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CCL20 C-C motif chemokine ligand 20 [ Homo sapiens (human) ]

Gene ID: 6364, updated on 23-Nov-2021

Summary

Official Symbol
CCL20provided by HGNC
Official Full Name
C-C motif chemokine ligand 20provided by HGNC
Primary source
HGNC:HGNC:10619
See related
Ensembl:ENSG00000115009 MIM:601960
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
CKb4; LARC; ST38; MIP3A; Exodus; MIP-3a; SCYA20; MIP-3-alpha
Summary
This antimicrobial gene belongs to the subfamily of small cytokine CC genes. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The protein encoded by this gene displays chemotactic activity for lymphocytes and can repress proliferation of myeloid progenitors. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]
Expression
Biased expression in gall bladder (RPKM 83.4), urinary bladder (RPKM 31.6) and 7 other tissues See more
Orthologs
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Genomic context

See CCL20 in Genome Data Viewer
Location:
2q36.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (227813842..227817556)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (228678558..228682272)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 8 Neighboring gene ATP binding cassette subfamily G member 2 (Junior blood group) pseudogene Neighboring gene teratocarcinoma-derived growth factor 1 pseudogene 2 Neighboring gene dynein assembly factor with WD repeats 1

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

Associated conditions

Description Tests
Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness.
GeneReviews: Not available
Genetic variants associated with disordered eating.
GeneReviews: Not available

HIV-1 interactions

Replication interactions

Interaction Pubs
Clinical samples from HIV-1 infected patients have upregulated levels of CCL20 (MIP3A) and IFNG in serum PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of chemokine (C-C motif) ligand 20 (CCL20) in human B cells PubMed
env CXCR4-tropic and CXCR4/CCR5 dual-tropic HIV-1 gp120 proteins inhibit B cell chemotaxis toward CXCL12, CCL20, and CCL21, and gp120-induced p38 MAPK activation is triggered by CCL21 and CCL20 PubMed
env HIV-1 gp120 modulates expression of the chemokines, GRO-alpha (CXCL1), GRO-gamma, NAP2, IL-8 (CXCL8), IP-10 (CXCL10), MIP-1beta, MIP-1alpha, RANTES, and MIP-3alpha, in PBMCs and MDMs PubMed
Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 inhibits activation of PBMCs and upregulates the expression of MIP-3A in peptide-treated PBMCs PubMed
Nef nef HIV-1 Nef inhibits IFN-gamma-induced apoptosis and upregulates TNF-alpha, IL-6 and MIP-3alpha production by Caco-2 cells while downregulates IL-10 production PubMed
Pr55(Gag) gag Inoculation with pMIP-3alpha three days before pGag injection enhances Gag-specific Ab response as compared with simultaneous inoculation PubMed
Tat tat HIV-1 Tat upregulates the expression of chemokine (C-C motif) ligand 20 (CCL20) in human primary T cells PubMed
Vpr vpr HIV-1 Vpr downregulates the expression of CCL20 in human monocyte-derived dendritic cells 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
enables CCR chemokine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables CCR6 chemokine receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chemokine activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in G protein-coupled receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in T cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in calcium-mediated signaling using intracellular calcium source IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
involved_in cellular response to interferon-gamma IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to interleukin-1 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to tumor necrosis factor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chemokine-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in defense response to bacterium IEA
Inferred from Electronic Annotation
more info
 
involved_in immune response TAS
Traceable Author Statement
more info
PubMed 
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in lymphocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in monocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neutrophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of ERK1 and ERK2 cascade IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within positive regulation of T cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in signal transduction TAS
Traceable Author Statement
more info
PubMed 
involved_in thymocyte migration ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in extracellular region TAS
Traceable Author Statement
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
C-C motif chemokine 20
Names
CC chemokine LARC
beta chemokine exodus-1
chemokine (C-C motif) ligand 20
liver and activation-regulated chemokine
macrophage inflammatory protein 3 alpha
small inducible cytokine subfamily A (Cys-Cys), member 20
small-inducible cytokine A20

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_001130046.2NP_001123518.1  C-C motif chemokine 20 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001123518.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    BC020698, U77035
    Consensus CDS
    CCDS46536.1
    UniProtKB/Swiss-Prot
    P78556
    Related
    ENSP00000386273.3, ENST00000409189.7
    Conserved Domains (1) summary
    cd01119
    Location:2989
    Chemokine_CC_DCCL; subgroup of the Chemokine_CC subgroup based on the presence of a DCCL motif involving the two N-terminal cysteine residues; includes a number of small inducible cytokines capable of reversibly inhibiting normal hematopoietic progenitor proliferation by ...
  2. NM_004591.3NP_004582.1  C-C motif chemokine 20 isoform 1 precursor

    See identical proteins and their annotated locations for NP_004582.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    D17012, D86955, U77035
    Consensus CDS
    CCDS2469.1
    UniProtKB/Swiss-Prot
    P78556
    Related
    ENSP00000351671.4, ENST00000358813.5
    Conserved Domains (1) summary
    cd01119
    Location:3090
    Chemokine_CC_DCCL; subgroup of the Chemokine_CC subgroup based on the presence of a DCCL motif involving the two N-terminal cysteine residues; includes a number of small inducible cytokines capable of reversibly inhibiting normal hematopoietic progenitor proliferation by ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    227813842..227817556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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