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

Gene ID: 1211, updated on 1-Jun-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
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (36190855..36212062)
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:22231
    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:22225
    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_001184762.1NP_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:22213
    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:22243
    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.

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..36212062
    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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