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    Ccl20 C-C motif chemokine ligand 20 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 29538, updated on 27-Nov-2024

    Summary

    Official Symbol
    Ccl20provided by RGD
    Official Full Name
    C-C motif chemokine ligand 20provided by RGD
    Primary source
    RGD:3646
    See related
    EnsemblRapid:ENSRNOG00000015992 AllianceGenome:RGD:3646
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    ST38; Scya20
    Summary
    Enables chemokine activity. Involved in cellular response to molecule of bacterial origin; chemotaxis; and positive regulation of macromolecule biosynthetic process. Located in extracellular space. Used to study transient cerebral ischemia. Biomarker of brain ischemia and ulcerative colitis. Orthologous to human CCL20 (C-C motif chemokine ligand 20). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 24.8), Thymus (RPKM 15.2) and 4 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Ccl20 in Genome Data Viewer
    Location:
    9q35
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (91837139..91839736)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (84389031..84391629)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (88918359..88921017)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 19 member 3 Neighboring gene small cysteine and glycine repeat-containing protein 6-like Neighboring gene dynein assembly factor with WD repeats 1 Neighboring gene SPHK1 interactor, AKAP domain containing

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables CCR6 chemokine receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables CCR6 chemokine receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables chemokine activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chemokine activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables cytokine activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in T cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in T cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in antimicrobial humoral immune response mediated by antimicrobial peptide ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in calcium-mediated signaling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in calcium-mediated signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell chemotaxis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to lipoteichoic acid IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of T cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of interleukin-1 alpha production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT involved_in regulation of T cell cytokine production ISO
    Inferred from Sequence Orthology
    more info
     
    NOT involved_in regulation of T-helper 17 cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thymocyte migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in thymocyte migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    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_019233.2NP_062106.1  C-C motif chemokine 20 precursor

      See identical proteins and their annotated locations for NP_062106.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      P97884
      UniProtKB/TrEMBL
      A6JWB9
      Conserved Domains (1) summary
      cd01119
      Location:2990
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      91837139..91839736
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006245164.5XP_006245226.1  C-C motif chemokine 20 isoform X1

      UniProtKB/TrEMBL
      A0A8L2QAZ9
      Related
      ENSRNOP00000021730.2, ENSRNOT00000021730.5
      Conserved Domains (1) summary
      cd01119
      Location:2889
      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 ...