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    CLTA clathrin light chain A [ Homo sapiens (human) ]

    Gene ID: 1211, updated on 26-Oct-2020

    Summary

    Official Symbol
    CLTAprovided by HGNC
    Official Full Name
    clathrin light chain Aprovided by HGNC
    Primary source
    HGNC:HGNC:2090
    See related
    Ensembl:ENSG00000122705 MIM:118960
    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
    LCA
    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. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in colon (RPKM 66.3), kidney (RPKM 59.1) and 25 other tissues See more
    Orthologs

    Genomic context

    See CLTA in Genome Data Viewer
    Location:
    9p13.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109.20200815 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (36190855..36212059)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (36190853..36212059)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene GLI pathogenesis related 2 Neighboring gene calicin Neighboring gene glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase Neighboring gene uncharacterized LOC102724322 Neighboring gene RNA, U4 small nuclear 53, pseudogene Neighboring gene high mobility group box 3 pseudogene 24

    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

    Replication interactions

    Interaction Pubs
    Knockdown of clathrin, light chain A (CLTA) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    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 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 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 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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    GTPase binding IEA
    Inferred from Electronic Annotation
    more info
     
    clathrin heavy chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    clathrin heavy chain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    molecular_function ND
    No biological Data available
    more info
     
    peptide binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    antigen processing and presentation of exogenous peptide antigen via MHC class II TAS
    Traceable Author Statement
    more info
     
    cell cycle 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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 
    cytoplasmic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    endolysosome membrane TAS
    Traceable Author Statement
    more info
     
    membrane HDA PubMed 
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    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
     
    spindle IEA
    Inferred from Electronic Annotation
    more info
     
    synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    clathrin light chain A
    Names
    clathrin, light polypeptide (Lca)

    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_001076677.3NP_001070145.1  clathrin light chain A isoform c

      See identical proteins and their annotated locations for NP_001070145.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon, compared to variant 2, resulting in a shorter protein (isoform c).
      Source sequence(s)
      CA306784, DQ270158, DT220470
      Consensus CDS
      CCDS43802.1
      UniProtKB/Swiss-Prot
      P09496
      Related
      ENSP00000379848.2, ENST00000396603.6
      Conserved Domains (1) summary
      pfam01086
      Location:20231
      Clathrin_lg_ch; Clathrin light chain
    2. NM_001184760.2NP_001171689.1  clathrin light chain A isoform d

      See identical proteins and their annotated locations for NP_001171689.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon, compared to variant 2, resulting in a shorter protein (isoform d), compared to isoform b.
      Source sequence(s)
      AK295692, CA306784, DT220470
      Consensus CDS
      CCDS55306.1
      UniProtKB/Swiss-Prot
      P09496
      Related
      ENSP00000419746.1, ENST00000470744.5
      Conserved Domains (1) summary
      pfam01086
      Location:20225
      Clathrin_lg_ch; Clathrin light chain
    3. NM_001184761.2NP_001171690.1  clathrin light chain A isoform e

      See identical proteins and their annotated locations for NP_001171690.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two alternate in-frame exons and uses an alternate splice site in the 3' terminal exon that causes a translational frameshift compared to variant 2. These differences result in a shorter protein (isoform e), compared to isoform b.
      Source sequence(s)
      BM423666, CA306784, DT220470
      Conserved Domains (1) summary
      pfam01086
      Location:22161
      Clathrin_lg_ch; Clathrin light chain
    4. NM_001184762.2NP_001171691.1  clathrin light chain A isoform f

      See identical proteins and their annotated locations for NP_001171691.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks four alternate in-frame exons, compared to variant 2, resulting in a shorter protein (isoform f), compared to isoform b.
      Source sequence(s)
      BI090227, CA306784, DT220470
      Consensus CDS
      CCDS55307.1
      UniProtKB/Swiss-Prot
      P09496
      Related
      ENSP00000437508.1, ENST00000540080.5
      Conserved Domains (1) summary
      pfam01086
      Location:22161
      Clathrin_lg_ch; Clathrin light chain
    5. NM_001311203.2NP_001298132.1  clathrin light chain A isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) uses an alternate splice junction in the first exon and lacks an alternate in-frame segment compared to variant 2. The resulting isoform (g) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform b.
      Source sequence(s)
      CA306784, CN300759, DT220470
      Conserved Domains (1) summary
      pfam01086
      Location:9135
      Clathrin_lg_ch; Clathrin light chain
    6. NM_001311204.2NP_001298133.1  clathrin light chain A isoform h

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks an alternate in-frame segment compared to variant 2. The resulting isoform (h) has the same N- and C-termini but is shorter compared to isoform b.
      Source sequence(s)
      BI600540, CA306784, DT220470
      Consensus CDS
      CCDS83364.1
      UniProtKB/TrEMBL
      C9J8P9
      Related
      ENSP00000417698.1, ENST00000466396.5
      Conserved Domains (1) summary
      pfam01086
      Location:22191
      Clathrin_lg_ch; Clathrin light chain
    7. NM_001311205.2NP_001298134.1  clathrin light chain A isoform i

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) lacks an alternate in-frame segment and an alternate in-frame exon compared to variant 2. The resulting isoform (i) has the same N- and C-termini but is shorter compared to isoform b.
      Source sequence(s)
      CA306784, DN991152, DT220470
      Conserved Domains (1) summary
      pfam01086
      Location:22173
      Clathrin_lg_ch; Clathrin light chain
    8. NM_001311206.2NP_001298135.1  clathrin light chain A isoform j

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) lacks an alternate exon and an alternate in-frame segment compared to variant 2. The resulting isoform (j) is shorter at the N-terminus and lacks an internal segment compared to isoform b.
      Source sequence(s)
      BF797444, CA306784, DT220470
      Conserved Domains (1) summary
      pfam01086
      Location:296
      Clathrin_lg_ch; Clathrin light chain
    9. NM_001833.4NP_001824.1  clathrin light chain A isoform a

      See identical proteins and their annotated locations for NP_001824.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks alternate in-frame exons compared to variant 2, resulting in a shorter protein (isoform a), compared to isoform b.
      Source sequence(s)
      BC009201, DT220470
      Consensus CDS
      CCDS6600.1
      UniProtKB/Swiss-Prot
      P09496
      Related
      ENSP00000242284.6, ENST00000345519.10
      Conserved Domains (1) summary
      pfam01086
      Location:20213
      Clathrin_lg_ch; Clathrin light chain
    10. NM_007096.4NP_009027.1  clathrin light chain A isoform b

      See identical proteins and their annotated locations for NP_009027.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript variant and encodes the longest isoform (b).
      Source sequence(s)
      CA306784, DT220470, M20471
      Consensus CDS
      CCDS6601.1
      UniProtKB/Swiss-Prot
      P09496
      Related
      ENSP00000242285.6, ENST00000242285.10
      Conserved Domains (1) summary
      pfam01086
      Location:20243
      Clathrin_lg_ch; Clathrin light chain

    RNA

    1. NR_132349.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) lacks three alternate exons 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)
      AK291078, CA306784, CA441539, DT220470

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

      Range
      36190855..36212059
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447409.1XP_024303177.1  clathrin light chain A isoform X3

      Conserved Domains (1) summary
      pfam01086
      Location:9135
      Clathrin_lg_ch; Clathrin light chain
    2. XM_017014258.1XP_016869747.1  clathrin light chain A isoform X2

    3. XM_017014257.1XP_016869746.1  clathrin light chain A isoform X1

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