Cxcl12 (C-X-C motif chemokine ligand 12) - Rat Genome Database

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Pathways
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Gene: Cxcl12 (C-X-C motif chemokine ligand 12) Ictidomys tridecemlineatus
Analyze
Symbol: Cxcl12
Name: C-X-C motif chemokine ligand 12
RGD ID: 12653120
Description: ENCODES a protein that exhibits chemokine activity (inferred); chemokine receptor binding (inferred); CXCR chemokine receptor binding (inferred); INVOLVED IN adult locomotory behavior (ortholog); animal organ regeneration (ortholog); antimicrobial humoral immune response mediated by antimicrobial peptide (ortholog); PARTICIPATES IN hypoxia inducible factor pathway; syndecan signaling pathway; ASSOCIATED WITH anti-basement membrane glomerulonephritis (ortholog); brain ischemia (ortholog); breast carcinoma (ortholog); FOUND IN external side of plasma membrane (ortholog); extracellular space (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: C-X-C motif chemokine ligand 12, transcript variant X1; C-X-C motif chemokine ligand 12, transcript variant X2; stromal cell-derived factor 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721382,545,003 - 82,559,854 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366174,224,131 - 4,238,796 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366174,224,131 - 4,239,080 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult locomotory behavior  (ISO)
animal organ regeneration  (ISO)
antimicrobial humoral immune response mediated by antimicrobial peptide  (ISO)
blood vessel endothelial cell migration  (ISO)
brain development  (ISO)
branching involved in blood vessel morphogenesis  (ISO)
cell chemotaxis  (IEA)
cell-cell adhesion  (ISO)
cellular response to chemokine  (IEA)
chemokine (C-X-C motif) ligand 12 signaling pathway  (IEA)
chemokine-mediated signaling pathway  (IEA)
chemotaxis  (IEA)
CXCL12-activated CXCR4 signaling pathway  (IEA)
defense response  (IEA)
detection of mechanical stimulus involved in sensory perception of pain  (ISO)
detection of temperature stimulus involved in sensory perception of pain  (ISO)
dopaminergic neuron differentiation  (ISO)
germ cell development  (ISO)
germ cell migration  (ISO)
immune response  (IEA)
induction of positive chemotaxis  (ISO)
integrin activation  (IEA)
motor neuron axon guidance  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of dendritic cell apoptotic process  (IEA)
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage  (IEA)
negative regulation of leukocyte tethering or rolling  (IEA)
neuron migration  (ISO)
positive regulation of axon extension involved in axon guidance  (ISO)
positive regulation of calcium ion import  (ISO)
positive regulation of cell adhesion  (IEA,ISO)
positive regulation of cell migration  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of chemotaxis  (ISO)
positive regulation of dopamine secretion  (ISO)
positive regulation of endothelial cell proliferation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of monocyte chemotaxis  (IEA)
positive regulation of myoblast fusion  (ISO)
positive regulation of neuron differentiation  (ISO)
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
positive regulation of T cell migration  (IEA,ISO)
positive regulation of vasculature development  (IEA)
regulation of calcium ion transport  (ISO)
regulation of cell migration  (ISO)
response to hypoxia  (ISO)
response to mechanical stimulus  (ISO)
response to peptide hormone  (ISO)
response to ultrasound  (ISO)
signal transduction  (IEA)
T cell chemotaxis  (ISO)
T cell proliferation  (ISO)
telencephalon cell migration  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Cxcl12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721382,545,003 - 82,559,854 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366174,224,131 - 4,238,796 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366174,224,131 - 4,239,080 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CXCL12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381044,370,165 - 44,385,097 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1044,370,165 - 44,386,493 (-)EnsemblGRCh38hg38GRCh38
GRCh371044,865,613 - 44,880,545 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361044,185,611 - 44,200,548 (-)NCBINCBI36Build 36hg18NCBI36
Build 341044,192,516 - 44,200,551NCBI
Celera1040,869,153 - 40,884,099 (-)NCBICelera
Cytogenetic Map10q11.21NCBI
HuRef1041,391,945 - 41,406,899 (-)NCBIHuRef
CHM1_11044,904,782 - 44,919,728 (-)NCBICHM1_1
T2T-CHM13v2.01045,251,013 - 45,265,954 (-)NCBIT2T-CHM13v2.0
Cxcl12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396117,145,496 - 117,158,329 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6117,145,496 - 117,158,328 (+)EnsemblGRCm39 Ensembl
GRCm386117,168,535 - 117,181,368 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6117,168,535 - 117,181,367 (+)EnsemblGRCm38mm10GRCm38
MGSCv376117,118,553 - 117,131,386 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366117,134,182 - 117,146,986 (+)NCBIMGSCv36mm8
Celera6118,991,272 - 119,004,105 (+)NCBICelera
Cytogenetic Map6F1NCBI
cM Map654.81NCBI
Cxcl12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84152,060,781 - 152,073,628 (+)NCBIGRCr8
mRatBN7.24150,388,326 - 150,401,173 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4150,388,325 - 150,401,168 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4156,650,651 - 156,663,492 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04152,434,709 - 152,447,550 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04151,057,585 - 151,070,426 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04149,261,044 - 149,273,891 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4149,261,044 - 149,273,891 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04215,195,689 - 215,208,536 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44153,503,576 - 153,516,423 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14153,748,473 - 153,755,186 (+)NCBI
Celera4139,267,343 - 139,280,188 (+)NCBICelera
Cytogenetic Map4q42NCBI
Cxcl12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555461,929,269 - 1,941,690 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555461,929,269 - 1,941,690 (-)NCBIChiLan1.0ChiLan1.0
CXCL12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2857,109,201 - 57,125,606 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11057,114,523 - 57,132,612 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01041,296,975 - 41,384,864 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11044,476,962 - 44,564,231 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1044,552,480 - 44,564,231 (-)Ensemblpanpan1.1panPan2
CXCL12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1282,895,916 - 2,903,543 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha283,126,200 - 3,137,772 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0283,070,799 - 3,082,409 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl283,070,793 - 3,099,455 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1282,868,050 - 2,879,621 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0282,906,153 - 2,917,718 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0283,043,671 - 3,055,243 (+)NCBIUU_Cfam_GSD_1.0
CXCL12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1491,516,431 - 91,552,752 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11491,516,383 - 91,543,857 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21499,990,204 - 100,017,171 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CXCL12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1940,005,580 - 40,020,513 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl940,011,439 - 40,020,494 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605646,393,964 - 46,408,906 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cxcl12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249221,261,228 - 1,273,758 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249221,261,228 - 1,273,755 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSSTOT00000005943   ⟹   ENSSTOP00000005317
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049366174,229,802 - 4,238,796 (-)Ensembl
RefSeq Acc Id: ENSSTOT00000036328   ⟹   ENSSTOP00000029959
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049366174,224,131 - 4,238,796 (-)Ensembl
RefSeq Acc Id: XM_005334408   ⟹   XP_005334465
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440721382,545,003 - 82,556,831 (+)NCBI
SpeTri2.0NW_0049366174,227,154 - 4,239,080 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005334409   ⟹   XP_005334466
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440721382,545,022 - 82,559,854 (+)NCBI
SpeTri2.0NW_0049366174,224,131 - 4,239,029 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005334465 (Get FASTA)   NCBI Sequence Viewer  
  XP_005334466 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000005317.2
  ENSSTOP00000029959.1
GenBank Protein KAG3265026 (Get FASTA)   NCBI Sequence Viewer  
  KAG3265027 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_005334466   ⟸   XM_005334409
- Peptide Label: isoform X2
- UniProtKB: A0A287D8U4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005334465   ⟸   XM_005334408
- Peptide Label: isoform X1
- UniProtKB: I3M6Z7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000029959   ⟸   ENSSTOT00000036328
RefSeq Acc Id: ENSSTOP00000005317   ⟸   ENSSTOT00000005943
Protein Domains
Chemokine interleukin-8-like


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000005950 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000005943.3 UniProtKB/TrEMBL
  ENSSTOT00000036328.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/TrEMBL
InterPro Chemokine_b/g/d UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/TrEMBL
  CXC_Chemokine_domain UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/TrEMBL
NCBI Gene Cxcl12 ENTREZGENE
PANTHER SMALL INDUCIBLE CYTOKINE A UniProtKB/TrEMBL
  STROMAL CELL-DERIVED FACTOR 1 UniProtKB/TrEMBL
Pfam IL8 UniProtKB/TrEMBL
PRINTS INTERLEUKIN8 UniProtKB/TrEMBL
SMART SCY UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/TrEMBL
UniProt A0A287D8U4 ENTREZGENE, UniProtKB/TrEMBL
  I3M6Z7 ENTREZGENE, UniProtKB/TrEMBL