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Gene: Ccl21 (C-C motif chemokine ligand 21) Rattus norvegicus

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Symbol:

Ccl21

Name:

C-C motif chemokine ligand 21

RGD ID:

1311996

Description:

Predicted to enable CCR7 chemokine receptor binding activity and chemokine activity. Predicted to be involved in several processes, including positive regulation of intracellular signal transduction; regulation of leukocyte migration; and regulation of plasma membrane bounded cell projection assembly. Predicted to act upstream of or within induction of positive chemotaxis; lymph node development; and positive regulation of T cell migration. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human CCL21 (C-C motif chemokine ligand 21); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

C-C motif chemokine 21; Ccl21b; chemokine (C-C motif) ligand 21; chemokine (C-C motif) ligand 21B; chemokine (C-C motif) ligand 21b (serine); LOC298006; MGC105669; small inducible cytokine A21

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CCL21 (C-C motif chemokine ligand 21)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Ccl21a (C-C motif chemokine ligand 21 (serine))	RGD	RGD
Chinchilla lanigera (long-tailed chinchilla):	Ccl21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CCL21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CCL21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ccl21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CCL21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CCL21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ccl21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Ccl21 (C-C motif chemokine ligand 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CCL21 (C-C motif chemokine ligand 21)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ccl21a (C-C motif chemokine ligand 21 (serine))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ccl21b (C-C motif chemokine ligand 21B (leucine))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ccl21e (C-C motif chemokine ligand 21E)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ccl21f (C-C motif chemokine ligand 21F)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ccl21d (C-C motif chemokine ligand 21D)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	61,776,411 - 61,777,515 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	5	61,776,413 - 61,777,540 (-)	Ensembl				GRCr8
mRatBN7.2	5	56,980,557 - 56,981,661 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	56,980,558 - 56,981,686 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	5	58,954,871 - 58,955,975 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	60,773,700 - 60,774,804 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	60,759,810 - 60,760,914 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	58,197,678 - 58,198,782 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	58,197,680 - 58,198,782 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	5	62,722,614 - 62,723,718 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	5	59,238,897 - 59,240,001 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	5	55,572,689 - 55,573,793 (-)	NCBI		Celera
RGSC_v3.1	5	59,239,077 - 59,240,180 (-)	NCBI
Cytogenetic Map	5	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Cytomegalovirus Infections (ISO)

pulmonary fibrosis (ISO)

rheumatoid arthritis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-nitropyrene (ISO)

17beta-estradiol (EXP,ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

3,4-methylenedioxymethamphetamine (ISO)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

aflatoxin B1 (ISO)

amphibole asbestos (ISO)

arsane (ISO)

arsenic atom (ISO)

Azoxymethane (ISO)

benzo[a]pyrene (ISO)

beta-naphthoflavone (EXP)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bromoacetate (ISO)

Butylbenzyl phthalate (EXP,ISO)

cadmium atom (ISO)

cantharidin (ISO)

capecitabine (ISO)

carbon nanotube (ISO)

copper atom (EXP)

copper(0) (EXP)

dextran sulfate (ISO)

dibutyl phthalate (ISO)

diethyl phthalate (ISO)

dihydroxyacetone (ISO)

diisobutyl phthalate (ISO)

diisononyl phthalate (ISO)

dimethylarsinic acid (EXP)

dioxygen (EXP)

disodium selenite (ISO)

diuron (EXP)

doxorubicin (ISO)

fenofibrate (EXP)

folic acid (ISO)

fragrance (ISO)

furan (EXP)

glyphosate (EXP)

hydrogen peroxide (ISO)

indole-3-methanol (EXP)

iron(2+) sulfate (anhydrous) (ISO)

kojic acid (ISO)

L-ascorbic acid (ISO)

lipopolysaccharide (ISO)

maneb (ISO)

metformin (ISO)

methotrexate (ISO)

monosodium L-glutamate (ISO)

N-nitrosodiethylamine (EXP,ISO)

nickel atom (ISO)

nitrofen (EXP)

oxybenzone (EXP)

ozone (ISO)

paclitaxel (EXP)

paraquat (EXP,ISO)

PCB138 (EXP)

pirinixic acid (EXP)

propanal (ISO)

pyridaben (ISO)

resveratrol (EXP)

silicon dioxide (EXP,ISO)

sodium arsenite (ISO)

taurodeoxycholic acid (ISO)

tetrachloromethane (EXP)

thioacetamide (EXP)

titanium dioxide (ISO)

usnic acid (ISO)

valproic acid (ISO)

vinclozolin (EXP)

zearalenone (ISO)

zinc molecular entity (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

antimicrobial humoral immune response mediated by antimicrobial peptide (ISO)

CCL21-activated CCR7 signaling pathway (IEA,ISO)

cell chemotaxis (IEA,ISO)

cell maturation (ISO)

cellular response to chemokine (ISO)

cellular response to prostaglandin E stimulus (IEA,ISO)

chemokine (C-C motif) ligand 21 signaling pathway (ISO)

chemotaxis (IEA)

dendritic cell chemotaxis (IEA,ISO)

dendritic cell dendrite assembly (ISO)

establishment of T cell polarity (IEA,ISO)

G protein-coupled receptor signaling pathway (IEA,ISO)

immune response (IEA)

immunological synapse formation (ISO)

induction of positive chemotaxis (ISO)

inflammatory response (IEA)

lymph node development (ISO)

mesangial cell-matrix adhesion (IEA,ISO)

negative regulation of dendritic cell apoptotic process (IEA,ISO)

negative regulation of dendritic cell dendrite assembly (ISO)

negative regulation of leukocyte tethering or rolling (IEA,ISO)

positive regulation of actin filament polymerization (IEA,ISO)

positive regulation of canonical NF-kappaB signal transduction (IEA,ISO)

positive regulation of cell adhesion mediated by integrin (IEA,ISO)

positive regulation of cell motility (IEA,ISO)

positive regulation of cell-matrix adhesion (IEA,ISO)

positive regulation of chemotaxis (ISO)

positive regulation of dendritic cell antigen processing and presentation (ISO)

positive regulation of ERK1 and ERK2 cascade (IEA,ISO)

positive regulation of filopodium assembly (IEA,ISO)

positive regulation of glycoprotein biosynthetic process (ISO)

positive regulation of JNK cascade (IEA,ISO)

positive regulation of myeloid dendritic cell chemotaxis (IEA,ISO)

positive regulation of neutrophil chemotaxis (IEA,ISO)

positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (IEA,ISO)

positive regulation of phospholipase C/protein kinase C signal transduction (IEA,ISO)

positive regulation of pseudopodium assembly (IEA,ISO)

positive regulation of receptor-mediated endocytosis (ISO)

positive regulation of T cell chemotaxis (ISO)

positive regulation of T cell migration (IEA,ISO)

release of sequestered calcium ion into cytosol (IEA,ISO)

ruffle organization (IEA,ISO)

T cell costimulation (ISO)

Cellular Component

extracellular region (IEA)

extracellular space (IEA)

Molecular Function

CCR7 chemokine receptor binding (ISO)

chemokine activity (IEA,ISO)

chemokine receptor binding (IEA,ISO)

cytokine activity (IEA)

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	CCR7 deficiency leads to leukocyte activation and increased clearance in response to pulmonary Pseudomonas aeruginosa infection.	Eppert BL, etal., Infect Immun. 2010 May;78(5):2099-107. Epub 2010 Feb 22.
2.	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.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Dendritic cells accumulate in human fibrotic interstitial lung disease.	Marchal-Somme J, etal., Am J Respir Crit Care Med. 2007 Nov 15;176(10):1007-14. Epub 2007 Aug 23.
5.	The chemokine binding protein M3 prevents diabetes induced by multiple low doses of streptozotocin.	Martin AP, etal., J Immunol. 2007 Apr 1;178(7):4623-31.
6.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
7.	GOA pipeline	RGD automated data pipeline
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Characterization of cytomegalovirus disease in solid organ transplant recipients by markers of inflammation in plasma.	Rollag H, etal., PLoS One. 2013 Apr 8;8(4):e60767. doi: 10.1371/journal.pone.0060767. Print 2013.

Additional References at PubMed

PMID:9507024	PMID:9548511	PMID:11242036	PMID:12200351	PMID:12477932	PMID:12609829	PMID:12729902	PMID:12732660	PMID:12949249	PMID:14592837	PMID:15059845	PMID:15569314
PMID:15778365	PMID:15845453	PMID:18308860	PMID:21051556	PMID:23341447	PMID:23620790	PMID:33089280	PMID:33651836

Genomics

Comparative Map Data

Ccl21
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	61,776,411 - 61,777,515 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	5	61,776,413 - 61,777,540 (-)	Ensembl				GRCr8
mRatBN7.2	5	56,980,557 - 56,981,661 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	56,980,558 - 56,981,686 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	5	58,954,871 - 58,955,975 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	60,773,700 - 60,774,804 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	60,759,810 - 60,760,914 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	58,197,678 - 58,198,782 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	58,197,680 - 58,198,782 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	5	62,722,614 - 62,723,718 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	5	59,238,897 - 59,240,001 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	5	55,572,689 - 55,573,793 (-)	NCBI		Celera
RGSC_v3.1	5	59,239,077 - 59,240,180 (-)	NCBI
Cytogenetic Map	5	q22	NCBI

CCL21
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	34,709,005 - 34,710,136 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	34,709,005 - 34,710,167 (-)	Ensembl			hg38	GRCh38
GRCh37	9	34,709,002 - 34,710,133 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	34,699,002 - 34,700,147 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	9	34,699,001 - 34,700,147	NCBI
Celera	9	34,640,475 - 34,641,620 (-)	NCBI		Celera
Cytogenetic Map	9	p13.3	NCBI
HuRef	9	34,663,256 - 34,664,418 (-)	NCBI		HuRef
CHM1_1	9	34,708,790 - 34,709,952 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	9	34,728,031 - 34,729,162 (-)	NCBI		T2T-CHM13v2.0

Ccl21a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	42,772,860 - 42,773,991 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	42,772,860 - 42,773,993 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	4	42,772,860 - 42,773,991 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	42,772,860 - 42,773,993 (-)	Ensembl			mm10	GRCm38
MGSCv37	4	42,786,392 - 42,787,523 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	4	42,794,620 - 42,795,751 (-)	NCBI		MGSCv36	mm8
Cytogenetic Map	4	A5	NCBI
cM Map	4	22.43	NCBI

Ccl21
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955472	1,427,710 - 1,429,102 (+)	Ensembl
ChiLan1.0	NW_004955472	1,427,660 - 1,428,771 (+)	NCBI	ChiLan1.0	ChiLan1.0

CCL21
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	11	89,886,250 - 89,895,097 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	89,892,190 - 89,901,037 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	34,545,248 - 34,546,801 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	35,353,768 - 35,354,924 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	35,353,768 - 35,354,924 (-)	Ensembl			panPan2	panpan1.1

CCL21
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	11	51,375,107 - 51,375,790 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	11	50,003,106 - 50,003,792 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	11	52,316,124 - 52,316,815 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	11	52,315,730 - 52,336,844 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	11	50,978,674 - 50,979,359 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	11	50,846,574 - 50,847,257 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	11	51,611,593 - 51,612,281 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Ccl21
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	166,240,383 - 166,241,531 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936524	2,788,341 - 2,789,016 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936524	2,787,963 - 2,789,116 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CCL21
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	10	32,093,763 - 32,096,224 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	10	32,093,783 - 32,094,482 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	10	36,233,288 - 36,233,987 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CCL21
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	12	45,787,118 - 45,788,506 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	45,787,356 - 45,908,711 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666038	43,020,959 - 43,022,109 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Ccl21
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624736	39,121,466 - 39,122,962 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624736	39,121,575 - 39,122,708 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Ccl21
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	1	3,744,532 - 3,745,656 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Ccl21
13 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	71
Count of miRNA genes:	58
Interacting mature miRNAs:	67
Transcripts:	ENSRNOT00000023951
Prediction methods:	Miranda, Rnahybrid, Targetscan
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1578776	Stresp18	Stress response QTL 18	2.9		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	5	32751649	77751649	Rat
1298067	Scl15	Serum cholesterol level QTL 15	4.8	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	38011670	83011670	Rat
1300115	Hrtrt7	Heart rate QTL 7	2.76		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	5	52665372	94894052	Rat
6907115	Mcs29	Mammary carcinoma susceptibility QTL 29			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	38004331	83004331	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	44924861	153890773	Rat
1358353	Srcrtb2	Stress Responsive Cort Basal QTL 2	3.48	0.003	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	23671493	79046465	Rat
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	38207390	136631402	Rat
634305	Mamtr1	Mammary tumor resistance QTL 1		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	17576633	62576633	Rat
1331801	Rf33	Renal function QTL 33	4.149		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	48523123	134369373	Rat
1598807	Glom12	Glomerulus QTL 12	2.7		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	5	38011670	83011670	Rat
1302786	Kidm8	Kidney mass QTL 8	28.15		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	5	38011670	83011670	Rat
1331782	Rf36	Renal function QTL 36	3.296		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	39019942	102105896	Rat
6903292	Stl28	Serum triglyceride level QTL 28	2.6	0.0073	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	5	33311673	78311673	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	51657967	166600247	Rat
1578767	Stresp17	Stress response QTL 17	4.3	0.01	blood aldosterone amount (VT:0005346)	plasma aldosterone level (CMO:0000551)	5	32751649	77751649	Rat
1641922	Alcrsp8	Alcohol response QTL 8			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	5	17486080	62486080	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	55124766	172190305	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	39985948	84985948	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	6922282	81330203	Rat
6903306	Scl35	Serum cholesterol QTL 35	2.6	0.0073	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	33311673	78311673	Rat
1576317	Eutr2	Estrogen induced uterine response QTL 2		0.01	uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	39526924	84526924	Rat
1331773	Scl26	Serum cholesterol level QTL 26	3.065		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	48523123	91770353	Rat
70189	Mcs5	Mammary carcinoma susceptibility QTL 5	10.51		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	60601597	137492949	Rat
1331771	Rf35	Renal function QTL 35	4.36965		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	10019064	91770353	Rat
61359	Eaex	Experimental allergic encephalomyelitis QTL x	3		nervous system integrity trait (VT:0010566)	post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)	5	60511627	105511627	Rat
8662454	Vetf3	Vascular elastic tissue fragility QTL 3	27.4		artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	5	7065535	74335773	Rat
2290448	Scl54	Serum cholesterol level QTL 54	2.93		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	36460764	136631402	Rat
1641903	Alcrsp3	Alcohol response QTL 3			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	17486080	62486080	Rat
1331756	Rf34	Renal function QTL 34	4.16275		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	10019064	87027358	Rat
8552954	Pigfal14	Plasma insulin-like growth factor 1 level QTL 14	9		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	26023211	71023211	Rat
2316959	Gluco59	Glucose level QTL 59	4.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	56546393	101546393	Rat
1600358	Mamtr5	Mammary tumor resistance QTL 5			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	23671493	68671493	Rat

Markers in Region

RH130156

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	56,980,647 - 56,980,866 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	58,197,769 - 58,197,987	NCBI	Rnor6.0
Rnor_5.0	5	62,722,705 - 62,722,923	UniSTS	Rnor5.0
RGSC_v3.4	5	59,238,988 - 59,239,206	UniSTS	RGSC3.4
Celera	5	55,572,780 - 55,572,998	UniSTS
Cytogenetic Map	5	q22	UniSTS

Ccl21a

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	56,980,692 - 56,981,115 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	58,197,814 - 58,198,236	NCBI	Rnor6.0
Rnor_5.0	5	62,722,750 - 62,723,172	UniSTS	Rnor5.0
RGSC_v3.4	5	59,239,033 - 59,239,455	UniSTS	RGSC3.4
Celera	5	55,572,825 - 55,573,247	UniSTS
Cytogenetic Map	5	q22	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	11	51	74	80	79	48	27	48	6	250	110	9	47	68	90	31	1	1

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001008513	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC110351	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC086571	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473962	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ218040	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220091	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223815	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225478	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226079	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233622	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234695	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000023951 ⟹ ENSRNOP00000023951

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	5	61,776,413 - 61,777,540 (-)	Ensembl
mRatBN7.2 Ensembl	5	56,980,559 - 56,981,686 (-)	Ensembl
Rnor_6.0 Ensembl	5	58,197,680 - 58,198,782 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000117300 ⟹ ENSRNOP00000080937

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	56,980,558 - 56,981,686 (-)	Ensembl

RefSeq Acc Id:

NM_001008513 ⟹ NP_001008513

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	61,776,411 - 61,777,515 (-)	NCBI
mRatBN7.2	5	56,980,557 - 56,981,661 (-)	NCBI
Rnor_6.0	5	58,197,678 - 58,198,782 (-)	NCBI
Rnor_5.0	5	62,722,614 - 62,723,718 (-)	NCBI
RGSC_v3.4	5	59,238,897 - 59,240,001 (-)	RGD
Celera	5	55,572,689 - 55,573,793 (-)	RGD

Sequence:

show sequence

GTCCATCTCACCTACAGCTCTGGTCTCATCCTCAACTCAACCACAGCCATGGCTCAGATGCTGG
CTCTGAGCCTCCTTAGCTTGGTCCTGGTTCTCTGCGTCCCGTGGACCCAAGGCAGTGACGGAGG
GGGTCAGGACTGCTGTCTTAGGTACAGCCAGAAGAAGATTCCCTACAACATTGTCCGAGGCTAC
AGGAAGCAAGAACCGAGCCTAGGTTGCCCCATCCCAGCAATCCTGTTCGCACCCCGGAAGCAAT
CTCAGCCTGAGCTATGCGCAAACCCTGAGGAAGCCTGGGTGCAGAAGCTGATGCGACGTCTGGA
CCAGCCTCCAGCCCCAGGGAAACAAAACTGCAGGAAGAATCGAGGAACCTCTAAGTCTGGGAAG
AAAGGAAGGGGCTCCAAAGGCTGCAAGGGGACTGAACAGACAGACTCCAAGAGGGTATCCCAGT
GACATGCCTGGAGTCCAGGAAGTCCTCCGTGAACTTCAACCTGAGTGCTTCACAGTCCAACTCA
CAGGCAAAGAGGGAGCTAGAGAGCAGAAAGACTCAGGGGCCCCAGAGCAGTCACCTCATGCTGG
CCTTGTCACACCCTTGTCTGCTTCAACCATCACATCTGCATGGCCGTCCCTTTCTTCTATGGCG
GAGCGGCCTTCCCTGGGATAGACCTAGGGAGTCAGAAGAAAGAGTGTCTCCCAGGGAAGGAAGA
AGGAGACAGCAGGACTGTCCCCTCTAGGAGGTCACTCAGGTCCCAAGACCTGCACTTGCTCTCC
ATGGCACCCTTCCTTTTTCCTTGCACCTATGATATATACCTAACTGAATAAAAAGCTGGTCCAG
CCTCAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001008513	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH86571	(Get FASTA)	NCBI Sequence Viewer
	EDL98707	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000023951
	ENSRNOP00000023951.4

RefSeq Acc Id:	NP_001008513 ⟸ NM_001008513
- Peptide Label:	precursor
- UniProtKB:	Q5RJN3 (UniProtKB/TrEMBL), A6IIY7 (UniProtKB/TrEMBL), A0A8I5ZU27 (UniProtKB/TrEMBL), F8WFI8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAQMLALSLLSLVLVLCVPWTQGSDGGGQDCCLRYSQKKIPYNIVRGYRKQEPSLGCPIPAILF APRKQSQPELCANPEEAWVQKLMRRLDQPPAPGKQNCRKNRGTSKSGKKGRGSKGCKGTEQTDS KRVSQ hide sequence

Ensembl Acc Id:

ENSRNOP00000023951 ⟸ ENSRNOT00000023951

Ensembl Acc Id:

ENSRNOP00000080937 ⟸ ENSRNOT00000117300

Protein Domains

Chemokine interleukin-8-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5RJN3-F1-model_v2	AlphaFold	Q5RJN3	1-133	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693663

Promoter ID:

EPDNEW_R4187

Type:

single initiation site

Name:

Ccl21_1

Description:

C-C motif chemokine ligand 21

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	58,198,806 - 58,198,866	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311996	AgrOrtholog
BioCyc Gene	G2FUF-41533	BioCyc
Ensembl Genes	ENSRNOG00000034290	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000023951	ENTREZGENE
	ENSRNOT00000023951.8	UniProtKB/TrEMBL
Gene3D-CATH	2.40.50.40	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7304213	IMAGE-MGC_LOAD
InterPro	Chemokine_b/g/d	UniProtKB/TrEMBL
	Chemokine_IL8	UniProtKB/TrEMBL
	Interleukin_8-like_sf	UniProtKB/TrEMBL
KEGG Report	rno:298006	UniProtKB/TrEMBL
MGC_CLONE	MGC:105669	IMAGE-MGC_LOAD
NCBI Gene	298006	ENTREZGENE
PANTHER	PTHR12015	UniProtKB/TrEMBL
	PTHR12015:SF72	UniProtKB/TrEMBL
Pfam	IL8	UniProtKB/TrEMBL
PhenoGen	Ccl21	PhenoGen
RatGTEx	ENSRNOG00000034290	RatGTEx
SMART	SCY	UniProtKB/TrEMBL
Superfamily-SCOP	Chemokine_IL8	UniProtKB/TrEMBL
UniProt	A0A8I5ZU27	ENTREZGENE
	A6IIY7	ENTREZGENE, UniProtKB/TrEMBL
	F8WFI8	ENTREZGENE, UniProtKB/TrEMBL
	Q5RJN3	ENTREZGENE
UniProt Secondary	Q5RJN3	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-03-08	Ccl21	C-C motif chemokine ligand 21	Ccl21	chemokine (C-C motif) ligand 21	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2011-04-29	Ccl21	chemokine (C-C motif) ligand 21	Ccl21b	chemokine (C-C motif) ligand 21B	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2011-04-14	Ccl21b	chemokine (C-C motif) ligand 21B	Ccl21b	chemokine (C-C motif) ligand 21b	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2010-04-20	Ccl21b	chemokine (C-C motif) ligand 21b	Ccl21b	chemokine (C-C motif) ligand 21b (serine)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Ccl21b	chemokine (C-C motif) ligand 21b (serine)	Ccl21b_predicted	chemokine (C-C motif) ligand 21b (serine) (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Ccl21b_predicted	chemokine (C-C motif) ligand 21b (serine) (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD