle IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of hyaluronan biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of hyaluronan biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of protein localization to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in osteoblast differentiation HDA PubMed 
    involved_in receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in receptor-mediated endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of mitotic spindle organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retrograde transport, endosome to Golgi IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in transferrin transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of clathrin coat IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of clathrin coat NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of clathrin coat of coated pit IEA
    Inferred from Electronic Annotation
    more info
     
    part_of clathrin coat of trans-Golgi network vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    part_of clathrin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of clathrin complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in clathrin-coated endocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in clathrin-coated endocytic vesicle NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in clathrin-coated vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endolysosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular vesicle HDA PubMed 
    located_in focal adhesion HDA PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
     
    located_in melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    located_in mitotic spindle IDA
    Inferred from Direct Assay
    more info
     
    located_in mitotic spindle microtubule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in spindle IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in spindle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    clathrin heavy chain 1
    Names
    clathrin heavy chain on chromosome 17
    clathrin, heavy polypeptide (Hc)
    clathrin, heavy polypeptide-like 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_047043.1 RefSeqGene

      Range
      5001..82268
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001288653.2NP_001275582.1  clathrin heavy chain 1 isoform 2

      See identical proteins and their annotated locations for NP_001275582.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is longer compared to isoform 1.
      Source sequence(s)
      AC091271, AK127134
      Consensus CDS
      CCDS74115.1
      UniProtKB/TrEMBL
      A0A087WVQ6
      Related
      ENSP00000479606.1, ENST00000621829.4
      Conserved Domains (6) summary
      smart00299
      Location:12781420
      CLH; Clathrin heavy chain repeat homology
      sd00006
      Location:11091135
      TPR; TPR repeat [structural motif]
      pfam01394
      Location:202238
      Clathrin_propel; Clathrin propeller repeat
      pfam00637
      Location:14311565
      Clathrin; Region in Clathrin and VPS
      pfam09268
      Location:335358
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:360425
      Clathrin_H_link; Clathrin-H-link
    2. NM_004859.4NP_004850.1  clathrin heavy chain 1 isoform 1

      See identical proteins and their annotated locations for NP_004850.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter protein (isoform 1).
      Source sequence(s)
      AC091271, BC054489
      Consensus CDS
      CCDS32696.1
      UniProtKB/Swiss-Prot
      Q00610
      Related
      ENSP00000269122.3, ENST00000269122.8
      Conserved Domains (6) summary
      smart00299
      Location:12741416
      CLH; Clathrin heavy chain repeat homology
      sd00006
      Location:11051131
      TPR; TPR repeat [structural motif]
      pfam00637
      Location:9791119
      Clathrin; Region in Clathrin and VPS
      pfam01394
      Location:198234
      Clathrin_propel; Clathrin propeller repeat
      pfam09268
      Location:331354
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:356421
      Clathrin_H_link; Clathrin-H-link

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

      Range
      59619895..59696956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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