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CLTC clathrin heavy chain [ Homo sapiens (human) ]

Gene ID: 1213, updated on 24-Nov-2020

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

Genomic context

See CLTC in Genome Data Viewer
Location:
17q23.1
Exon count:
32
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (59619895..59696956)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57697050..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
RNA binding HDA PubMed 
clathrin light chain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin light chain binding IPI
Inferred from Physical Interaction
more info
PubMed 
disordered domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
low-density lipoprotein particle receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
structural molecule activity NAS
Non-traceable Author Statement
more info
PubMed 
ubiquitin-specific protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway, planar cell polarity pathway TAS
Traceable Author Statement
more info
 
amyloid-beta clearance by transcytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
antigen processing and presentation of exogenous peptide antigen via MHC class II TAS
Traceable Author Statement
more info
 
autophagy IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
clathrin coat assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin coat assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
clathrin-dependent endocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport NAS
Non-traceable Author Statement
more info
PubMed 
low-density lipoprotein particle clearance TAS
Traceable Author Statement
more info
 
low-density lipoprotein particle receptor catabolic process TAS
Traceable Author Statement
more info
 
membrane organization TAS
Traceable Author Statement
more info
 
mitotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of hyaluronan biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of hyaluronan biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein localization to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
osteoblast differentiation HDA PubMed 
receptor internalization IMP
Inferred from Mutant Phenotype
more info
PubMed 
receptor-mediated endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
receptor-mediated endocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mitotic spindle organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
transferrin transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
clathrin coat IMP
Inferred from Mutant Phenotype
more info
PubMed 
clathrin coat NAS
Non-traceable Author Statement
more info
PubMed 
clathrin coat of coated pit IEA
Inferred from Electronic Annotation
more info
 
clathrin coat of trans-Golgi network vesicle IEA
Inferred from Electronic Annotation
more info
 
clathrin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin complex IDA
Inferred from Direct Assay
more info
PubMed 
clathrin-coated endocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin-coated endocytic vesicle NAS
Non-traceable Author Statement
more info
PubMed 
clathrin-coated endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endolysosome membrane TAS
Traceable Author Statement
more info
 
endosome IDA
Inferred from Direct Assay
more info
 
extracellular exosome HDA PubMed 
extracellular vesicle HDA PubMed 
focal adhesion HDA PubMed 
lysosome IDA
Inferred from Direct Assay
more info
 
melanosome IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
mitotic spindle IDA
Inferred from Direct Assay
more info
 
mitotic spindle microtubule IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
spindle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spindle IDA
Inferred from Direct Assay
more info
PubMed 
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)

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]
    pfam01394
    Location:198234
    Clathrin_propel; Clathrin propeller repeat
    pfam00637
    Location:14271561
    Clathrin; Region in Clathrin and VPS
    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 109.20201120

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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