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

Gene ID: 6364, updated on 2-Oct-2018

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; Vega:OTTHUMG00000133189
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

Genomic context

See CCL20 in Genome Data Viewer
Location:
2q36.3
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (227813842..227817564)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (228678558..228682280)

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness.
NHGRI GWA Catalog
Genetic variants associated with disordered eating.
NHGRI GWA Catalog

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 BioSystems

  • Chemokine receptors bind chemokines, organism-specific biosystem (from REACTOME)
    Chemokine receptors bind chemokines, organism-specific biosystemChemokine receptors are cytokine receptors found on the surface of certain cells, which interact with a type of cytokine called a chemokine. Following interaction, these receptors trigger a flux of i...
  • Chemokine signaling pathway, organism-specific biosystem (from KEGG)
    Chemokine signaling pathway, organism-specific biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
  • Chemokine signaling pathway, conserved biosystem (from KEGG)
    Chemokine signaling pathway, conserved biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
  • Class A/1 (Rhodopsin-like receptors), organism-specific biosystem (from REACTOME)
    Class A/1 (Rhodopsin-like receptors), organism-specific biosystemRhodopsin-like receptors (class A/1) are the largest group of GPCRs and are the best studied group from a functional and structural point of view. They show great diversity at the sequence level and ...
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • EBV LMP1 signaling, organism-specific biosystem (from WikiPathways)
    EBV LMP1 signaling, organism-specific biosystem
    EBV LMP1 signaling
  • G alpha (i) signalling events, organism-specific biosystem (from REACTOME)
    G alpha (i) signalling events, organism-specific biosystemThe classical signalling mechanism for G alpha (i) is inhibition of the cAMP dependent pathway through inhibition of adenylate cyclase. Decreased production of cAMP from ATP results in decreased act...
  • GPCR downstream signaling, organism-specific biosystem (from REACTOME)
    GPCR downstream signaling, organism-specific biosystemG protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it h...
  • GPCR ligand binding, organism-specific biosystem (from REACTOME)
    GPCR ligand binding, organism-specific biosystemThere are more than 800 G-protein coupled receptor (GPCRs) in the human genome, making it the largest receptor superfamily. GPCRs are also the largest class of drug targets, involved in virtually all...
  • IL-17 signaling pathway, organism-specific biosystem (from KEGG)
    IL-17 signaling pathway, organism-specific biosystemThe interleukin 17 (IL-17) family, a subset of cytokines consisting of IL-17A-F, plays crucial roles in both acute and chronic inflammatory responses. IL-17A, the hallmark cytokine of the newly defi...
  • IL-17 signaling pathway, conserved biosystem (from KEGG)
    IL-17 signaling pathway, conserved biosystemThe interleukin 17 (IL-17) family, a subset of cytokines consisting of IL-17A-F, plays crucial roles in both acute and chronic inflammatory responses. IL-17A, the hallmark cytokine of the newly defi...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Interleukin-10 signaling, organism-specific biosystem (from REACTOME)
    Interleukin-10 signaling, organism-specific biosystemInterleukin-10 (IL10) was originally described as a factor named cytokine synthesis inhibitory factor that inhibited T-helper (Th) 1 activation and Th1 cytokine production (Fiorentino et al. 1989). ...
  • Peptide ligand-binding receptors, organism-specific biosystem (from REACTOME)
    Peptide ligand-binding receptors, organism-specific biosystemThese receptors, a subset of the Class A/1 (Rhodopsin-like) family, all bind peptide ligands which include the chemokines, opioids and somatostatins.
  • Rheumatoid arthritis, organism-specific biosystem (from KEGG)
    Rheumatoid arthritis, organism-specific biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
  • Rheumatoid arthritis, conserved biosystem (from KEGG)
    Rheumatoid arthritis, conserved biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by GPCR, organism-specific biosystem (from REACTOME)
    Signaling by GPCR, organism-specific biosystemG protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors i...
  • Signaling by Interleukins, organism-specific biosystem (from REACTOME)
    Signaling by Interleukins, organism-specific biosystemInterleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but a...
  • TNF signaling pathway, organism-specific biosystem (from KEGG)
    TNF signaling pathway, organism-specific biosystemTumor necrosis factor (TNF), as a critical cytokine, can induce a wide range of intracellular signal pathways including apoptosis and cell survival as well as inflammation and immunity. Activated TNF...
  • TNF signaling pathway, conserved biosystem (from KEGG)
    TNF signaling pathway, conserved biosystemTumor necrosis factor (TNF), as a critical cytokine, can induce a wide range of intracellular signal pathways including apoptosis and cell survival as well as inflammation and immunity. Activated TNF...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
CCR chemokine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
CCR6 chemokine receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
chemokine activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 
T cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium-mediated signaling using intracellular calcium source IDA
Inferred from Direct Assay
more info
PubMed 
cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
cellular response to interferon-gamma IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to interleukin-1 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to tumor necrosis factor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
defense response to bacterium IEA
Inferred from Electronic Annotation
more info
 
immune response TAS
Traceable Author Statement
more info
PubMed 
inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lymphocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
monocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neutrophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of T cell migration IDA
Inferred from Direct Assay
more info
PubMed 
regulation of signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
thymocyte migration ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular IEA
Inferred from Electronic Annotation
more info
 

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)

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_001130046.1NP_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, U64197, U77035
    Consensus CDS
    CCDS46536.1
    UniProtKB/Swiss-Prot
    P78556
    Related
    ENSP00000386273.3, OTTHUMP00000164245, ENST00000409189.7, OTTHUMT00000256898
    Conserved Domains (1) summary
    cd01119
    Location:2989
    Chemokine_CC_DCCL; 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 ...
  2. NM_004591.2NP_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, U64197, U77035
    Consensus CDS
    CCDS2469.1
    UniProtKB/Swiss-Prot
    P78556
    Related
    ENSP00000351671.4, OTTHUMP00000204113, ENST00000358813.4, OTTHUMT00000331641
    Conserved Domains (1) summary
    cd01119
    Location:3090
    Chemokine_CC_DCCL; 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 ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    227813842..227817564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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