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    Clta clathrin light chain A [ Mus musculus (house mouse) ]

    Gene ID: 12757, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Cltaprovided by MGI
    Official Full Name
    clathrin light chain Aprovided by MGI
    Primary source
    MGI:MGI:894297
    See related
    Ensembl:ENSMUSG00000028478 AllianceGenome:MGI:894297
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    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 encoding different isoforms. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in placenta adult (RPKM 111.5), CNS E18 (RPKM 91.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Clta in Genome Data Viewer
    Location:
    4 B1; 4 23.09 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (44003816..44032846)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (44003816..44032846)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E7964 Neighboring gene predicted gene, 30377 Neighboring gene GLI pathogenesis-related 2 Neighboring gene STARR-positive B cell enhancer ABC_E1275 Neighboring gene STARR-seq mESC enhancer starr_10063 Neighboring gene STARR-positive B cell enhancer ABC_E6167 Neighboring gene calicin Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:44025298-44025528 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:44035322-44035529 Neighboring gene glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase Neighboring gene STARR-seq mESC enhancer starr_10067 Neighboring gene STARR-positive B cell enhancer ABC_E7965 Neighboring gene prothymosin alpha, pseudogene 2 Neighboring gene STARR-positive B cell enhancer ABC_E10233

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Clathrin: anatomy of a coat protein. Smith CJ, et al. Trends Cell Biol, 1999 Sep. PMID 10461185
    2. Comprehensive analysis of alternative splicing and functionality in neuronal differentiation of P19 cells. Suzuki H, et al. PLoS One, 2011 Feb 18. PMID 21365003, Free PMC Article
    3. Clathrin light chains' role in selective endocytosis influences antibody isotype switching. Wu S, et al. Proc Natl Acad Sci U S A, 2016 Aug 30. PMID 27540116, Free PMC Article
    4. Clathrin light chains CLCa and CLCb have non-redundant roles in epithelial lumen formation. Chen Y, et al. Life Sci Alliance, 2024 Jan. PMID 37923360, Free PMC Article
    5. Clathrin light chain diversity regulates membrane deformation in vitro and synaptic vesicle formation in vivo. Redlingshöfer L, et al. Proc Natl Acad Sci U S A, 2020 Sep 22. PMID 32907943, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clathrin light chains CLCa and CLCb have non-redundant roles in epithelial lumen formation.
      Title: Clathrin light chains CLCa and CLCb have non-redundant roles in epithelial lumen formation.
    2. Clathrin light chains' role in selective endocytosis influences antibody isotype switching.
      Title: Clathrin light chains' role in selective endocytosis influences antibody isotype switching.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables GTPase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables clathrin heavy chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables clathrin heavy chain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables peptide binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in clathrin coat assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in clathrin-dependent endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of clathrin coat ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of clathrin vesicle coat IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in clathrin-coated pit ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in clathrin-coated vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic endocytic zone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in postsynaptic endocytic zone IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in postsynaptic endocytic zone cytoplasmic component IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in presynaptic endocytic zone membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in spindle IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in synaptic vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in synaptic vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    clathrin light chain A
    Names
    clathrin, light polypeptide (Lca)
    clathryn light chain (LCA2)

    NCBI Reference Sequences (RefSeq)

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    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_001080384.3 → NP_001073853.1  clathrin light chain A isoform a

      See identical proteins and their annotated locations for NP_001073853.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and lacks alternate in-frame exons, compared to variant 2, resulting in a shorter protein (isoform a), compared to isoform b.
      Source sequence(s)
      AL732563
      Consensus CDS
      CCDS38748.1
      UniProtKB/TrEMBL
      Q3THU7, Q6PFA2
      Related
      ENSMUSP00000103478.4, ENSMUST00000107846.10
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 213
      Clathrin_lg_ch; Clathrin light chain

    2. NM_001080385.2 → NP_001073854.1  clathrin light chain A isoform b

      See identical proteins and their annotated locations for NP_001073854.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (b).
      Source sequence(s)
      AL732563
      Consensus CDS
      CCDS38746.1
      UniProtKB/Swiss-Prot
      O08585
      UniProtKB/TrEMBL
      B1AWD9
      Related
      ENSMUSP00000103483.4, ENSMUST00000107851.10
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 243
      Clathrin_lg_ch; Clathrin light chain

    3. NM_001080386.2 → NP_001073855.1  clathrin light chain A isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple in-frame differences in the 5' coding region, compared to variant 2, resulting in a shorter protein (isoform d), compared to isoform b.
      Source sequence(s)
      AL732563
      Consensus CDS
      CCDS38749.1
      UniProtKB/TrEMBL
      B1AWE0, Q3THU7
      Related
      ENSMUSP00000103477.4, ENSMUST00000107845.4
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 215
      Clathrin_lg_ch; Clathrin light chain

    4. NM_001290470.2 → NP_001277399.1  clathrin light chain A isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region, compared to variant 2. It encodes isoform e, which is shorter than isoform b.
      Source sequence(s)
      AL732563
      Consensus CDS
      CCDS71377.1
      UniProtKB/TrEMBL
      B1AWE1, Q3THU7
      Related
      ENSMUSP00000103479.4, ENSMUST00000107847.10
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 225
      Clathrin_lg_ch; Clathrin light chain

    5. NM_001369156.1 → NP_001356085.1  clathrin light chain A isoform f

      Status: REVIEWED

      Source sequence(s)
      AL732563, FO707511
      UniProtKB/Swiss-Prot
      O08585
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 234
      Clathrin_lg_ch; Clathrin light chain

    6. NM_001369157.1 → NP_001356086.1  clathrin light chain A isoform g

      Status: REVIEWED

      Source sequence(s)
      AL732563
      UniProtKB/Swiss-Prot
      O08585
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 241
      Clathrin_lg_ch; Clathrin light chain

    7. NM_001369158.1 → NP_001356087.1  clathrin light chain A isoform h

      Status: REVIEWED

      Source sequence(s)
      AL732563
      UniProtKB/Swiss-Prot
      O08585
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 229
      Clathrin_lg_ch; Clathrin light chain

    8. NM_001369159.1 → NP_001356088.1  clathrin light chain A isoform i

      Status: REVIEWED

      Source sequence(s)
      AL732563
      UniProtKB/TrEMBL
      Q3THU7
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 223
      Clathrin_lg_ch; Clathrin light chain

    9. NM_016760.3 → NP_058040.2  clathrin light chain A isoform c

      See identical proteins and their annotated locations for NP_058040.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon, compared to variant 2, resulting in a shorter protein (isoform c), compared to isoform b.
      Source sequence(s)
      AL732563
      Consensus CDS
      CCDS38747.1
      UniProtKB/Swiss-Prot
      O08585
      UniProtKB/TrEMBL
      B1AWD8
      Related
      ENSMUSP00000103481.4, ENSMUST00000107849.10
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 231
      Clathrin_lg_ch; Clathrin light chain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      44003816..44032846
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006537587.2 → XP_006537650.1  clathrin light chain A isoform X1

      See identical proteins and their annotated locations for XP_006537650.1

      UniProtKB/Swiss-Prot
      O08585
      UniProtKB/TrEMBL
      B1AWD9
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 243
      Clathrin_lg_ch; Clathrin light chain

    2. XM_030253143.1 → XP_030109003.1  clathrin light chain A isoform X1

      UniProtKB/Swiss-Prot
      O08585
      UniProtKB/TrEMBL
      B1AWD9
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 243
      Clathrin_lg_ch; Clathrin light chain

    3. XM_030253145.1 → XP_030109005.1  clathrin light chain A isoform X2

      UniProtKB/Swiss-Prot
      O08585
      UniProtKB/TrEMBL
      B1AWD8
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 231
      Clathrin_lg_ch; Clathrin light chain

    4. XM_030253146.1 → XP_030109006.1  clathrin light chain A isoform X3

      UniProtKB/TrEMBL
      B1AWE1, Q3THU7
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 225
      Clathrin_lg_ch; Clathrin light chain

    5. XM_036163622.1 → XP_036019515.1  clathrin light chain A isoform X4

      UniProtKB/TrEMBL
      Q3THU7
      Conserved Domains (1) summary
      pfam01086
      Location:20 → 223
      Clathrin_lg_ch; Clathrin light chain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O08585.2 GenPept UniProtKB/Swiss-Prot:O08585

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