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    CLTB clathrin light chain B [ Homo sapiens (human) ]

    Gene ID: 1212, updated on 13-Feb-2019

    Summary

    Official Symbol
    CLTBprovided by HGNC
    Official Full Name
    clathrin light chain Bprovided by HGNC
    Primary source
    HGNC:HGNC:2091
    See related
    Ensembl:ENSG00000175416 MIM:118970
    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
    LCB
    Summary
    Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in esophagus (RPKM 44.6), skin (RPKM 37.3) and 25 other tissues See more
    Orthologs

    Genomic context

    See CLTB in Genome Data Viewer
    Location:
    5q35.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (176392455..176416569, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (175819456..175843570, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene microRNA 1271 Neighboring gene ADP ribosylation factor like GTPase 10 Neighboring gene NOP16 nucleolar protein Neighboring gene HIG1 hypoxia inducible domain family member 2A Neighboring gene Fas associated factor family member 2 Neighboring gene collagen alpha-1(III) chain-like Neighboring gene ring finger protein 44 Neighboring gene cadherin related family member 2

    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 FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes PubMed
    Gag-Pol 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 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
    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
    Pol gag-pol Clathrin stabilizes HIV-1 Pol proteins in HIV-1 infected cells PubMed
    Vpr 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 BioSystems

    • Arf1 pathway, organism-specific biosystem (from Pathway Interaction Database)
      Arf1 pathway, organism-specific biosystem
      Arf1 pathway
    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Bacterial invasion of epithelial cells, organism-specific biosystem (from KEGG)
      Bacterial invasion of epithelial cells, organism-specific biosystemMany pathogenic bacteria can invade phagocytic and non-phagocytic cells and colonize them intracellularly, then become disseminated to other cells. Invasive bacteria induce their own uptake by non-ph...
    • Bacterial invasion of epithelial cells, conserved biosystem (from KEGG)
      Bacterial invasion of epithelial cells, conserved biosystemMany pathogenic bacteria can invade phagocytic and non-phagocytic cells and colonize them intracellularly, then become disseminated to other cells. Invasive bacteria induce their own uptake by non-ph...
    • Beta-catenin independent WNT signaling, organism-specific biosystem (from REACTOME)
      Beta-catenin independent WNT signaling, organism-specific biosystemHumans and mice have 19 identified WNT proteins that were originally classified as either 'canonical' or 'non-canonical' depending upon whether they were able to transform the mouse mammary epithelia...
    • Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
      Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystemRecruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-...
    • Clathrin derived vesicle budding, organism-specific biosystem (from REACTOME)
      Clathrin derived vesicle budding, organism-specific biosystemThere at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the cl...
    • Clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
      Clathrin-mediated endocytosis, organism-specific biosystemClathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • EPH-Ephrin signaling, organism-specific biosystem (from REACTOME)
      EPH-Ephrin signaling, organism-specific biosystemDuring the development process cell migration and adhesion are the main forces involved in morphing the cells into critical anatomical structures. The ability of a cell to migrate to its correct dest...
    • EPH-ephrin mediated repulsion of cells, organism-specific biosystem (from REACTOME)
      EPH-ephrin mediated repulsion of cells, organism-specific biosystemDespite high-affinity multimeric interaction between EPHs and ephrins (EFNs), the cellular response to EPH-EFN engagement is usually repulsion between the two cells and signal termination. These repu...
    • Endocrine and other factor-regulated calcium reabsorption, organism-specific biosystem (from KEGG)
      Endocrine and other factor-regulated calcium reabsorption, organism-specific biosystemCalcium (Ca2+) is essential for numerous physiological functions including intracellular signalling processes, neuronal excitability, muscle contraction and bone formation. Therefore, its homeostasis...
    • Endocrine and other factor-regulated calcium reabsorption, conserved biosystem (from KEGG)
      Endocrine and other factor-regulated calcium reabsorption, conserved biosystemCalcium (Ca2+) is essential for numerous physiological functions including intracellular signalling processes, neuronal excitability, muscle contraction and bone formation. Therefore, its homeostasis...
    • Endocytosis, organism-specific biosystem (from KEGG)
      Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
    • Endocytosis, conserved biosystem (from KEGG)
      Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
    • Formation of annular gap junctions, organism-specific biosystem (from REACTOME)
      Formation of annular gap junctions, organism-specific biosystemGap junction plaque internalization and the disruption cell communication requires a reorganization of Cx molecular interactions. Proteins including Dab-2, AP-2, Dynamin and Myosin VI associate w...
    • Gap junction degradation, organism-specific biosystem (from REACTOME)
      Gap junction degradation, organism-specific biosystemThe half-life of Cx is very short (1 to 5h) compared to other junctional proteins (Laird et al., 1995 ; Fallon and Goudenough, 1981). Connexins are targeted for degradation by the proteasome and the...
    • Gap junction trafficking, organism-specific biosystem (from REACTOME)
      Gap junction trafficking, organism-specific biosystemGap junctions are intercellular communication channels formed from Cx (connexin) protein subunits (see Segretain and Falk 2004 and Evans et al. 2006 for comprehensive reviews). Connexins are transpor...
    • Gap junction trafficking and regulation, organism-specific biosystem (from REACTOME)
      Gap junction trafficking and regulation, organism-specific biosystemGap junctions are clusters of intercellular channels connecting adjacent cells and permitting the direct exchange of ions and small molecules between cells. These channels are composed of two hemicha...
    • Huntington's disease, organism-specific biosystem (from KEGG)
      Huntington's disease, organism-specific biosystemHuntington disease (HD) is an autosomal-dominant neurodegenerative disorder that primarily affects medium spiny striatal neurons (MSN). The symptoms are choreiform, involuntary movements, personality...
    • Huntington's disease, conserved biosystem (from KEGG)
      Huntington's disease, conserved biosystemHuntington disease (HD) is an autosomal-dominant neurodegenerative disorder that primarily affects medium spiny striatal neurons (MSN). The symptoms are choreiform, involuntary movements, personality...
    • Lysosome, organism-specific biosystem (from KEGG)
      Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
    • Lysosome, conserved biosystem (from KEGG)
      Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
    • Lysosome Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
      Lysosome Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
    • Membrane Trafficking, organism-specific biosystem (from REACTOME)
      Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
    • PCP/CE pathway, organism-specific biosystem (from REACTOME)
      PCP/CE pathway, organism-specific biosystemThe planar cell polarity (PCP) pathway controls the establishment of polarity within the plane of a sheet of cells. PCP was initially characterized in Drosophila, where it controls the arrangement o...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by Wnt, organism-specific biosystem (from REACTOME)
      Signaling by Wnt, organism-specific biosystemWNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Sai...
    • Synaptic vesicle cycle, organism-specific biosystem (from KEGG)
      Synaptic vesicle cycle, organism-specific biosystemCommunication between neurons is mediated by the release of neurotransmitter from synaptic vesicles (SVs). At the nerve terminal, SVs cycle through repetitive episodes of exocytosis and endocytosis. ...
    • Synaptic vesicle cycle, conserved biosystem (from KEGG)
      Synaptic vesicle cycle, conserved biosystemCommunication between neurons is mediated by the release of neurotransmitter from synaptic vesicles (SVs). At the nerve terminal, SVs cycle through repetitive episodes of exocytosis and endocytosis. ...
    • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
      Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
    • WNT5A-dependent internalization of FZD2, FZD5 and ROR2, organism-specific biosystem (from REACTOME)
      WNT5A-dependent internalization of FZD2, FZD5 and ROR2, organism-specific biosystemInternalization of FZD2, FZD5 and ROR2 after WNT5A binding is thought to occur in a clathrin-dependent manner and is required for the activation of RAC signaling (Kurayoshi et al, 2007; Sato et al, 2...
    • WNT5A-dependent internalization of FZD4, organism-specific biosystem (from REACTOME)
      WNT5A-dependent internalization of FZD4, organism-specific biosystemWNT5A induces internalization of FZD4 in a manner that depends upon PKC-mediated phosphorylation of DVL2. Uptake of FZD4 appears to occur in a clathrin, AP-2 and ARBB2-dependent mannner (Chen et al,...
    • trans-Golgi Network Vesicle Budding, organism-specific biosystem (from REACTOME)
      trans-Golgi Network Vesicle Budding, organism-specific biosystemAfter passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membran...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    clathrin heavy chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    peptide binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    clathrin coat assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    clathrin-dependent endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    membrane organization TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    ciliary membrane IEA
    Inferred from Electronic Annotation
    more info
     
    clathrin coat ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 vesicle coat IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    clathrin-coated endocytic vesicle NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    postsynaptic endocytic zone cytoplasmic component IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    presynaptic endocytic zone membrane IEA
    Inferred from Electronic Annotation
    more info
     
    synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    trans-Golgi network IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    clathrin light chain B
    Names
    clathrin, light chain (Lcb)
    clathrin, light polypeptide (Lcb)

    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.

    mRNA and Protein(s)

    1. NM_001364126.1NP_001351055.1  clathrin light chain B isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 2. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform b.
      Source sequence(s)
      AC138956
      Conserved Domains (1) summary
      pfam01086
      Location:14141
      Clathrin_lg_ch; Clathrin light chain
    2. NM_001364127.1NP_001351056.1  clathrin light chain B isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (d) has a shorter and distinct C-terminus compared to isoform b.
      Source sequence(s)
      AC138956
      Consensus CDS
      CCDS87350.1
      Conserved Domains (1) summary
      pfam01086
      Location:163
      Clathrin_lg_ch; Clathrin light chain
    3. NM_001834.3NP_001825.1  clathrin light chain B isoform a

      See identical proteins and their annotated locations for NP_001825.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 2, resulting in a shorter isoform (a) compared to isoform b.
      Source sequence(s)
      BC006332, CN409237, M20470
      Consensus CDS
      CCDS4402.1
      UniProtKB/Swiss-Prot
      P09497
      UniProtKB/TrEMBL
      A0A024R7S3
      Related
      ENSP00000310812.4, ENST00000345807.6
      Conserved Domains (1) summary
      pfam01086
      Location:1208
      Clathrin_lg_ch; Clathrin light chain
    4. NM_007097.3NP_009028.1  clathrin light chain B isoform b

      See identical proteins and their annotated locations for NP_009028.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (b).
      Source sequence(s)
      BC006332, CN409237, M20469
      Consensus CDS
      CCDS4403.1
      UniProtKB/Swiss-Prot
      P09497
      Related
      ENSP00000309415.4, ENST00000310418.8
      Conserved Domains (1) summary
      pfam01086
      Location:1226
      Clathrin_lg_ch; Clathrin light chain

    RNA

    1. NR_045724.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an additional exon in the center region, which results in an early translation termination and a nonsense-mediated mRNA decay candidate, compared to variant 2. The transcript does not encode a functinal protein.
      Source sequence(s)
      AK300200, BC006332, CN409237, M20470
    2. NR_157088.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate exon compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC138956

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

      Range
      176392455..176416569 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009026.1XP_016864515.1  clathrin light chain B isoform X1

      Conserved Domains (1) summary
      pfam01086
      Location:14141
      Clathrin_lg_ch; Clathrin light chain
    2. XM_017009027.2XP_016864516.1  clathrin light chain B isoform X2

      UniProtKB/TrEMBL
      B4DTF9
      Related
      ENSP00000422978.1, ENST00000510734.5
      Conserved Domains (1) summary
      pfam01086
      Location:163
      Clathrin_lg_ch; Clathrin light chain

    RNA

    1. XR_001741995.2 RNA Sequence

    2. XR_001741996.2 RNA Sequence

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