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

Gene ID: 1212, updated on 9-Feb-2020

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
109.20191205 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (176392452..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 Functions

What'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 PubChem

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_001364126.2NP_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
    Related
    ENSP00000498943.1, ENST00000651832.1
    Conserved Domains (1) summary
    pfam01086
    Location:163
    Clathrin_lg_ch; Clathrin light chain
  3. NM_001834.5NP_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)
    AC138956
    Consensus CDS
    CCDS4402.1
    UniProtKB/Swiss-Prot
    P09497
    UniProtKB/TrEMBL
    A0A024R7S3
    Related
    ENSP00000310812.4, ENST00000345807.7
    Conserved Domains (1) summary
    pfam01086
    Location:1208
    Clathrin_lg_ch; Clathrin light chain
  4. NM_007097.4NP_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)
    AC138956
    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_045724.2 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)
    AC138956
  2. NR_157088.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC138956

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    176392452..176416569 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001741996.2 RNA Sequence

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