Ccl20 (C-C motif chemokine ligand 20) - Rat Genome Database

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Gene: Ccl20 (C-C motif chemokine ligand 20) Rattus norvegicus
Analyze
Symbol: Ccl20
Name: C-C motif chemokine ligand 20
RGD ID: 3646
Description: 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); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; rheumatoid arthritis pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: beta chemokine exodus-1; beta-chemokine exodus-1; C-C motif chemokine 20; CC chemokine LARC; CC chemokine ST38; chemokine (C-C motif) ligand 20; liver and activation-regulated chemokine; macrophage inflammatory protein 3 alpha; MIP-3-alpha; Scya20; small inducible cytokine subfamily A20; small-inducible cytokine A20; ST38
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8991,837,139 - 91,839,736 (+)NCBIGRCr8
mRatBN7.2984,389,031 - 84,391,629 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl984,388,904 - 84,391,629 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx992,819,272 - 92,821,849 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,947,738 - 97,950,315 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0996,330,459 - 96,333,051 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0988,918,359 - 88,921,017 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,918,433 - 88,921,001 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,662,765 - 88,665,379 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4982,440,965 - 82,443,542 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1982,624,383 - 82,626,960 (+)NCBI
Celera981,830,990 - 81,833,567 (+)NCBICelera
Cytogenetic Map9q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-hydroxypropanoic acid  (ISO)
2-tert-butylhydroquinone  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3-chlorophenol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-Nitrofluoranthene  (ISO)
3-phenylprop-2-enal  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6alpha-methylprednisolone  (ISO)
acrolein  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (EXP,ISO)
alpha-Zearalanol  (EXP)
ammonium chloride  (EXP)
amphotericin B  (ISO)
andrographolide  (ISO)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
asperentin  (ISO)
azathioprine  (ISO)
Bardoxolone methyl  (ISO)
barium sulfate  (EXP)
benzalkonium chloride  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (EXP)
beta-lapachone  (ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
Botulinum toxin type A  (ISO)
Brevianamide A  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
ceric oxide  (EXP,ISO)
chenodeoxycholic acid  (ISO)
chloroprene  (ISO)
chromium(6+)  (ISO)
ciglitazone  (ISO)
cisplatin  (ISO)
cobalt atom  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
deoxycholic acid  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dibenzofuran  (EXP)
dibutyl phthalate  (EXP)
dichlorine  (ISO)
diethyl malate  (ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP,ISO)
eugenol  (ISO)
fentanyl  (EXP)
ferric oxide  (EXP)
flavonoids  (EXP)
formaldehyde  (ISO)
fragrance  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
gemcitabine  (ISO)
gentamycin  (EXP)
glutathione  (ISO)
hexachlorobenzene  (EXP)
hydrogen peroxide  (ISO)
indoxyl sulfate  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
lidocaine  (EXP)
linuron  (ISO)
lipopolysaccharide  (ISO)
lipoteichoic acid  (EXP)
malathion  (ISO)
melphalan  (ISO)
mercury dichloride  (EXP)
mesalamine  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP)
Muraglitazar  (EXP)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-Nitrosopyrrolidine  (ISO)
naphthalenes  (EXP)
naproxen  (EXP)
neoechinulin A  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
niclosamide  (EXP,ISO)
nicotinamide  (ISO)
o-anisidine  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
PD 0325901  (ISO)
pentanal  (ISO)
peptidoglycan  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluoroundecanoic acid  (ISO)
phenobarbital  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
piroxicam  (ISO)
poly(I:C)  (ISO)
potassium bromate  (EXP,ISO)
potassium dichromate  (ISO)
prednisolone  (ISO)
propanal  (ISO)
prostaglandin E2  (ISO)
pyrrolidine dithiocarbamate  (EXP)
rac-lactic acid  (ISO)
raloxifene  (ISO)
razoxane  (EXP)
resveratrol  (ISO)
ritonavir  (ISO)
rofecoxib  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (EXP)
sirtinol  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium aurothiomalate  (ISO)
sodium dichromate  (EXP)
sodium dodecyl sulfate  (ISO)
sterigmatocystin  (ISO)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
sumatriptan  (EXP)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
taurocholic acid  (ISO)
tenofovir disoproxil fumarate  (ISO)
titanium dioxide  (EXP,ISO)
TMC-120A  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
troglitazone  (EXP,ISO)
Tryptanthrine  (ISO)
Tungsten carbide  (ISO)
tunicamycin  (ISO)
undecane  (EXP)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zinc atom  (EXP,ISO)
zinc dichloride  (ISO)
zinc oxide  (EXP)
zinc(0)  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
extracellular space  (IBA,IDA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Increased presence of dendritic cells and dendritic cell chemokines in the sinus mucosa of chronic rhinosinusitis with nasal polyps and allergic fungal rhinosinusitis. Ayers CM, etal., Int Forum Allergy Rhinol. 2011 Jul-Aug;1(4):296-302. doi: 10.1002/alr.20046. Epub 2011 Apr 11.
2. Orchestration of inflammation and adaptive immunity in Borrelia burgdorferi-induced arthritis by neutrophil-activating protein A. Codolo G, etal., Arthritis Rheum. 2013 May;65(5):1232-42. doi: 10.1002/art.37875.
3. CCL20/macrophage inflammatory protein 3alpha and tumor necrosis factor alpha production by primary uterine epithelial cells in response to treatment with lipopolysaccharide or Pam3Cys. Crane-Godreau MA and Wira CR, Infect Immun. 2005 Jan;73(1):476-84.
4. Expression of inflammatory chemokines combined with local tumor destruction enhances tumor regression and long-term immunity. Crittenden M, etal., Cancer Res. 2003 Sep 1;63(17):5505-12.
5. Baicalin down-regulates the expression of macrophage migration inhibitory factor (MIF) effectively for rats with ulcerative colitis. Dai SX, etal., Phytother Res. 2012 Apr;26(4):498-504. doi: 10.1002/ptr.3581. Epub 2011 Sep 2.
6. Lateral fluid percussion injury of the brain induces CCL20 inflammatory chemokine expression in rats. Das M, etal., J Neuroinflammation. 2011 Oct 31;8:148. doi: 10.1186/1742-2094-8-148.
7. Age-related T-cell cytokine profile parallels corneal disease severity in Sjogren's syndrome-like keratoconjunctivitis sicca in CD25KO mice. De Paiva CS, etal., Rheumatology (Oxford). 2010 Feb;49(2):246-58. doi: 10.1093/rheumatology/kep357. Epub 2009 Dec 9.
8. The CCR6/CCL20 axis mediates Th17 cell migration to the ocular surface in dry eye disease. Dohlman TH, etal., Invest Ophthalmol Vis Sci. 2013 Jun 12;54(6):4081-91. doi: 10.1167/iovs.12-11216.
9. [Expression of CCL20 and CXCR4 in epidermal condyloma acuminatum lesions]. Feng JY, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2007 Apr;27(4):418-20.
10. Cytokine and chemokine expression in the skin from patients with maculopapular exanthema to drugs. Fernandez TD, etal., Allergy. 2008 Jun;63(6):712-9. doi: 10.1111/j.1398-9995.2007.01607.x. Epub 2008 Mar 29.
11. Elevated CCR6+ CD4+ T lymphocytes in tissue compared with blood and induction of CCL20 during the asthmatic late response. Francis JN, etal., Clin Exp Immunol. 2008 Jun;152(3):440-7. doi: 10.1111/j.1365-2249.2008.03657.x. Epub 2008 Apr 16.
12. Hypothermia-enhanced splenic cytokine gene expression is independent of the sympathetic nervous system. Ganta CK, etal., Am J Physiol Regul Integr Comp Physiol. 2006 Sep;291(3):R558-65.
13. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. TNF inhibition rapidly down-regulates multiple proinflammatory pathways in psoriasis plaques. Gottlieb AB, etal., J Immunol. 2005 Aug 15;175(4):2721-9.
15. Up-regulation of macrophage inflammatory protein-3 alpha/CCL20 and CC chemokine receptor 6 in psoriasis. Homey B, etal., J Immunol. 2000 Jun 15;164(12):6621-32.
16. Expression profile of chemokines and chemokine receptors in epithelial cell layers of oral lichen planus. Ichimura M, etal., J Oral Pathol Med. 2006 Mar;35(3):167-74.
17. Detection and localization of Mip-3alpha/LARC/Exodus, a macrophage proinflammatory chemokine, and its CCR6 receptor in human pancreatic cancer. Kleeff J, etal., Int J Cancer. 1999 May 17;81(4):650-7.
18. Up-regulation of chemokine ligand 20 in chronic rhinosinusitis. Lee JH, etal., Arch Otolaryngol Head Neck Surg. 2006 May;132(5):537-41.
19. Sensitization to Per a 2 of the American cockroach correlates with more clinical severity among airway allergic patients in Taiwan. Lee MF, etal., Ann Allergy Asthma Immunol. 2012 Apr;108(4):243-8. doi: 10.1016/j.anai.2012.01.014. Epub 2012 Feb 14.
20. CCR6 is required for epidermal trafficking of gammadelta-T cells in an IL-23-induced model of psoriasiform dermatitis. Mabuchi T, etal., J Invest Dermatol. 2013 Jan;133(1):164-71. doi: 10.1038/jid.2012.260. Epub 2012 Aug 16.
21. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
22. IL-22, but not IL-17, dominant environment in cutaneous T-cell lymphoma. Miyagaki T, etal., Clin Cancer Res. 2011 Dec 15;17(24):7529-38. doi: 10.1158/1078-0432.CCR-11-1192. Epub 2011 Nov 2.
23. Chemokine signatures in the skin disorders of Lyme borreliosis in Europe: predominance of CXCL9 and CXCL10 in erythema migrans and acrodermatitis and CXCL13 in lymphocytoma. Mullegger RR, etal., Infect Immun. 2007 Sep;75(9):4621-8. Epub 2007 Jul 2.
24. Inducible expression of a CC chemokine liver- and activation-regulated chemokine (LARC)/macrophage inflammatory protein (MIP)-3 alpha/CCL20 by epidermal keratinocytes and its role in atopic dermatitis. Nakayama T, etal., Int Immunol. 2001 Jan;13(1):95-103.
25. Dendritic cell subsets and immunological milieu in inflammatory human papilloma virus-related skin lesions. Nakayama Y, etal., J Dermatol Sci. 2011 Sep;63(3):173-83. doi: 10.1016/j.jdermsci.2011.05.006. Epub 2011 Jun 6.
26. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Dermatophagoides farinae extract induces severe atopic dermatitis in NC/Nga mice, which is effectively suppressed by the administration of tacrolimus ointment. Oshio T, etal., Int Immunopharmacol. 2009 Apr;9(4):403-11. doi: 10.1016/j.intimp.2008.12.013. Epub 2009 Jan 20.
28. Neutropenia enhances lung dendritic cell recruitment in response to Aspergillus via a cytokine-to-chemokine amplification loop. Park SJ, etal., J Immunol. 2010 Nov 15;185(10):6190-7. doi: 10.4049/jimmunol.1002064. Epub 2010 Oct 6.
29. Deletion of interferon-gamma delays onset and severity of dacryoadenitis in CD25KO mice. Pelegrino FS, etal., Arthritis Res Ther. 2012 Nov 1;14(6):R234.
30. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
31. High glucose induces macrophage inflammatory protein-3 alpha in renal proximal tubule cells via a transforming growth factor-beta 1 dependent mechanism. Qi W, etal., Nephrol Dial Transplant. 2007 Nov;22(11):3147-53. Epub 2007 Jul 29.
32. GOA pipeline RGD automated data pipeline
33. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
34. Protein expression changes during human triple negative breast cancer cell line progression to lymph node metastasis in a xenografted model in nude mice. Roberti MP, etal., Cancer Biol Ther. 2012 Sep;13(11):1123-40. doi: 10.4161/cbt.21187. Epub 2012 Jul 24.
35. Oral administration of oleic or linoleic acid accelerates the inflammatory phase of wound healing. Rodrigues HG, etal., J Invest Dermatol. 2012 Jan;132(1):208-15. doi: 10.1038/jid.2011.265. Epub 2011 Sep 1.
36. MCP-1 and MIP3-alpha serum levels in acute liver failure and molecular adsorbent recirculating system (MARS) treatment: a pilot study. Roth GA, etal., Scand J Gastroenterol. 2009;44(6):745-51. doi: 10.1080/00365520902770086.
37. Corneal epithelial cells and stromal keratocytes efficently produce CC chemokine-ligand 20 (CCL20) and attract cells expressing its receptor CCR6 in mouse herpetic stromal keratitis. Shirane J, etal., Curr Eye Res. 2004 May;28(5):297-306.
38. Up-regulation of CC chemokine ligand 20 and its receptor CCR6 in the lesional skin of early systemic sclerosis. Tao J, etal., Eur J Dermatol. 2011 Sep-Oct;21(5):731-6. doi: 10.1684/ejd.2011.1469.
39. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
40. Macrophage inflammatory protein-3alpha plays a key role in the inflammatory cascade in rat focal cerebral ischemia. Terao Y, etal., Neurosci Res. 2009 May;64(1):75-82. doi: 10.1016/j.neures.2009.01.017. Epub 2009 Feb 13.
41. A novel rat CC chemokine, identified by targeted differential display, is upregulated in brain inflammation. Utans-Schneitz U, etal., J Neuroimmunol 1998 Dec 1;92(1-2):179-90.
42. Transcriptional regulation of inflammatory and extracellular matrix-regulating genes in cerebral arteries following experimental subarachnoid hemorrhage in rats. Laboratory investigation. Vikman P, etal., J Neurosurg. 2007 Nov;107(5):1015-22.
43. Late angiotensin II receptor blockade in progressive rat mesangioproliferative glomerulonephritis: new insights into mechanisms. Villa L, etal., J Pathol. 2013 Apr;229(5):672-84. doi: 10.1002/path.4151. Epub 2013 Mar 5.
44. Gene expression profiles of nasal polyps associated with allergic rhinitis. Wu J, etal., Am J Otolaryngol. 2009 Jan-Feb;30(1):24-32. doi: 10.1016/j.amjoto.2008.01.003. Epub 2008 Jul 9.
Additional References at PubMed
PMID:9862452   PMID:12081481   PMID:12949249   PMID:19050256   PMID:19109182   PMID:20068036   PMID:23620790   PMID:23765988   PMID:24638065   PMID:25122636   PMID:26704184   PMID:30619251  


Genomics

Comparative Map Data
Ccl20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8991,837,139 - 91,839,736 (+)NCBIGRCr8
mRatBN7.2984,389,031 - 84,391,629 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl984,388,904 - 84,391,629 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx992,819,272 - 92,821,849 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,947,738 - 97,950,315 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0996,330,459 - 96,333,051 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0988,918,359 - 88,921,017 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,918,433 - 88,921,001 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,662,765 - 88,665,379 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4982,440,965 - 82,443,542 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1982,624,383 - 82,626,960 (+)NCBI
Celera981,830,990 - 81,833,567 (+)NCBICelera
Cytogenetic Map9q35NCBI
CCL20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382227,813,842 - 227,817,556 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2227,805,739 - 227,817,564 (+)EnsemblGRCh38hg38GRCh38
GRCh372228,678,558 - 228,682,272 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362228,386,814 - 228,390,494 (+)NCBINCBI36Build 36hg18NCBI36
Build 342228,504,074 - 228,507,755NCBI
Celera2222,448,001 - 222,451,723 (+)NCBICelera
Cytogenetic Map2q36.3NCBI
HuRef2220,520,976 - 220,524,697 (+)NCBIHuRef
CHM1_12228,684,755 - 228,688,476 (+)NCBICHM1_1
T2T-CHM13v2.02228,296,236 - 228,299,949 (+)NCBIT2T-CHM13v2.0
Ccl20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39183,094,487 - 83,096,888 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl183,094,487 - 83,096,888 (+)EnsemblGRCm39 Ensembl
GRCm38183,116,766 - 83,119,167 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl183,116,766 - 83,119,167 (+)EnsemblGRCm38mm10GRCm38
MGSCv37183,113,341 - 83,115,742 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36182,995,806 - 82,998,190 (+)NCBIMGSCv36mm8
Celera183,181,441 - 83,183,842 (+)NCBICelera
Cytogenetic Map1C5NCBI
cM Map142.69NCBI
Ccl20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554536,846,549 - 6,850,031 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554536,846,625 - 6,850,007 (-)NCBIChiLan1.0ChiLan1.0
CCL20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213130,426,843 - 130,430,630 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B130,441,887 - 130,445,600 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B115,052,768 - 115,056,479 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B233,862,505 - 233,866,225 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B233,862,505 - 233,866,225 (+)Ensemblpanpan1.1panPan2
CCL20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12540,506,385 - 40,509,903 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2540,506,753 - 40,509,709 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2541,124,207 - 41,127,161 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02540,753,667 - 40,756,954 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2540,753,401 - 40,756,953 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12540,689,847 - 40,692,573 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02540,531,942 - 40,534,671 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02540,704,782 - 40,707,510 (+)NCBIUU_Cfam_GSD_1.0
Ccl20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303182,698,770 - 182,701,593 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365258,237,831 - 8,240,974 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365258,238,128 - 8,240,974 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCL20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.115129,172,743 - 129,176,069 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215143,050,303 - 143,053,630 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCL20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110113,815,099 - 113,836,562 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10113,832,573 - 113,835,736 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604085,618,590 - 85,622,439 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccl20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248432,017,738 - 2,021,153 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccl20
33 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:40
Count of miRNA genes:39
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000021730
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
12879506Pur33Proteinuria QTL 33urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat

Markers in Region
AB015136  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2984,391,211 - 84,391,296 (+)MAPPERmRatBN7.2
Rnor_6.0988,920,586 - 88,920,670NCBIRnor6.0
Rnor_5.0988,664,962 - 88,665,046UniSTSRnor5.0
RGSC_v3.4982,443,125 - 82,443,209UniSTSRGSC3.4
Celera981,833,150 - 81,833,234UniSTS
Cytogenetic Map9q34UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 1 49 47 52 64 35 18 35 6 160 71 39 44 40 29

Sequence


Ensembl Acc Id: ENSRNOT00000021730   ⟹   ENSRNOP00000021730
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl984,388,904 - 84,391,629 (+)Ensembl
Rnor_6.0 Ensembl988,918,433 - 88,921,001 (+)Ensembl
RefSeq Acc Id: NM_019233   ⟹   NP_062106
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8991,837,159 - 91,839,736 (+)NCBI
mRatBN7.2984,389,052 - 84,391,629 (+)NCBI
Rnor_6.0988,918,426 - 88,921,003 (+)NCBI
Rnor_5.0988,662,765 - 88,665,379 (+)NCBI
RGSC_v3.4982,440,965 - 82,443,542 (+)RGD
Celera981,830,990 - 81,833,567 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245164   ⟹   XP_006245226
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8991,837,139 - 91,839,736 (+)NCBI
mRatBN7.2984,389,031 - 84,391,629 (+)NCBI
Rnor_6.0988,918,359 - 88,921,017 (+)NCBI
Rnor_5.0988,662,765 - 88,665,379 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_062106 (Get FASTA)   NCBI Sequence Viewer  
  XP_006245226 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB61459 (Get FASTA)   NCBI Sequence Viewer  
  AAC78294 (Get FASTA)   NCBI Sequence Viewer  
  EDL75527 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021730.2
GenBank Protein P97884 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_062106   ⟸   NM_019233
- Peptide Label: precursor
- UniProtKB: P97884 (UniProtKB/Swiss-Prot),   A6JWB9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245226   ⟸   XM_006245164
- Peptide Label: isoform X1
- UniProtKB: A0A8L2QAZ9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000021730   ⟸   ENSRNOT00000021730
Protein Domains
Chemokine interleukin-8-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P97884-F1-model_v2 AlphaFold P97884 1-96 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696804
Promoter ID:EPDNEW_R7328
Type:single initiation site
Name:Ccl20_1
Description:C-C motif chemokine ligand 20
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0988,918,422 - 88,918,482EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3646 AgrOrtholog
BioCyc Gene G2FUF-26966 BioCyc
Ensembl Genes ENSRNOG00000015992 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021730.4 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Chemokine_b/g/d UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_CC_DCCL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29538 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29538 ENTREZGENE
PANTHER C-C MOTIF CHEMOKINE 20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12015 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam IL8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccl20 PhenoGen
RatGTEx ENSRNOG00000015992 RatGTEx
SMART SCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC203208
UniProt A0A8L2QAZ9 ENTREZGENE, UniProtKB/TrEMBL
  A6JWB9 ENTREZGENE, UniProtKB/TrEMBL
  CCL20_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Ccl20  C-C motif chemokine ligand 20  Ccl20  chemokine (C-C motif) ligand 20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Ccl20  chemokine (C-C motif) ligand 20  Scya20  small inducible cytokine subfamily A20  Symbol and Name updated 1299863 APPROVED
2002-06-10 Scya20  small inducible cytokine subfamily A20      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation expression is induced by TNF in the brain 69987