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.... See more...

Aliases for CCL21 Gene

Aliases for CCL21 Gene

  • C-C Motif Chemokine Ligand 21 2 3 5
  • 6Ckine 2 3 4
  • SLC 2 3 4
  • Small Inducible Cytokine Subfamily A (Cys-Cys), Member 21 2 3
  • Efficient Chemoattractant For Lymphocytes 2 3
  • Secondary Lymphoid Tissue Chemokine 2 3
  • Chemokine (C-C Motif) Ligand 21 2 3
  • Beta Chemokine Exodus-2 2 3
  • C-C Motif Chemokine 21 3 4
  • SCYA21 3 4
  • CKb9 2 3
  • TCA4 2 3
  • ECL 2 3
  • Secondary Lymphoid-Tissue Chemokine 4
  • Small-Inducible Cytokine A21 4
  • Beta-Chemokine Exodus-2 4
  • Exodus-2 2
  • CCL21 5

External Ids for CCL21 Gene

Previous HGNC Symbols for CCL21 Gene

  • SCYA21

Previous GeneCards Identifiers for CCL21 Gene

  • GC09M035021
  • GC09M034878
  • GC09M034699
  • GC09M034663

Summaries for CCL21 Gene

Entrez Gene Summary for CCL21 Gene

  • 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]

GeneCards Summary for CCL21 Gene

CCL21 (C-C Motif Chemokine Ligand 21) is a Protein Coding gene. Diseases associated with CCL21 include Gastric Lymphoma and Secondary Progressive Multiple Sclerosis. Among its related pathways are Signaling by GPCR and PEDF Induced Signaling. Gene Ontology (GO) annotations related to this gene include chemokine activity and CCR7 chemokine receptor binding. An important paralog of this gene is CX3CL1.

UniProtKB/Swiss-Prot Summary for CCL21 Gene

  • Inhibits hemopoiesis and stimulates chemotaxis. Chemotactic in vitro for thymocytes and activated T-cells, but not for B-cells, macrophages, or neutrophils. Shows preferential activity towards naive T-cells. May play a role in mediating homing of lymphocytes to secondary lymphoid organs. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4.

Gene Wiki entry for CCL21 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CCL21 Gene

Genomics for CCL21 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CCL21 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J034709 Promoter/Enhancer 0.7 EPDnew Ensembl ENCODE 250.7 +0.6 635 2.6 CCL21 FAM205BP IL11RA GALT FAM205A RPP25L GLULP4 CCL19 ENSG00000288583
GH09J033813 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 13.1 +892.7 892716 8.4 SP1 ZNF207 ZNF600 MYC IKZF1 POLR2A NFIC ZIC2 ZBTB10 YY1 UBE2R2 HSALNG0070812 UBE2R2-AS1 ENSG00000228352 ASS1P12 SMU1 NOL6 TCEA1P4 NFX1 CCL21
GH09J034373 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 13.2 +332.5 332476 8 SP1 ZNF207 MYC ZNF654 ZNF600 IKZF1 SIX5 KLF9 CEBPA ZNF10 MYORG C9orf24 NUDT2 PIGO ENSG00000228352 CCL21 NOL6 KIF24 UBAP1 HSALNG0070841
GH09J034675 Enhancer 0.9 Ensembl ENCODE 11.5 +34.4 34425 1.4 ZNF654 MYC IKZF1 CEBPB REST DEK CTCF THAP11 HCFC1 RAD21 piR-55107 ENSG00000230074 IL11RA GALT CCL21 ARID3C LOC730098 lnc-CCL21-1 ENSG00000288583 CCL19
GH09J034743 Enhancer 0.6 Ensembl ENCODE 11.7 -35.1 -35095 2.5 JUND PKNOX1 MEIS2 FOS CCL21 CCL19 PHF24 FAM205A piR-58297-493 piR-60985-131 ENSG00000288583
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCL21 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CCL21

Top Transcription factor binding sites by QIAGEN in the CCL21 gene promoter:
  • E47
  • GATA-2
  • HNF-3beta
  • Ik-3
  • IRF-1
  • p300
  • p53
  • Pax-4a

Genomic Locations for CCL21 Gene

Latest Assembly
chr9:34,709,005-34,710,136
(GRCh38/hg38)
Size:
1,132 bases
Orientation:
Minus strand

Previous Assembly
chr9:34,709,002-34,710,133
(GRCh37/hg19 by Entrez Gene)
Size:
1,132 bases
Orientation:
Minus strand

chr9:34,709,002-34,710,121
(GRCh37/hg19 by Ensembl)
Size:
1,120 bases
Orientation:
Minus strand

Genomic View for CCL21 Gene

Genes around CCL21 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCL21 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCL21 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCL21 Gene

Proteins for CCL21 Gene

  • Protein details for CCL21 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00585-CCL21_HUMAN
    Recommended name:
    C-C motif chemokine 21
    Protein Accession:
    O00585
    Secondary Accessions:
    • Q6ICR7

    Protein attributes for CCL21 Gene

    Size:
    134 amino acids
    Molecular mass:
    14646 Da
    Quaternary structure:
    • Monomer. Binds to CCR7. Interacts with PDPN; relocalizes PDPN to the basolateral membrane (PubMed:14978162).

    Three dimensional structures from OCA and Proteopedia for CCL21 Gene

neXtProt entry for CCL21 Gene

Post-translational modifications for CCL21 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CCL21 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CCL21 Gene

Domains & Families for CCL21 Gene

Gene Families for CCL21 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for CCL21 Gene

InterPro:
Blocks:
  • Small chemokine, C-C subfamily

Suggested Antigen Peptide Sequences for CCL21 Gene

GenScript: Design optimal peptide antigens:
  • Small-inducible cytokine A21 (CCL21_HUMAN)
  • cDNA, FLJ92167, Homo sapiens chemokine (C-C motif) ligand 21 (CCL21), mRNA (Q6ICR7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O00585

UniProtKB/Swiss-Prot:

CCL21_HUMAN :
  • Belongs to the intercrine beta (chemokine CC) family.
Family:
  • Belongs to the intercrine beta (chemokine CC) family.
genes like me logo Genes that share domains with CCL21: view

Function for CCL21 Gene

Molecular function for CCL21 Gene

UniProtKB/Swiss-Prot Function:
Inhibits hemopoiesis and stimulates chemotaxis. Chemotactic in vitro for thymocytes and activated T-cells, but not for B-cells, macrophages, or neutrophils. Shows preferential activity towards naive T-cells. May play a role in mediating homing of lymphocytes to secondary lymphoid organs. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4.

Phenotypes From GWAS Catalog for CCL21 Gene

Gene Ontology (GO) - Molecular Function for CCL21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA --
GO:0005515 protein binding IPI 14978162
GO:0008009 chemokine activity IEA,ISS --
GO:0031732 CCR7 chemokine receptor binding IEA,ISS --
GO:0042379 chemokine receptor binding IDA 23341447
genes like me logo Genes that share ontologies with CCL21: view
genes like me logo Genes that share phenotypes with CCL21: view

Animal Models for CCL21 Gene

MGI Knock Outs for CCL21:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCL21

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CCL21 Gene

Localization for CCL21 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCL21 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCL21 gene
Compartment Confidence
extracellular 5
plasma membrane 3
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
endosome 2
cytosol 2
lysosome 2
peroxisome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CCL21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA,TAS --
GO:0005615 extracellular space IEA,IBA 21873635
genes like me logo Genes that share ontologies with CCL21: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CCL21 Gene

Pathways & Interactions for CCL21 Gene

PathCards logo

SuperPathways for CCL21 Gene

SuperPathway Contained pathways
1 PEDF Induced Signaling
.94
.94
.73
.71
.62
.61
.57
.51
.47
.46
.43
2 TGF-Beta Pathway
.60
.60
.57
.51
.43
.40
3 Peptide ligand-binding receptors
4 Chemokine Superfamily Pathway: Human/Mouse Ligand-Receptor Interactions
5 Akt Signaling
.60
.60
.55
genes like me logo Genes that share pathways with CCL21: view

Pathways by source for CCL21 Gene

1 GeneGo (Thomson Reuters) pathway for CCL21 Gene
  • Apoptosis and survival Lymphotoxin-beta receptor signaling
28 Qiagen pathways for CCL21 Gene
  • Akt Signaling
  • all-trans-Retinoic Acid Signaling in Brain
  • Antioxidant Action of Vitamin-C
  • Chemokine Signaling
  • Endothelin-1 Signaling Pathway

SIGNOR curated interactions for CCL21 Gene

Activates:

Gene Ontology (GO) - Biological Process for CCL21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001768 establishment of T cell polarity IDA 12729902
GO:0001771 immunological synapse formation ISS --
GO:0001954 positive regulation of cell-matrix adhesion IDA 15569314
GO:0002407 dendritic cell chemotaxis IDA 15778365
GO:0002548 monocyte chemotaxis IBA 21873635
genes like me logo Genes that share ontologies with CCL21: view

Drugs & Compounds for CCL21 Gene

(3) Drugs for CCL21 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(6) Additional Compounds for CCL21 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CCL21: view

Transcripts for CCL21 Gene

mRNA/cDNA for CCL21 Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCL21

Alternative Splicing Database (ASD) splice patterns (SP) for CCL21 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b
SP1:
SP2:

Relevant External Links for CCL21 Gene

GeneLoc Exon Structure for
CCL21

Expression for CCL21 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CCL21 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CCL21 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x11.1) and Thyroid (x7.7).

Protein differential expression in normal tissues from HIPED for CCL21 Gene

This gene is overexpressed in Esophagus (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCL21 Gene



Protein tissue co-expression partners for CCL21 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CCL21

SOURCE GeneReport for Unigene cluster for CCL21 Gene:

Hs.57907

mRNA Expression by UniProt/SwissProt for CCL21 Gene:

O00585-CCL21_HUMAN
Tissue specificity: Highly expressed in high endothelial venules of lymph nodes, spleen and appendix. Intermediate levels found in small intestine, thyroid gland and trachea. Low level expression in thymus, bone marrow, liver, and pancreas. Also found in tonsil, fetal heart and fetal spleen.

Evidence on tissue expression from TISSUES for CCL21 Gene

  • Spleen(4.8)
  • Pancreas(4.4)
  • Lymph node(4.2)
  • Intestine(4)
  • Liver(3.1)
  • Heart(3)
  • Lung(2.9)
  • Skin(2.9)
  • Thyroid gland(2.8)
  • Muscle(2.8)
  • Stomach(2.8)
  • Blood(2.7)
  • Kidney(2.5)
  • Bone marrow(2.4)
  • Nervous system(2.2)
  • Adrenal gland(2.2)
genes like me logo Genes that share expression patterns with CCL21: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CCL21 Gene

Orthologs for CCL21 Gene

This gene was present in the common ancestor of mammals.

Orthologs for CCL21 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CCL21 29 30
  • 100 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CCL21 29
  • 87.22 (n)
Cow
(Bos Taurus)
Mammalia CCL21 29 30
  • 83.97 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Gm13304 29 16 30
  • 79.95 (n)
OneToMany
Ccl21a 16 30
  • 71 (a)
OneToMany
Ccl21b 16 30
  • 71 (a)
OneToMany
Gm10591 16 30
  • 71 (a)
OneToMany
Gm21541 30
  • 71 (a)
OneToMany
CCL21A 30
  • 71 (a)
OneToMany
Ccl21c 30 30 30
  • 71 (a)
OneToMany
Ccl21d 16
Rat
(Rattus norvegicus)
Mammalia Ccl21 29
  • 79.17 (n)
Oppossum
(Monodelphis domestica)
Mammalia CCL21 30
  • 56 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CCL21 30
  • 38 (a)
OneToOne
Species where no ortholog for CCL21 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for CCL21 Gene

ENSEMBL:
Gene Tree for CCL21 (if available)
TreeFam:
Gene Tree for CCL21 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCL21: view image
Alliance of Genome Resources:
Additional Orthologs for CCL21

Paralogs for CCL21 Gene

(20) SIMAP similar genes for CCL21 Gene using alignment to 3 proteins:

  • CCL21_HUMAN
  • Q5VZ73_HUMAN
  • Q6ICR7_HUMAN
genes like me logo Genes that share paralogs with CCL21: view

Variants for CCL21 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CCL21 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs142807238 Benign: not provided 34,709,583(-) T/C
NM_002989.4(CCL21):c.288A>G (p.Pro96=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CCL21 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CCL21 Gene

Variant ID Type Subtype PubMed ID
esv3620335 CNV gain 21293372
nsv1125318 OTHER inversion 24896259
nsv509301 CNV insertion 20534489
nsv614157 CNV loss 21841781
nsv831544 CNV gain 17160897

Variation tolerance for CCL21 Gene

Residual Variation Intolerance Score: 50.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.14; 3.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCL21 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCL21
Leiden Open Variation Database (LOVD)
CCL21

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCL21 Gene

Disorders for CCL21 Gene

MalaCards: The human disease database

(12) MalaCards diseases for CCL21 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
gastric lymphoma
  • lymphoma of the stomach
secondary progressive multiple sclerosis
  • secondary-progressive ms
polyradiculoneuropathy
scrapie
skin carcinoma in situ
  • carcinoma in situ of skin
- elite association - COSMIC cancer census association via MalaCards
Search CCL21 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CCL21

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CCL21: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CCL21 Gene

Publications for CCL21 Gene

  1. Molecular cloning of a novel human CC chemokine secondary lymphoid-tissue chemokine that is a potent chemoattractant for lymphocytes and mapped to chromosome 9p13. (PMID: 9235955) Nagira M … Yoshie O (The Journal of biological chemistry 1997) 2 3 4 22
  2. A chemokine expressed in lymphoid high endothelial venules promotes the adhesion and chemotaxis of naive T lymphocytes. (PMID: 9419363) Gunn MD … Williams LT (Proceedings of the National Academy of Sciences of the United States of America 1998) 3 4 22
  3. Secondary lymphoid-tissue chemokine is a functional ligand for the CC chemokine receptor CCR7. (PMID: 9507024) Yoshida R … Yoshie O (The Journal of biological chemistry 1998) 3 4 22
  4. β-Arrestin recruitment and G protein signaling by the atypical human chemokine decoy receptor CCX-CKR. (PMID: 23341447) Watts AO … Vischer HF (The Journal of biological chemistry 2013) 3 4
  5. Solution structure of CCL21 and identification of a putative CCR7 binding site. (PMID: 22221265) Love M … Veldkamp CT (Biochemistry 2012) 3 4

Products for CCL21 Gene

  • Addgene plasmids for CCL21

Sources for CCL21 Gene