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CCL21 Gene

protein-coding   GIFtS: 61
GCID: GC09M034709

Chemokine (C-C Motif) Ligand 21

(Previous names: small inducible cytokine subfamily A (Cys-Cys), member 21)
(Previous symbol: SCYA21)
Microbiology & Infectious Diseases Congress
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at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chemokine (C-C Motif) Ligand 211 2     CKb92
SCYA211 2 3 5     ECL2
SLC2 3 5     TCA42
Small Inducible Cytokine Subfamily A (Cys-Cys), Member 211 2     C-C Motif Chemokine 212
Beta Chemokine Exodus-21 2     Beta-Chemokine Exodus-23
Efficient Chemoattractant For Lymphocytes1 2     Secondary Lymphoid-Tissue Chemokine3
Secondary Lymphoid Tissue Chemokine1 2     Small-Inducible Cytokine A213
6Ckine2 3     

External Ids:    HGNC: 106201   Entrez Gene: 63662   Ensembl: ENSG000001370777   OMIM: 6027375   UniProtKB: O005853   

Export aliases for CCL21 gene to outside databases

Previous GC identifers: GC09M035021 GC09M034878 GC09M034699 GC09M034663


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CCL21 Gene:
This 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, May 2013)

GeneCards Summary for CCL21 Gene:
CCL21 (chemokine (C-C motif) ligand 21) is a protein-coding gene. Diseases associated with CCL21 include thymic hyperplasia, and chronic inflammatory demyelinating polyradiculoneuropathy. GO annotations related to this gene include CCR7 chemokine receptor binding and chemokine activity.

UniProtKB/Swiss-Prot: CCL21_HUMAN, O00585
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

Gene Wiki entry for CCL21 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000009.12  NC_018920.2  NT_008413.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCL21 gene promoter:
         p53   p300   IRF-1   HNF-3beta   Ik-3   E47   GATA-2   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCL21 promoter sequence
   Search Chromatin IP Primers for CCL21

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCL21


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9p13   Ensembl cytogenetic band:  9p13.3   HGNC cytogenetic band: 9p13

CCL21 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCL21 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M034709:  view genomic region     (about GC identifiers)

Start:
34,709,002 bp from pter      End:
34,710,147 bp from pter
Size:
1,146 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CCL21_HUMAN, O00585 (See protein sequence)
Recommended Name: C-C motif chemokine 21 precursor  
Size: 134 amino acids; 14646 Da
Subunit: Monomer. Binds to CCR7
1 PDB 3D structure from and Proteopedia for CCL21:
2L4N (3D)    

Explore the universe of human proteins at neXtProt for CCL21: NX_O00585

Explore proteomics data for CCL21 at MOPED


See CCL21 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_002980.1  
ENSEMBL proteins: 
 ENSP00000259607   ENSP00000368069  
Reactome Protein details: O00585

CCL21 Human Recombinant Protein Products:

Browse Purified and Recombinant Proteins at EMD Millipore
R&D Systems Recombinant & Natural Proteins for CCL21 (CCL21/6Ckine)
Browse recombinant and purified proteins available from Enzo Life Sciences
OriGene Purified Protein for CCL21
OriGene Protein Over-expression Lysate for CCL21
OriGene MassSpec for CCL21
OriGene Custom Protein Services for CCL21
GenScript Purified and Recombinant Proteins for CCL21
Novus Biologicals CCL21 Proteins
Novus Biologicals CCL21 Lysates
Sino Biological Recombinant Protein for CCL21
Sino Biological Cell Lysate for CCL21
ProSpec Recombinant Protein for CCL21
Browse Proteins at Cloud-Clone Corp.

CCL21 Antibody Products:

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R&D Systems Antibodies for CCL21 (CCL21/6Ckine)
OriGene Antibodies for CCL21
OriGene Custom Antibody Services for CCL21
Novus Biologicals CCL21 Antibodies
Abcam antibodies for CCL21
Browse Antibodies at Cloud-Clone Corp.
ThermoFisher Antibodies for CCL21
LSBio Antibodies in human, mouse, rat for CCL21

CCL21 Assay Products:

Browse Kits and Assays available from EMD Millipore
OriGene Custom Assay Services for CCL21
R&D Systems Flow Cytometry Kits for CCL21 (CCL21/6Ckine)         (see all)
GenScript Custom Assay Services for CCL21
Browse Enzo Life Sciences for kits & assays
Browse ELISAs at Cloud-Clone Corp.
Browse CLIAs at Cloud-Clone Corp.


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
ENDOLIG: Endogenous ligands
CCL: Chemokine ligands

1 InterPro protein domain:
 IPR001811 Chemokine_IL8-like_dom

Graphical View of Domain Structure for InterPro Entry O00585

ProtoNet protein and cluster: O00585

1 Blocks protein domain: IPB000827 Small chemokine

UniProtKB/Swiss-Prot: CCL21_HUMAN, O00585
Similarity: Belongs to the intercrine beta (chemokine CC) family


CCL21 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: CCL21_HUMAN, O00585
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

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008009chemokine activity IDA15778365
GO:0031732CCR7 chemokine receptor binding ISS--
GO:0042379chemokine receptor binding IDA--
     
CCL21 for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for CCL21:
 Decreased G3BP1 protein expres 

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CCL21
   inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CCL21

   genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CCL21
   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CCL21

miRNA
Products:
    
Block miRNA regulation of human, mouse, rat CCL21 using miScript Target Protectors
3 qRT-PCR Assays for microRNAs that regulate CCL21:
hsa-miR-370 hsa-miR-331-5p hsa-miR-1910
SwitchGear 3'UTR luciferase reporter plasmidCCL21 3' UTR sequence
Inhib. RNA
Products:
    
OriGene RNAi products in human, mouse, rat for CCL21
Predesigned siRNA for gene silencing in human, mouse, rat CCL21

Gene Editing
Products:
DNA2.0 Custom Protein Engineering Service for CCL21

Clone
Products:
     
OriGene clones in human, mouse for CCL21 (see all 6)
OriGene ORF clones in mouse, rat for CCL21
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector: CCL21 (NM_002989)
Sino Biological Human cDNA Clone for CCL21
DNA2.0 Custom Codon Optimized Gene Synthesis Service for CCL21
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCL21

Cell Line
Products:
     
GenScript Custom overexpressing Cell Line Services for CCL21
Browse ESI BIO Cell Lines and PureStem Progenitors for CCL21 
In Situ Assay
Products:
   

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCL21


(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
CCL21_HUMAN, O00585: Secreted
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5
cytoskeleton1
lysosome1
nucleus1
plasma membrane1
vacuole1

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region TAS--
GO:0005615extracellular space IEA--

CCL21 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for CCL21 About   (see all 12)  
See pathways by source

SuperPathSelected contained pathways About (see all per SuperPath)
1PEDF Induced Signaling
MIF Regulation of Innate Immune Cells0.94
NFAT Signaling and Lymphocyte Interactions0.57
MIF Mediated Glucocorticoid Regulation0.94
PGC1Alpha Pathway0.51
PEDF Induced Signaling0.73
STAT3 Pathway0.47
all-trans-Retinoic Acid Signaling in Brain0.71
Endothelin-1 Signaling Pathway0.46
2Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions
Chemokine receptors bind chemokines0.81
Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions0.81
3LT-BetaR Pathway
Apoptosis and survival Lymphotoxin beta receptor signaling0.46
LT-BetaR Pathway0.46
4Chemokine Signaling
Chemokine signaling pathway0.33
Chemokine Signaling0.33
5TGF-Beta Pathway
TGF-Beta Pathway0.60
JNK Pathway0.51
MAPK Family Pathway0.60
Regulation of eIF4 and p70S6K0.43
JAK-STAT Pathway0.57
SOCS Pathway0.40

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways

1 R&D Systems Pathway for CCL21
    Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions

Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CCL21 (see all 28)
    LT-BetaR Pathway
Endothelin-1 Signaling Pathway
Molecular Mechanisms of Cancer
Antioxidant Action of Vitamin-C
NFAT Signaling and Lymphocyte Interactions

1 GeneGo (Thomson Reuters) Pathway for CCL21
    Apoptosis and survival Lymphotoxin-beta receptor signaling


2 Reactome Pathways for CCL21
    Chemokine receptors bind chemokines
G alpha (i) signalling events


3 Kegg Pathways  (Kegg details for CCL21):
    Cytokine-cytokine receptor interaction
Chemokine signaling pathway
NF-kappa B signaling pathway


CCL21 for pathways           About GeneDecksing

    Pathway & Disease-focused RT2 Profiler PCR Arrays including CCL21: 
          Cytokines & Chemokines in human mouse rat
          Inflammatory Response & Autoimmunity in human mouse rat
          Inflammatory Response & Autoimmunity 384HT in human mouse rat
          Chemokines & Receptors in human mouse rat

Interactions:

    GeneGlobe Interaction Network for CCL21

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for CCL21 (O005852, 3 ENSP000002596074) via UniProtKB, MINT, STRING, and/or I2D (see all 160)
InteractantInteraction Details
GeneCardExternal ID(s)
UBQLN4Q9NRR52, 3, ENSP000003572924MINT-2862960 I2D: score=3 STRING: ENSP00000357292
GOT2P005052, 3, ENSP000002452064MINT-8250756 I2D: score=2 STRING: ENSP00000245206
ACKR4Q9NPB93, ENSP000002498874I2D: score=3 STRING: ENSP00000249887
CCR7P322483, ENSP000002466574I2D: score=3 STRING: ENSP00000246657
IGFBP7Q162703, ENSP000002956664I2D: score=3 STRING: ENSP00000295666
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Gene Ontology (GO): Selected biological process terms (see all 34):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0001768establishment of T cell polarity IDA12729902
GO:0001771immunological synapse formation ISS--
GO:0001954positive regulation of cell-matrix adhesion IDA15569314
GO:0002407dendritic cell chemotaxis IDA15778365
GO:0002606positive regulation of dendritic cell antigen processing and presentation ISS--

CCL21 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for CCL21

9 Novoseek inferred chemical compound relationships for CCL21 gene    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
mip-3beta 84.5 2 12437666 (2)
teck 75.2 5 10706668 (3), 9886241 (1), 10967023 (1)
larc 70.7 6 9365118 (2), 10027395 (2), 10967023 (1)
ccl3 62.1 5 15818740 (1), 12651610 (1), 16106219 (1), 19726994 (1)
tarc 58.1 5 9365118 (2), 15890946 (2)
rantes 48.7 7 15818740 (1), 12847218 (1), 15233729 (1), 12667214 (1) (see all 5)
ccl4 31.9 5 12651610 (1), 16106219 (1), 18250572 (1), 19726994 (1)
pge2 24.4 5 19545899 (1), 12149218 (1)
calcium 0 6 9507024 (3), 10339465 (2), 15956285 (1)



CCL21 for compounds           About GeneDecksing



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for CCL21 gene: 
NM_002989.3  

Unigene Cluster for CCL21:

Chemokine (C-C motif) ligand 21
Hs.57907  [show with all ESTs]
Unigene Representative Sequence: BI838628
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000259607(uc003zvo.3) ENST00000378792
Congresses - knowledge worth sharing:
European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

miRNA
Products:
     
Block miRNA regulation of human, mouse, rat CCL21 using miScript Target Protectors
3 qRT-PCR Assays for microRNAs that regulate CCL21:
hsa-miR-370 hsa-miR-331-5p hsa-miR-1910
SwitchGear 3'UTR luciferase reporter plasmidCCL21 3' UTR sequence
Inhib. RNA
Products:
     
OriGene RNAi products in human, mouse, rat for CCL21
Predesigned siRNA for gene silencing in human, mouse, rat CCL21
Clone
Products:
     
OriGene clones in human, mouse for CCL21 (see all 6)
OriGene ORF clones in mouse, rat for CCL21
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector: CCL21 (NM_002989)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for CCL21
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCL21
Primer
Products:
    
OriGene qPCR primer pairs and template standards for CCL21
OriGene qSTAR qPCR primer pairs in human, mouse for CCL21
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CCL21
  QuantiTect SYBR Green Assays in human, mouse, rat CCL21
  QuantiFast Probe-based Assays in human, mouse, rat CCL21

Additional mRNA sequence: 

AB002409.1 AF001979.1 AK311901.1 AY358887.1 BC027918.1 CR450326.1 U88320.1 

2 DOTS entries:

DT.414858  DT.100748260 

Selected AceView cDNA sequences (see all 118):

CR450326 NM_002989 CB164244 AY358887 BI834167 AI224371 AI571892 BM704701 
BI838571 AA331228 AI707973 AI143228 AI718256 BC027918 AI707832 AI718192 
BE501196 AI719947 AA360212 AA027315 AI253757 CF530057 AI253634 AI185579 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for CCL21    About this scheme

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


ECgene alternative splicing isoforms for CCL21

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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CCL21 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGAGGAGGCA
CCL21 Expression
About this image

CCL21 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CCL21 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.57907

UniProtKB/Swiss-Prot: CCL21_HUMAN, O00585
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

    Pathway & Disease-focused RT2 Profiler PCR Arrays including CCL21: 
          Cytokines & Chemokines in human mouse rat
          Inflammatory Response & Autoimmunity in human mouse rat
          Inflammatory Response & Autoimmunity 384HT in human mouse rat
          Chemokines & Receptors in human mouse rat

Primer
Products:
OriGene qPCR primer pairs and template standards for CCL21
OriGene qSTAR qPCR primer pairs in human, mouse for CCL21
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CCL21
QuantiTect SYBR Green Assays in human, mouse, rat CCL21
QuantiFast Probe-based Assays in human, mouse, rat CCL21
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCL21

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for CCL21 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ccl21b5
Gm215411
chemokine (C-C motif) ligand 21B (leucine)5
predicted gene, 215411
79.95(n)1
71.43(a)1
  4 (22.12 cM)5
1008621771  NM_001270360.11  NP_001257289.11 
 422557675 


ENSEMBL Gene Tree for CCL21 (if available)
TreeFam Gene Tree for CCL21 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for CCL21 gene
Selected SIMAP similar genes for CCL21 using alignment to 3 protein entries:     CCL21_HUMAN (see all proteins) (see all similar genes):
CCL16    CCL3L1    CCL3L3    CCL19    CCL14    CCL20
CCL26    CCL3    CCL22    CCL4    CCL4L2    LOC728835
CCL18    CCL4L1    CCL11    CCL8    CCL5    CCL7

CCL21 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for CCL21 (see all 109)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1439033641,2
C--34708506(+) CAGGGC/TTGGAA 1 -- ds50010--------
rs1483731981,2
--34708611(+) CACTTA/GGAGGG 1 -- ds50010--------
rs1858990821,2
--34708898(+) TAGATG/TAGAAC 1 -- ds50010--------
rs109722031,2
C,F,A,H--34708899(-) TGTTCT/CCATCT 1 -- ds500130Minor allele frequency- C:0.13NA NS EA CSA WA 3050
rs109722041,2
C,F,H--34708946(-) GGTGGG/AGTCAC 1 -- ds500118Minor allele frequency- A:0.14NA NS EA CSA WA 2138
rs1415929521,2
--34708961(+) AGGAAA/CCTTGG 1 -- ds50010--------
rs1910587241,2
--34709039(+) GTTAGA/GTATAA 1 -- ut310--------
rs18019371,2
C,F--34709060(-) CCTCTT/GCCTTG 1 -- ut312Minor allele frequency- G:0.07NA WA 162
rs1475426251,2
--34709238(+) AGATGA/GGGTGG 1 -- ut310--------
rs115749161,2
C,F,H--34709239(-) ACCACC/TCCATC 1 -- ut31 ese311Minor allele frequency- T:0.04NA NS EA WA 1296

HapMap Linkage Disequilibrium report for CCL21 (34709002 - 34710147 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for CCL21:    About this table    
Variant IDTypeSubtypePubMed ID
nsv509301CNV Insertion20534489
nsv893040CNV Gain21882294
nsv831544CNV Gain17160897

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing CCL21
DNA2.0 Custom Variant and Variant Library Synthesis for CCL21

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 602737    OMIM disorders: --

Selected diseases for CCL21 (see all 64):    
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thymic hyperplasia    chronic inflammatory demyelinating polyradiculoneuropathy    gastric lymphoma    allergic contact dermatitis
central nervous system lymphoma    polyradiculoneuropathy    contact dermatitis    proliferative vitreoretinopathy
inclusion body myositis    guillain-barre syndrome    b-cell chronic lymphocytic leukemia    wegener's granulomatosis
common variable immunodeficiency    idiopathic pulmonary fibrosis    psoriatic arthritis    myositis
sjogren's syndrome    adult t-cell leukemia    malt lymphoma    spinal cord injury


CCL21 for disorders           About GeneDecksing

Selected Novoseek inferred disease relationships for CCL21 gene (see all 18)    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
sjogrens syndrome 25.8 1 18354239 (1)
tumors 25.4 15 14613584 (2), 14726959 (1), 15059899 (1), 17016763 (1) (see all 14)
melanoma b16 23.5 1 16112911 (1)
inflammation 21.9 8 17982129 (1), 16118351 (1), 19747210 (1), 11943728 (1) (see all 7)
autoimmune diseases 20.9 2 12393410 (1), 16887149 (1)
metastasis 14.4 4 20181250 (2), 17891505 (1)
necrosis 12.4 4 12186835 (1), 16106219 (1), 17223654 (1), 16618517 (1)
atherosclerotic plaque 12.3 1 10027395 (1)
cancer 5.06 3 14613584 (1), 16112911 (1), 15671487 (1)
multiple sclerosis 3.92 2 12576236 (1)

Genetic Association Database (GAD): CCL21
Human Genome Epidemiology (HuGE) Navigator: CCL21 (20 documents)

Export disorders for CCL21 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for CCL21 gene, integrated from 10 sources (see all 217):
(articles sorted by number of sources associating them with CCL21)
    Utopia: connect your pdf to the dynamic
world of online information

  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. (PubMed id 9235955)1, 2, 3, 9 Nagira M.... Yoshie O. (J. Biol. Chem. 1997)
  2. Secondary lymphoid-tissue chemokine is a functional ligand for the CC chemokine receptor CCR7. (PubMed id 9507024)1, 2, 9 Yoshida R.... Yoshie O. (J. Biol. Chem. 1998)
  3. A chemokine expressed in lymphoid high endothelial venules promotes the adhesion and chemotaxis of naive T lymphocytes. (PubMed id 9419363)1, 2, 9 Gunn M.D....Williams L.T. (Proc. Natl. Acad. Sci. U.S.A. 1998)
  4. Solution structure of CCL21 and identification of a putative CCR7 binding site. (PubMed id 22221265)1, 2 Love M.... Veldkamp C.T. (Biochemistry 2012)
  5. Endometriosis and autoimmune disease: association of susceptibility to moderate/severe endometriosis with CCL21 and HLA-DRB1. (PubMed id 20797713)1, 4 Sundqvist J....D'Hooghe T.M. (Fertil. Steril. 2011)
  6. Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. (PubMed id 19674979)1, 4 Hinks A....Thomson W. (Ann. Rheum. Dis. 2010)
  7. Association of a rheumatoid arthritis susceptibility variant at the CCL21 locus with premature mortality in inflammatory polyarthritis patients. (PubMed id 20461788)1, 4 Farragher T.M....Barton A. (amp 2010)
  8. A functionally relevant IRF5 haplotype is associated with reduced risk to Wegener's granulomatosis. (PubMed id 20049410)1, 4 Wieczorek S....Epplen J.T. (J. Mol. Med. 2010)
  9. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. (PubMed id 20444755)1, 4 Tan R.J....Barton A. (Ann. Rheum. Dis. 2010)
  10. Genetic variants in the prediction of rheumatoid arthritis. (PubMed id 20439292)1, 4 van der Helm-van Mil A.H....Huizinga T.W. (Ann. Rheum. Dis. 2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 6366 HGNC: 10620 AceView: CCL21 Ensembl:ENSG00000137077 euGenes: HUgn6366
ECgene: CCL21 Kegg: 6366 H-InvDB: CCL21

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for CCL21 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for CCL21 Genetics and Cytogenetics in Oncology and Haematology
Wikipedia http://en.wikipedia.org/wiki/CCL21

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for CCL21 gene:
Search GeneIP for patents involving CCL21

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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