U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Ccl20 C-C motif chemokine ligand 20 [ Mus musculus (house mouse) ]

Gene ID: 20297, updated on 11-Apr-2024

Summary

Official Symbol
Ccl20provided by MGI
Official Full Name
C-C motif chemokine ligand 20provided by MGI
Primary source
MGI:MGI:1329031
See related
Ensembl:ENSMUSG00000026166 AllianceGenome:MGI:1329031
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
CKb4; LARC; ST38; MIP3A; MIP-3A; Scya20; MIP-3[a]; exodus-1
Summary
Enables CCR6 chemokine receptor binding activity and cytokine activity. Involved in chemotaxis and thymocyte migration. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human CCL20 (C-C motif chemokine ligand 20). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in duodenum adult (RPKM 6.4), small intestine adult (RPKM 4.1) and 3 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:
1 C5; 1 42.69 cM
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (83094487..83096888)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (83116766..83119167)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_01489 Neighboring gene solute carrier family 19, member 3 Neighboring gene nascent polypeptide-associated complex alpha polypeptide pseudogene Neighboring gene STARR-seq mESC enhancer starr_01490 Neighboring gene keratin associated protein 28-13 Neighboring gene STARR-seq mESC enhancer starr_01492 Neighboring gene STARR-seq mESC enhancer starr_01493 Neighboring gene dynein assembly factor with WDR repeat domains 1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2) 
  • Endonuclease-mediated (5) 

Pathways from PubChem

General gene information

Markers

Gene Ontology Provided by MGI

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 CCR6 chemokine receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables chemokine activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables chemokine activity ISO
Inferred from Sequence Orthology
more info
 
enables cytokine activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in T cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide ISO
Inferred from Sequence Orthology
more info
 
involved_in calcium-mediated signaling using intracellular calcium source ISO
Inferred from Sequence Orthology
more info
 
involved_in cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell chemotaxis ISO
Inferred from Sequence Orthology
more info
 
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 chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in killing of cells of another organism ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
PubMed 
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of interleukin-1 alpha production ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of nitric-oxide synthase biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
NOT involved_in regulation of T cell cytokine production IDA
Inferred from Direct Assay
more info
PubMed 
NOT involved_in regulation of T-helper 17 cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
involved_in thymocyte migration IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular space ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
C-C motif chemokine 20
Names
CC chemokine LARC
CC chemokine ST38
MIP-3-alpha
beta-chemokine exodus-1
chemokine (C-C motif) ligand 20
liver and activation-regulated chemokine
macrophage inflammatory protein 3 alpha
small inducible cytokine subfamily A20
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_001159738.1NP_001153210.1  C-C motif chemokine 20 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001153210.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
    Source sequence(s)
    BC028504, BY026108
    Consensus CDS
    CCDS78638.1
    UniProtKB/TrEMBL
    F8WHA7, Q642U4
    Related
    ENSMUSP00000139923.2, ENSMUST00000186832.2
    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 ...
  2. NM_016960.2NP_058656.1  C-C motif chemokine 20 isoform 1 precursor

    See identical proteins and their annotated locations for NP_058656.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC028504, BX525886, BY026108
    Consensus CDS
    CCDS35632.1
    UniProtKB/Swiss-Prot
    O89093, Q9Z1X3
    UniProtKB/TrEMBL
    F8WHA7, Q54AI7
    Related
    ENSMUSP00000109064.3, ENSMUST00000113437.9
    Conserved Domains (1) summary
    cd01119
    Location:3191
    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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    83094487..83096888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)