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CCL21 C-C motif chemokine ligand 21 [ Homo sapiens (human) ]

Gene ID: 6366, updated on 24-Nov-2020

Summary

Official Symbol
CCL21provided by HGNC
Official Full Name
C-C motif chemokine ligand 21provided by HGNC
Primary source
HGNC:HGNC:10620
See related
Ensembl:ENSG00000137077 MIM:602737
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
ECL; SLC; CKb9; TCA4; 6Ckine; SCYA21
Summary
This antimicrobial gene is one of several CC cytokine genes clustered on the p-arm of chromosome 9. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. Similar to other chemokines the protein encoded by this gene inhibits hemopoiesis and stimulates chemotaxis. This protein is chemotactic in vitro for thymocytes and activated T cells, but not for B cells, macrophages, or neutrophils. The cytokine encoded by this gene may also play a role in mediating homing of lymphocytes to secondary lymphoid organs. It is a high affinity functional ligand for chemokine receptor 7 that is expressed on T and B lymphocytes and a known receptor for another member of the cytokine family (small inducible cytokine A19). [provided by RefSeq, Sep 2014]
Expression
Biased expression in lymph node (RPKM 1020.3), spleen (RPKM 170.8) and 2 other tissues See more
Orthologs

Genomic context

See CCL21 in Genome Data Viewer
Location:
9p13.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (34709005..34710136, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (34709002..34710164, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987063 Neighboring gene uncharacterized LOC730098 Neighboring gene C-C motif chemokine ligand 19 Neighboring gene family with sequence similarity 205 member A Neighboring gene PHD finger protein 24 Neighboring gene transmembrane protein C9orf144B pseudogene

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
Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
GeneReviews: Not available
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
GeneReviews: Not available
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
GeneReviews: Not available

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 enhances CCL-21-induced CD4+ T cell chemotaxis in a CXCR4- and CD4-dependent manner 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

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC34555

Gene Ontology Provided by GOA

Function Evidence Code Pubs
CCR chemokine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
CCR7 chemokine receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
chemokine activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine activity IDA
Inferred from Direct Assay
more info
PubMed 
chemokine activity ISS
Inferred from Sequence or Structural Similarity
more info
 
chemokine receptor binding IDA
Inferred from Direct Assay
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 IDA
Inferred from Direct Assay
more info
PubMed 
G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 
T cell costimulation ISS
Inferred from Sequence or Structural Similarity
more info
 
activation of GTPase activity IDA
Inferred from Direct Assay
more info
PubMed 
cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
cell maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
cellular response to chemokine ISS
Inferred from Sequence or Structural Similarity
more info
 
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 (C-C motif) ligand 21 signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
chemokine-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
dendritic cell dendrite assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
eosinophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
establishment of T cell polarity IDA
Inferred from Direct Assay
more info
PubMed 
immune response TAS
Traceable Author Statement
more info
PubMed 
immunological synapse formation ISS
Inferred from Sequence or Structural Similarity
more info
 
inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inflammatory response NAS
Non-traceable Author Statement
more info
PubMed 
lymphocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mesangial cell-matrix adhesion IDA
Inferred from Direct Assay
more info
PubMed 
monocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of dendritic cell apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of dendritic cell dendrite assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of leukocyte tethering or rolling IDA
Inferred from Direct Assay
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 ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of JNK cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of T cell chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of T cell migration IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of actin filament polymerization IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell adhesion mediated by integrin IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell motility IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell-matrix adhesion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of dendritic cell antigen processing and presentation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of filopodium assembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of glycoprotein biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of myeloid dendritic cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of neutrophil chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of phosphatidylinositol 3-kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein kinase B signaling IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of pseudopodium assembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of receptor-mediated endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
release of sequestered calcium ion into cytosol IDA
Inferred from Direct Assay
more info
PubMed 
response to prostaglandin E IDA
Inferred from Direct Assay
more info
PubMed 
ruffle organization IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
C-C motif chemokine 21
Names
Efficient Chemoattractant for Lymphocytes
beta chemokine exodus-2
chemokine (C-C motif) ligand 21
secondary lymphoid tissue chemokine
small inducible cytokine subfamily A (Cys-Cys), member 21

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_002989.4NP_002980.1  C-C motif chemokine 21 precursor

    See identical proteins and their annotated locations for NP_002980.1

    Status: REVIEWED

    Source sequence(s)
    BC027918, BI833188
    Consensus CDS
    CCDS6571.1
    UniProtKB/Swiss-Prot
    O00585
    UniProtKB/TrEMBL
    Q6ICR7
    Related
    ENSP00000259607.2, ENST00000259607.7
    Conserved Domains (1) summary
    cd01119
    Location:2991
    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 Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    34709005..34710136 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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