CCL21 (C-C motif chemokine ligand 21) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: CCL21 (C-C motif chemokine ligand 21) Sus scrofa
Analyze
Symbol: CCL21
Name: C-C motif chemokine ligand 21
RGD ID: 14152742
Description: ENCODES a protein that exhibits CCR7 chemokine receptor binding (ortholog); INVOLVED IN antimicrobial humoral immune response mediated by antimicrobial peptide (ortholog); cell maturation (ortholog); cellular response to chemokine (ortholog); ASSOCIATED WITH acromesomelic dysplasia, Maroteaux type (ortholog); anauxetic dysplasia (ortholog); autosomal recessive distal hereditary motor neuronopathy 2 (ortholog); FOUND IN extracellular region (inferred); extracellular space (inferred); INTERACTS WITH deoxynivalenol; zearalenone
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-C motif chemokine 21; chemokine (C-C motif) ligand 21; putative CCL21 chemokine
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1032,093,763 - 32,096,224 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11032,093,783 - 32,094,482 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21036,233,288 - 36,233,987 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
antimicrobial humoral immune response mediated by antimicrobial peptide  (ISO)
cell chemotaxis  (IEA)
cell maturation  (ISO)
cellular response to chemokine  (ISO)
cellular response to interleukin-1  (IBA)
cellular response to tumor necrosis factor  (IBA)
cellular response to type II interferon  (IBA)
chemokine (C-C motif) ligand 21 signaling pathway  (ISO)
chemokine-mediated signaling pathway  (IBA)
chemotaxis  (IEA)
dendritic cell chemotaxis  (IEA)
dendritic cell dendrite assembly  (ISO)
establishment of T cell polarity  (IEA)
G protein-coupled receptor signaling pathway  (IBA,IEA)
immune response  (IEA)
immunological synapse formation  (ISO)
induction of positive chemotaxis  (ISO)
inflammatory response  (IBA)
lymph node development  (ISO)
lymphocyte chemotaxis  (IBA)
mesangial cell-matrix adhesion  (IEA)
monocyte chemotaxis  (IBA)
negative regulation of dendritic cell apoptotic process  (IEA)
negative regulation of dendritic cell dendrite assembly  (ISO)
negative regulation of leukocyte tethering or rolling  (IEA)
neutrophil chemotaxis  (IBA)
positive regulation of actin filament polymerization  (IEA)
positive regulation of canonical NF-kappaB signal transduction  (IEA)
positive regulation of cell adhesion mediated by integrin  (IEA)
positive regulation of cell motility  (IEA)
positive regulation of cell-matrix adhesion  (IEA)
positive regulation of chemotaxis  (ISO)
positive regulation of dendritic cell antigen processing and presentation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (IBA,IEA)
positive regulation of filopodium assembly  (IEA)
positive regulation of glycoprotein biosynthetic process  (ISO)
positive regulation of JNK cascade  (IEA)
positive regulation of myeloid dendritic cell chemotaxis  (IEA)
positive regulation of neutrophil chemotaxis  (IEA)
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (IEA)
positive regulation of pseudopodium assembly  (IEA)
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)
response to prostaglandin E  (IEA)
ruffle organization  (IEA)
signal transduction  (IEA)
T cell costimulation  (ISO)

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:15242943   PMID:17145712   PMID:22301074   PMID:30032202   PMID:30711450  


Genomics

Comparative Map Data
CCL21
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1032,093,763 - 32,096,224 (+)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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38934,709,005 - 34,710,136 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl934,709,005 - 34,710,136 (-)EnsemblGRCh38hg38GRCh38
GRCh37934,709,002 - 34,710,133 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36934,699,002 - 34,700,147 (-)NCBINCBI36Build 36hg18NCBI36
Build 34934,699,001 - 34,700,147NCBI
Celera934,640,475 - 34,641,620 (-)NCBICelera
Cytogenetic Map9p13.3NCBI
HuRef934,663,256 - 34,664,418 (-)NCBIHuRef
CHM1_1934,708,790 - 34,709,952 (-)NCBICHM1_1
T2T-CHM13v2.0934,728,031 - 34,729,162 (-)NCBIT2T-CHM13v2.0
Ccl21a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39442,772,860 - 42,773,991 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl442,772,860 - 42,773,993 (-)EnsemblGRCm39 Ensembl
GRCm38442,772,860 - 42,773,991 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl442,772,860 - 42,773,993 (-)EnsemblGRCm38mm10GRCm38
MGSCv37442,786,392 - 42,787,523 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36442,794,620 - 42,795,751 (-)NCBIMGSCv36mm8
Cytogenetic Map4A5NCBI
cM Map422.43NCBI
Ccl21
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8561,776,411 - 61,777,515 (-)NCBIGRCr8
mRatBN7.2556,980,557 - 56,981,661 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl556,980,558 - 56,981,686 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx558,954,871 - 58,955,975 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0560,773,700 - 60,774,804 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0560,759,810 - 60,760,914 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
NHGRI_mPanPan1-v21189,886,250 - 89,895,097 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1989,892,190 - 89,901,037 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0934,545,248 - 34,546,801 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1935,353,768 - 35,354,924 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl935,353,768 - 35,354,924 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01152,316,124 - 52,316,815 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1152,315,730 - 52,336,844 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11150,978,674 - 50,979,359 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01150,846,574 - 50,847,257 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01151,611,593 - 51,612,281 (-)NCBIUU_Cfam_GSD_1.0
Ccl21
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947166,240,383 - 166,241,531 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365242,788,341 - 2,789,016 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365242,787,963 - 2,789,116 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCL21
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11245,787,118 - 45,788,506 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1245,787,356 - 45,908,711 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603843,020,959 - 43,022,109 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccl21
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473639,121,466 - 39,122,962 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473639,121,575 - 39,122,708 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CCL21
9 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 3 2 4 2
Low 7 2 3 1 2 23 2 1 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001005151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AEMK02000074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ585194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK233720 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK233740 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK233904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK233936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK345072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346857 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK346960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK347052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK352389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY312067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU155482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FP236727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GFLN01125901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSSSCT00000051779   ⟹   ENSSSCP00000036350
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1032,093,763 - 32,096,224 (+)Ensembl
RefSeq Acc Id: NM_001005151   ⟹   NP_001005151
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11032,093,783 - 32,094,482 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001005151   ⟸   NM_001005151
- Peptide Label: precursor
- UniProtKB: Q6EKW3 (UniProtKB/TrEMBL),   A0A4X1USM3 (UniProtKB/TrEMBL),   F1S3U5 (UniProtKB/TrEMBL),   Q5K4L1 (UniProtKB/TrEMBL),   A0A8D1R4F7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000036350   ⟸   ENSSSCT00000051779

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000038162 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005045579 UniProtKB/TrEMBL
  ENSSSCG00015015691 UniProtKB/TrEMBL
  ENSSSCG00025051683 UniProtKB/TrEMBL
  ENSSSCG00030052262 UniProtKB/TrEMBL
  ENSSSCG00035046374 UniProtKB/TrEMBL
  ENSSSCG00040033105 UniProtKB/TrEMBL
  ENSSSCG00045003019 UniProtKB/TrEMBL
  ENSSSCG00050034856 UniProtKB/TrEMBL
  ENSSSCG00055018473 UniProtKB/TrEMBL
  ENSSSCG00060060436 UniProtKB/TrEMBL
  ENSSSCG00065069892 UniProtKB/TrEMBL
  ENSSSCG00070019612 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000051779 ENTREZGENE
  ENSSSCT00000051779.3 UniProtKB/TrEMBL
  ENSSSCT00005073721.1 UniProtKB/TrEMBL
  ENSSSCT00015020854.1 UniProtKB/TrEMBL
  ENSSSCT00025070712.1 UniProtKB/TrEMBL
  ENSSSCT00030072879.1 UniProtKB/TrEMBL
  ENSSSCT00035061673.1 UniProtKB/TrEMBL
  ENSSSCT00040044694.1 UniProtKB/TrEMBL
  ENSSSCT00045004851.1 UniProtKB/TrEMBL
  ENSSSCT00050046872.1 UniProtKB/TrEMBL
  ENSSSCT00055036316.1 UniProtKB/TrEMBL
  ENSSSCT00060082493.1 UniProtKB/TrEMBL
  ENSSSCT00065095975.1 UniProtKB/TrEMBL
  ENSSSCT00070038773.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/TrEMBL
InterPro Chemokine_b/g/d UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/TrEMBL
KEGG Report ssc:448797 UniProtKB/TrEMBL
NCBI Gene CCL21 ENTREZGENE
PANTHER PTHR12015 UniProtKB/TrEMBL
  PTHR12015:SF72 UniProtKB/TrEMBL
Pfam IL8 UniProtKB/TrEMBL
SMART SCY UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/TrEMBL
UniProt A0A4X1USM3 ENTREZGENE
  A0A8D1R4F7 ENTREZGENE, UniProtKB/TrEMBL
  F1S3U5 ENTREZGENE
  Q5K4L1 ENTREZGENE, UniProtKB/TrEMBL
  Q6EKW3 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A4X1USM3 UniProtKB/TrEMBL
  F1S3U5 UniProtKB/TrEMBL
VGNC ID VGNC:95485 ENTREZGENE