U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 6364, updated on 17-Jun-2024

    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; AllianceGenome:HGNC:10619
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CCL20 in Genome Data Viewer
    Location:
    2q36.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (227813842..227817556)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (228296236..228299949)
    105.20220307 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 BRD4-independent group 4 enhancer GRCh37_chr2:228682495-228683694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:228725143-228725642 Neighboring gene CRIPTO 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

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables CCR chemokine receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in T cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in calcium-mediated signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 chemokine-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    involved_in positive regulation of GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within positive regulation of T cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     

    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)

    NEW Try the new Transcript table

    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, Q53S51, Q99664
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      228296236..228299949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)