Ccl21a (chemokine (C-C motif) ligand 21A (serine)) - Rat Genome Database

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Gene: Ccl21a (chemokine (C-C motif) ligand 21A (serine)) Mus musculus
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Symbol: Ccl21a
Name: chemokine (C-C motif) ligand 21A (serine)
RGD ID: 1323746
MGI Page MGI
Description: Enables CCR7 chemokine receptor binding activity and chemokine activity. Involved in several processes, including dendritic cell dendrite assembly; negative regulation of dendritic cell dendrite assembly; and positive regulation of T cell chemotaxis. Acts upstream of or within induction of positive chemotaxis and lymph node development. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Is expressed in branchial arch; hemolymphoid system; lymph sac; renal vasculature; and trunk. Orthologous to human CCL21 (C-C motif chemokine ligand 21); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 100038965; 6CKBAC; 6CKBAC2; 6Cki; 6Ckine; ALP; AW987545; beta chemokine exodus-2; beta-chemokine exodus-2; C-C motif chemokine 21-like; C-C motif chemokine 21a; C-C motif chemokine 21b; c-C motif chemokine 21b-like; CC chemokine 6Ckine-ser; CCL21-Ser; CKb9; Exodus; exodus-2; Gm1987; MGC107632; plt; predicted gene 1987; S; Scya; Scya2; Scya21; SCYA21a; Scya21b; SLC; small inducible cytokine A21a; small-inducible cytokine A21a; small-inducible cytokine A21b; Tca; Tca4; thymus-derived chemotactic agent 4
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39442,772,860 - 42,773,991 (-)NCBIGRCm39mm39
GRCm39 Ensembl442,772,860 - 42,773,993 (-)Ensembl
GRCm38442,772,860 - 42,773,991 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl442,772,860 - 42,773,993 (-)EnsemblGRCm38mm10GRCm38
MGSCv37442,786,392 - 42,787,523 (-)NCBIGRCm37mm9NCBIm37
MGSCv36442,794,620 - 42,795,751 (-)NCBImm8
Cytogenetic Map4A5NCBI
cM Map422.43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of GTPase activity  (ISO)
antimicrobial humoral immune response mediated by antimicrobial peptide  (ISO)
cell chemotaxis  (ISO)
cell maturation  (IDA)
cellular response to chemokine  (IMP)
cellular response to interferon-gamma  (IBA)
cellular response to interleukin-1  (IBA)
cellular response to tumor necrosis factor  (IBA)
chemokine (C-C motif) ligand 21 signaling pathway  (IMP)
chemokine-mediated signaling pathway  (IBA)
chemotaxis  (IEA)
dendritic cell chemotaxis  (IDA,ISO)
dendritic cell dendrite assembly  (IDA)
eosinophil chemotaxis  (IBA)
establishment of T cell polarity  (ISO)
G protein-coupled receptor signaling pathway  (IBA,ISO)
immune response  (IEA)
immunological synapse formation  (IDA)
induction of positive chemotaxis  (IDA)
inflammatory response  (IBA)
killing of cells of other organism  (ISO)
lymph node development  (IMP)
lymphocyte chemotaxis  (IBA)
mesangial cell-matrix adhesion  (ISO)
monocyte chemotaxis  (IBA)
negative regulation of dendritic cell apoptotic process  (ISO)
negative regulation of dendritic cell dendrite assembly  (IDA)
negative regulation of leukocyte tethering or rolling  (ISO)
neutrophil chemotaxis  (IBA)
positive regulation of actin filament polymerization  (ISO)
positive regulation of cell adhesion mediated by integrin  (ISO)
positive regulation of cell motility  (ISO)
positive regulation of cell-matrix adhesion  (ISO)
positive regulation of chemotaxis  (IDA)
positive regulation of dendritic cell antigen processing and presentation  (IDA)
positive regulation of ERK1 and ERK2 cascade  (IBA,ISO)
positive regulation of filopodium assembly  (ISO)
positive regulation of glycoprotein biosynthetic process  (IDA)
positive regulation of GTPase activity  (IBA)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
positive regulation of JNK cascade  (ISO)
positive regulation of macrophage chemotaxis  (NAS)
positive regulation of myeloid dendritic cell chemotaxis  (ISO)
positive regulation of neutrophil chemotaxis  (ISO)
positive regulation of phosphatidylinositol 3-kinase activity  (ISO)
positive regulation of protein kinase activity  (ISO)
positive regulation of protein kinase B signaling  (ISO)
positive regulation of pseudopodium assembly  (ISO)
positive regulation of receptor-mediated endocytosis  (IDA)
positive regulation of T cell chemotaxis  (IMP)
positive regulation of T cell migration  (ISO)
release of sequestered calcium ion into cytosol  (ISO)
response to prostaglandin E  (ISO)
ruffle organization  (ISO)
T cell costimulation  (IDA)

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8405042   PMID:9022021   PMID:9257816   PMID:9300671   PMID:9419363   PMID:9507024   PMID:9531599   PMID:9548511   PMID:9927507   PMID:10329455   PMID:10349636   PMID:10523616  
PMID:10620605   PMID:11042159   PMID:11070085   PMID:11076861   PMID:11093154   PMID:11123313   PMID:11148224   PMID:11217851   PMID:11739486   PMID:11801632   PMID:11907075   PMID:11927535  
PMID:11944948   PMID:12055211   PMID:12077273   PMID:12080938   PMID:12093871   PMID:12200351   PMID:12466851   PMID:12477932   PMID:12496447   PMID:12609829   PMID:12707342   PMID:12732660  
PMID:12750361   PMID:14617751   PMID:15302902   PMID:15302903   PMID:15358618   PMID:15470021   PMID:15489334   PMID:15534368   PMID:15845449   PMID:15845453   PMID:15857154   PMID:16141072  
PMID:16141073   PMID:16473829   PMID:16602821   PMID:16815646   PMID:16982861   PMID:17382312   PMID:17721537   PMID:18287559   PMID:18809240   PMID:19164599   PMID:19234195   PMID:19398761  
PMID:19468303   PMID:19625643   PMID:19783990   PMID:19923453   PMID:20201039   PMID:20231530   PMID:20237296   PMID:20504947   PMID:20562329   PMID:20605225   PMID:21044143   PMID:21267068  
PMID:21441897   PMID:21559281   PMID:21593766   PMID:21611855   PMID:21750661   PMID:21873635   PMID:21930767   PMID:22884357   PMID:23329049   PMID:23620790   PMID:23643685   PMID:23750244  
PMID:24368807   PMID:24813163   PMID:25378482   PMID:25398010   PMID:25620669   PMID:26876174   PMID:27031839   PMID:27400149   PMID:27666000   PMID:28336912   PMID:28611158   PMID:28709801  
PMID:29077526   PMID:29279353   PMID:29784760   PMID:29877568   PMID:30914733   PMID:30988302   PMID:31968244   PMID:31980640   PMID:32289156   PMID:32366944   PMID:33707780  


Genomics

Comparative Map Data
Ccl21a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39442,772,860 - 42,773,991 (-)NCBIGRCm39mm39
GRCm39 Ensembl442,772,860 - 42,773,993 (-)Ensembl
GRCm38442,772,860 - 42,773,991 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl442,772,860 - 42,773,993 (-)EnsemblGRCm38mm10GRCm38
MGSCv37442,786,392 - 42,787,523 (-)NCBIGRCm37mm9NCBIm37
MGSCv36442,794,620 - 42,795,751 (-)NCBImm8
Cytogenetic Map4A5NCBI
cM Map422.43NCBI
CCL21
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl934,709,005 - 34,710,136 (-)EnsemblGRCh38hg38GRCh38
GRCh38934,709,005 - 34,710,136 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37934,709,002 - 34,710,133 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36934,699,002 - 34,700,147 (-)NCBINCBI36hg18NCBI36
Build 34934,699,001 - 34,700,147NCBI
Celera934,640,475 - 34,641,620 (-)NCBI
Cytogenetic Map9p13.3NCBI
HuRef934,663,256 - 34,664,418 (-)NCBIHuRef
CHM1_1934,708,790 - 34,709,952 (-)NCBICHM1_1
Ccl21
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2556,980,557 - 56,981,661 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl556,980,558 - 56,981,686 (-)Ensembl
Rnor_6.0558,197,678 - 58,198,782 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl558,197,680 - 58,198,782 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0562,722,614 - 62,723,718 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4559,238,897 - 59,240,001 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1559,239,077 - 59,240,180 (-)NCBI
Celera555,572,689 - 55,573,793 (-)NCBICelera
Cytogenetic Map5q22NCBI
Ccl21
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554721,427,710 - 1,429,102 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554721,427,660 - 1,428,771 (+)NCBIChiLan1.0ChiLan1.0
CCL21
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1935,353,768 - 35,354,924 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl935,353,768 - 35,354,924 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0934,545,248 - 34,546,801 (-)NCBIMhudiblu_PPA_v0panPan3
CCL21
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11151,375,107 - 51,375,790 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1150,003,106 - 50,003,792 (-)NCBI
ROS_Cfam_1.01152,316,124 - 52,316,815 (-)NCBI
UMICH_Zoey_3.11150,978,674 - 50,979,359 (-)NCBI
UNSW_CanFamBas_1.01150,846,574 - 50,847,257 (-)NCBI
UU_Cfam_GSD_1.01151,611,593 - 51,612,281 (-)NCBI
Ccl21
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947166,240,383 - 166,241,531 (-)NCBI
SpeTri2.0NW_0049365242,787,963 - 2,789,116 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCL21
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1031,933,733 - 32,094,583 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11032,093,783 - 32,094,482 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21036,233,288 - 36,233,987 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCL21
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11245,787,118 - 45,788,506 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1245,787,356 - 45,908,711 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603843,020,959 - 43,022,109 (+)NCBIVero_WHO_p1.0
Ccl21
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473639,121,575 - 39,122,708 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
AW987545  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4A5UniSTS
cM Map413.34UniSTS
cM Map413.3UniSTS
cM Map413.3UniSTS
Whitehead/MRC_RH4664.9UniSTS
AI159701  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4A5UniSTS
cM Map413.3UniSTS
cM Map413.34UniSTS
cM Map413.3UniSTS
Whitehead/MRC_RH4664.83UniSTS
Whitehead/MRC_RH4663.97UniSTS
Ccl21a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4A5UniSTS
cM Map413.34UniSTS
cM Map413.3UniSTS
cM Map413.3UniSTS
cM Map413.3UniSTS
cM Map413.34UniSTS
cM Map413.3UniSTS
Ccl21a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4A5UniSTS
cM Map413.34UniSTS
cM Map413.3UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11567249Elorr3_methanol induced loss of righting response 3 (mouse)43722677156183778Mouse
10401905Sicd3_mseizure-induced cell death 3 (mouse)Not determined4939552543760862Mouse
10401115Pgia35_mproteoglycan induced arthritis 35 (mouse)Not determined41256237746562509Mouse
12880405Jcdq1_mjoint cartilage degeneration QTL 1 (mouse)41256237746562509Mouse
4142318Lyr2_mlymphoma resistance 2 (mouse)Not determined1401045763365441Mouse
4142047Mvwf3_mmodifier of von Willebrand factor 3 (mouse)Not determined14010457117215009Mouse
1301203Alcp8_malcohol preference locus 8 (mouse)Not determined41739516051395290Mouse
1301237Alcp7_malcohol preference locus 7 (mouse)Not determined41739516051395290Mouse
4141555Nbwa2_mNZB and NZW autoimmunity 2 (mouse)Not determined41789251551892635Mouse
4141911W6q15_mweight 6 weeks QTL 15 (mouse)Not determined1789261689063979Mouse
1357645Lvrq9_mliver weight QTL 9 (mouse)Not determined41789261689063979Mouse
1357453Kidq4_mkidney weight QTL 4 (mouse)Not determined41789261689063979Mouse
39128211Lwq22_mliver weight QTL 22 (mouse)41789261689063979Mouse
25440481Moaq1_mmodifier of alien QTL 1 (mouse)41950000046000000Mouse
1300769Pcyts2_mplasmacytoma susceptibility 2 (mouse)Not determined42211194456112145Mouse
1302058Hrtfm3_mheart failure modifier 3 (mouse)Not determined42211194456112145Mouse
1302075Bdln6_mbody length 6 (mouse)Not determined42237344856373612Mouse
1301437Scon1_msucrose consumption 1 (mouse)Not determined42237344856373612Mouse
1301697Sluc18_msusceptibility to lung cancer 18 (mouse)Not determined42237344856373612Mouse
1302184Aaom1_mautoimmune aoritis in MRL mice 1 (mouse)Not determined42432229946332776Mouse
1300574Im2_mimmunoregulatory 2 (mouse)Not determined42807768262077816Mouse
1301586Stheal3_msoft tissue heal 3 (mouse)Not determined42865844262658566Mouse
1357877Synch1_msynechia 1 (mouse)Not determined42870992562710107Mouse
1301990Arvm1_mautoimmune renal vasculitis 1 (mouse)Not determined42933264663332776Mouse
4142290Ssrq9_mstress response QTL 9 (mouse)Not determined3439516046332776Mouse
1301792Hdlq10_mHDL QTL 10 (mouse)Not determined43585970769859853Mouse
1300977Mopkd1_mmodifier of polycystic kidney disease progression 1 (mouse)Not determined43655083970550967Mouse
26884449Sklq2_mskull length QTL 2, 5 week (mouse)436700000129100000Mouse
1302116Bbaa1_mB.burgdorferi-associated arthritis 1 (mouse)Not determined43825093072251078Mouse
10412178Habiir2_mhyperoxic acute lung injury imprinted region 2 (mouse)Not determined43945212663365441Mouse
1301786Bpq3_mblood pressure QTL 3 (mouse)Not determined44240224076402381Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:233
Count of miRNA genes:181
Interacting mature miRNAs:209
Transcripts:ENSMUST00000095114
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000095114   ⟹   ENSMUSP00000092732
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl442,772,860 - 42,773,993 (-)Ensembl
GRCm38.p6 Ensembl442,772,860 - 42,773,993 (-)Ensembl
RefSeq Acc Id: NM_011124   ⟹   NP_035254
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39442,772,860 - 42,773,991 (-)NCBI
GRCm38442,772,860 - 42,773,991 (-)ENTREZGENE
MGSCv37442,786,392 - 42,787,523 (-)RGD
cM Map4 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_035254   ⟸   NM_011124
- Peptide Label: precursor
- UniProtKB: P84444 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000092732   ⟸   ENSMUST00000095114

Promoters
RGD ID:6883160
Promoter ID:EPDNEW_M5031
Type:multiple initiation site
Name:Ccl21a_1
Description:Mus musculus chemokine (C-C motif) ligand 21A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38442,773,992 - 42,774,052EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1349183 AgrOrtholog
  MGI:3780156 AgrOrtholog
Ensembl Genes ENSMUSG00000057744
  ENSMUSG00000094686 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000092732 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000095114 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro CCL21 UniProtKB/Swiss-Prot
  Chemokine_b/g/d UniProtKB/Swiss-Prot
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot
  Interleukin_8-like_sf UniProtKB/Swiss-Prot
KEGG Report mmu:18829 UniProtKB/Swiss-Prot
MGD MGI:1349183 ENTREZGENE
NCBI Gene 18829 ENTREZGENE
PANTHER PTHR12015 UniProtKB/Swiss-Prot
  PTHR12015:SF72 UniProtKB/Swiss-Prot
Pfam IL8 UniProtKB/Swiss-Prot
PhenoGen Ccl21a PhenoGen
SMART SCY UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot
UniProt CC21A_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O09002 UniProtKB/Swiss-Prot
  O09006 UniProtKB/Swiss-Prot
  Q3U1J2 UniProtKB/Swiss-Prot
  Q91V84 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-10-29 Ccl21a  chemokine (C-C motif) ligand 21A (serine)  Gm1987  predicted gene 1987  Data Merged 737654 PROVISIONAL
2011-07-27 Ccl21a  chemokine (C-C motif) ligand 21A (serine)  Ccl21a  chemokine (C-C motif) ligand 21A  Symbol and/or name change 5135510 APPROVED