Cxcl12 C-X-C motif chemokine ligand 12 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cxcl12provided by RGD
Official Full Name: C-X-C motif chemokine ligand 12provided by RGD
Primary source: RGD:3651
See related: Ensembl:ENSRNOG00000013589
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Sdf1
Summary: a chemoattractant molecule; involved in cell migration [RGD, Feb 2006]
Expression: Biased expression in Spleen (RPKM 358.2), Liver (RPKM 284.3) and 9 other tissues See more
Orthologs: human mouse all

Genomic context

Location:: 4q42

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
106	current	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (149261044..149273891)
104	previous assembly	Rnor_5.0 (GCF_000001895.4)	4	NC_005103.3 (215195689..215208536)

Chromosome 4 - NC_005103.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

the inhibition of SDF1CXC4 signaling by the activation of A2A receptor and subsequent increase in the level of cAMP may be a potential method to ameliorate pulmonary arterial hypertension.
Title: Adenosine A(2A) receptor activation reverses hypoxia‑induced rat pulmonary artery smooth muscle cell proliferation via cyclic AMP‑mediated inhibition of the SDF1‑CXC4 signaling pathway.
The aim of the present study was to assess whether fibrosis markers, estrogen receptor (ER)alpha and the stromal derived factor (SDF)1/CXC chemokine receptor type 4 (CXCR4) axis are abnormally expressed in Intrauterine adhesions endometrium.
Title: Abnormal expression of fibrosis markers, estrogen receptor α and stromal derived factor‑1/chemokine (C‑X‑C motif) receptor‑4 axis in intrauterine adhesions.
Both bone marrow-derived endothelial progenitor cells and gastric endothelial cells express SDF-1 and CXCR4, which indicates direct paracrine interactions between these cells during neovascularization.
Title: In vitro model of vasculo-angiogenesis: demonstration that bone marrow derived endothelial progenitor cells form new hybrid capillary blood vessels jointly with gastric endothelial cells.
Activation of the SDF-1alpha/CXCR4 axis and NPS2143 could counteract CaSR activation.
Title: Stromal Cell-Derived Factor-1<i>α</i> Alleviates Calcium-Sensing Receptor Activation-Mediated Ischemia/Reperfusion Injury by Inhibiting Caspase-3/Caspase-9-Induced Cell Apoptosis in Rat Free Flaps.
we established the neurodegenerative role of MMP2 in cleaving SDF-1alpha to a neurotoxic fragment SDF-1(5-67).
Title: Traumatic brain injury induced matrix metalloproteinase2 cleaves CXCL12α (stromal cell derived factor 1α) and causes neurodegeneration.
the upregulation of CXCL12 via TNF-alpha/IL-1beta-dependent STAT3 activation contributes to oxaliplatin-induced chronic pain.
Title: Activation of STAT3-mediated CXCL12 up-regulation in the dorsal root ganglion contributes to oxaliplatin-induced chronic pain.
the lower expression levels of CXCR4 and p-AKT may be responsible for the impaired osteogenic ability and lower chemotactic activity towards SDF-1alpha of OVX-bone marrow mesenchymal stem cells .
Title: In vitro cell behaviors of bone mesenchymal stem cells derived from normal and postmenopausal osteoporotic rats.
The SDF-1alpha/CXCR4 axis drives proliferation and hypertrophy of and collagen production by CFs, PGVSMCs, and GMCs, particularly in cells from genetically hypertensive animals and when DPP4 is inhibited.
Title: SDF-1α (Stromal Cell-Derived Factor 1α) Induces Cardiac Fibroblasts, Renal Microvascular Smooth Muscle Cells, and Glomerular Mesangial Cells to Proliferate, Cause Hypertrophy, and Produce Collagen.
Findings from this study demonstrate that co-transplanting SDF-1-MSCs with NSCs improved motor functions and enhanced axon densities surrounding the lesion.
Title: Co-transplantation of mesenchymal and neural stem cells and overexpressing stromal-derived factor-1 for treating spinal cord injury.
therapeutic benefits of mesenchymal stem transplantation in neonatal hyperoxia-induced lung injury are in part mediated by SDF-1, through anti-inflammatory and angiogenesis promoting mechanisms.
Title: Stromal derived factor-1 mediates the lung regenerative effects of mesenchymal stem cells in a rodent model of bronchopulmonary dysplasia.

Submit: New GeneRIF Correction See all GeneRIFs (130)

Variation

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Pathways from BioSystems

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Axon guidance, organism-specific biosystem (from KEGG)
Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
Axon guidance, conserved biosystem (from KEGG)
Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
Chemokine receptors bind chemokines, organism-specific biosystem (from REACTOME)
Chemokine receptors bind chemokines, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Chemokine signaling pathway, organism-specific biosystem (from KEGG)
Chemokine signaling pathway, organism-specific biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
Chemokine signaling pathway, conserved biosystem (from KEGG)
Chemokine signaling pathway, conserved biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
Class A/1 (Rhodopsin-like receptors), organism-specific biosystem (from REACTOME)
Class A/1 (Rhodopsin-like receptors), organism-specific biosystemcomputationally inferred pathway (not manually curated)
Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
G alpha (i) signalling events, organism-specific biosystem (from REACTOME)
G alpha (i) signalling events, organism-specific biosystemcomputationally inferred pathway (not manually curated)
GPCR downstream signaling, organism-specific biosystem (from REACTOME)
GPCR downstream signaling, organism-specific biosystemcomputationally inferred pathway (not manually curated)
GPCR ligand binding, organism-specific biosystem (from REACTOME)
GPCR ligand binding, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Intestinal immune network for IgA production, organism-specific biosystem (from KEGG)
Intestinal immune network for IgA production, organism-specific biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
Intestinal immune network for IgA production, conserved biosystem (from KEGG)
Intestinal immune network for IgA production, conserved biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
Leukocyte transendothelial migration, organism-specific biosystem (from KEGG)
Leukocyte transendothelial migration, organism-specific biosystemLeukocyte migaration from the blood into tissues is vital for immune surveillance and inflammation. During this diapedesis of leukocytes, the leukocytes bind to endothelial cell adhesion molecules (C...
Leukocyte transendothelial migration, conserved biosystem (from KEGG)
Leukocyte transendothelial migration, conserved biosystemLeukocyte migaration from the blood into tissues is vital for immune surveillance and inflammation. During this diapedesis of leukocytes, the leukocytes bind to endothelial cell adhesion molecules (C...
NF-kappa B signaling pathway, organism-specific biosystem (from KEGG)
NF-kappa B signaling pathway, organism-specific biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
NF-kappa B signaling pathway, conserved biosystem (from KEGG)
NF-kappa B signaling pathway, conserved biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
Nuclear signaling by ERBB4, organism-specific biosystem (from REACTOME)
Nuclear signaling by ERBB4, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Pathways in cancer, organism-specific biosystem (from KEGG)
Pathways in cancer, organism-specific biosystem
Pathways in cancer
Peptide ligand-binding receptors, organism-specific biosystem (from REACTOME)
Peptide ligand-binding receptors, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Rheumatoid arthritis, organism-specific biosystem (from KEGG)
Rheumatoid arthritis, organism-specific biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
Rheumatoid arthritis, conserved biosystem (from KEGG)
Rheumatoid arthritis, conserved biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
Signal Transduction, organism-specific biosystem (from REACTOME)
Signal Transduction, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Signaling by ERBB4, organism-specific biosystem (from REACTOME)
Signaling by ERBB4, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Signaling by GPCR, organism-specific biosystem (from REACTOME)
Signaling by GPCR, organism-specific biosystemcomputationally inferred pathway (not manually curated)

General gene information

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Markers

D4Wox52 (e-PCR)
- UniSTS:518721

RH127482 (e-PCR)
- UniSTS:210792

RH138767 (e-PCR)
- UniSTS:220854

Cxcl12 (e-PCR), detects polymorphism
- UniSTS:502723

Cxcl12 (e-PCR), detects polymorphism
- UniSTS:506829

Homology

Homologs of the Cxcl12 gene: The Cxcl12 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, mouse, chicken, and frog.
Orthologs from Annotation Pipeline: 208 organisms have orthologs with human gene Cxcl12
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
CXCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
CXCR chemokine receptor binding	ISO Inferred from Sequence Orthology more info
chemokine activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
chemokine activity	ISO Inferred from Sequence Orthology more info
chemokine activity	TAS Traceable Author Statement more info	PubMed
chemokine receptor binding	ISO Inferred from Sequence Orthology more info
integrin binding	IEA Inferred from Electronic Annotation more info
integrin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
T cell proliferation	ISO Inferred from Sequence Orthology more info
adult locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
ameboidal-type cell migration	ISO Inferred from Sequence Orthology more info
animal organ regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
brain development	IEP Inferred from Expression Pattern more info	PubMed
brain development	ISO Inferred from Sequence Orthology more info
branching involved in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cell chemotaxis	ISO Inferred from Sequence Orthology more info
cell migration	TAS Traceable Author Statement more info	PubMed
cell-cell adhesion	ISO Inferred from Sequence Orthology more info
cellular response to chemokine	ISO Inferred from Sequence Orthology more info
chemokine (C-X-C motif) ligand 12 signaling pathway	IEA Inferred from Electronic Annotation more info
chemokine (C-X-C motif) ligand 12 signaling pathway	ISO Inferred from Sequence Orthology more info
chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
chemokine-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
defense response	IEA Inferred from Electronic Annotation more info
detection of mechanical stimulus involved in sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed
detection of temperature stimulus involved in sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed
dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
germ cell development	ISO Inferred from Sequence Orthology more info
germ cell migration	ISO Inferred from Sequence Orthology more info
immune response	IEA Inferred from Electronic Annotation more info
induction of positive chemotaxis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
induction of positive chemotaxis	ISO Inferred from Sequence Orthology more info
integrin activation	IEA Inferred from Electronic Annotation more info
integrin activation	ISO Inferred from Sequence Orthology more info
motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
negative regulation of dendritic cell apoptotic process	IEA Inferred from Electronic Annotation more info
negative regulation of dendritic cell apoptotic process	ISO Inferred from Sequence Orthology more info
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	IEA Inferred from Electronic Annotation more info
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	ISO Inferred from Sequence Orthology more info
negative regulation of leukocyte tethering or rolling	IEA Inferred from Electronic Annotation more info
negative regulation of leukocyte tethering or rolling	ISO Inferred from Sequence Orthology more info
neuron migration	IDA Inferred from Direct Assay more info	PubMed
positive regulation of T cell migration	IEA Inferred from Electronic Annotation more info
positive regulation of T cell migration	ISO Inferred from Sequence Orthology more info
positive regulation of axon extension involved in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of calcium ion import	ISO Inferred from Sequence Orthology more info
positive regulation of cell adhesion	IEA Inferred from Electronic Annotation more info
positive regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
positive regulation of cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of dopamine secretion	IDA Inferred from Direct Assay more info	PubMed
positive regulation of endothelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of monocyte chemotaxis	IEA Inferred from Electronic Annotation more info
positive regulation of monocyte chemotaxis	ISO Inferred from Sequence Orthology more info
positive regulation of myoblast fusion	ISO Inferred from Sequence Orthology more info
positive regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
regulation of calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
regulation of cell migration	ISO Inferred from Sequence Orthology more info
response to heat	IEP Inferred from Expression Pattern more info	PubMed
response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
response to peptide hormone	IEP Inferred from Expression Pattern more info	PubMed
response to radiation	IEP Inferred from Expression Pattern more info	PubMed
response to ultrasound	IEP Inferred from Expression Pattern more info	PubMed
telencephalon cell migration	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
external side of plasma membrane	ISO Inferred from Sequence Orthology more info
extracellular space	IDA Inferred from Direct Assay more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed
plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: stromal cell-derived factor 1

Names: SDF-1 gamma; chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1); stromal cell-derived factor-1 gamma

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001033882.1 → NP_001029054.1 stromal cell-derived factor 1 isoform beta precursor

See identical proteins and their annotated locations for NP_001029054.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an internal exon and uses an alternate penultimate exon, compared to variant 1, resulting in a novel 3' coding region and 3' UTR. It encodes isoform beta which is longer and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AABR07061848, CK475409, CV081127

Conserved Domains (1) summary

cd00273
Location:27 → 88

Chemokine_CXC; Chemokine_CXC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members ...
NM_001033883.1 → NP_001029055.1 stromal cell-derived factor 1 isoform gamma precursor

See identical proteins and their annotated locations for NP_001029055.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate 3' structure compared to variant 1, resulting in a novel 3' coding region and longer 3' UTR. It encodes isoform gamma which is longer and has a distinct C-terminus, compared to isoform alpha.

Source sequence(s)

AABR07061848, AF217564, CK475409

UniProtKB/TrEMBL

Q80YV8

Related

ENSRNOP00000059574.1, ENSRNOT00000066670.3

Conserved Domains (1) summary

cd00273
Location:27 → 88

Chemokine_CXC; Chemokine_CXC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members ...
NM_022177.3 → NP_071513.1 stromal cell-derived factor 1 isoform alpha precursor

See identical proteins and their annotated locations for NP_071513.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the isoform alpha.

Source sequence(s)

AF209976, BC078737, CK475409

UniProtKB/TrEMBL

Q9QZD1

Conserved Domains (1) summary

cd00273
Location:27 → 88

Chemokine_CXC; Chemokine_CXC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members ...