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

Gene ID: 12757, updated on 17-Mar-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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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
  • 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 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
  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: anatomy of a coat protein. Smith CJ, et al. Trends Cell Biol, 1999 Sep. PMID 10461185
  4. 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
  5. Neuron-specific expression of high-molecular-weight clathrin light chain. Wong DH, et al. J Neurosci, 1990 Sep. PMID 2204686, Free PMC Article

See all (42) 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)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (2) 

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
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within 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 cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
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 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
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
  
located_in postsynaptic endocytic zone cytoplasmic component IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in presynaptic endocytic zone membrane ISO
Inferred from Sequence Orthology
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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