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
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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)
106	current	Rn_Celera (GCF_000002265.2)	4	AC_000072.1 (139267343..139280188)
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 Functions

What's a GeneRIF?

Stromal cell-derived factor-1 regulates the secretion of interleukin-1beta in the temporomandibular joint of rats with synovial inflammation.
Title: Stromal cell-derived factor-1 regulates the secretion of interleukin-1β in the temporomandibular joint of rats with synovial inflammation.
HIF-1alpha/SDF-1/CXCR4 axis reduces neuronal apoptosis via enhancing the bone marrow-derived mesenchymal stromal cell migration in rats with traumatic brain injury.
Title: HIF-1α/SDF-1/CXCR4 axis reduces neuronal apoptosis via enhancing the bone marrow-derived mesenchymal stromal cell migration in rats with traumatic brain injury.
CXCL12/CXCR4 signaling contributes to neuropathic pain via central sensitization mechanisms in a rat spinal nerve ligation model.
Title: CXCL12/CXCR4 signaling contributes to neuropathic pain via central sensitization mechanisms in a rat spinal nerve ligation model.
Houshiheisan promotes angiogenesis via HIF-1alpha/VEGF and SDF-1/CXCR4 pathways: in vivo and in vitro.
Title: Houshiheisan promotes angiogenesis via HIF-1α/VEGF and SDF-1/CXCR4 pathways: in vivo and in vitro.
CXCL12 was identified as a potential molecular linker between Dex-induced skeletal cell apoptosis and chondroclastic/osteoclastic recruitment, as well as growth plate cartilage/bone loss, revealing a therapeutic potential of CXCL12 functional blockade in preventing bone growth defects during/after Dex treatment.
Title: Release of CXCL12 From Apoptotic Skeletal Cells Contributes to Bone Growth Defects Following Dexamethasone Therapy in Rats.
Implicating SDF1 signaling in epithelial canalization.
Title: The role of SDF1 in prostate epithelial morphogenesis.
SDF-1 mediated apoptosis of cardiomyocytes is TNF-alpha-dependent.
Title: SDF-1 induces TNF-mediated apoptosis in cardiac myocytes.
These findings indicate the participation of spinal CXCL12/CXCR4 and NR2B-containing NMDAR pathway in anti-hyperalgesic action of ANXA1 in OIH.
Title: Annexin 1 inhibits remifentanil-induced hyperalgesia and NMDA receptor phosphorylation via regulating spinal CXCL12/CXCR4 in rats.
Combined VEGF165 and SDF-1 gene therapy represents a potential strategy for improving vascular remodeling and recovery of neural function after cerebral infarction.
Title: Effect of combined VEGF<sub>165</sub>/ SDF-1 gene therapy on vascular remodeling and blood perfusion in cerebral ischemia.
CXCL12 plays a protective role in facial nerve injury and promotes Schwann cells autophagy and migration via PI3K-AKT-mTOR signaling pathway.
Title: CXCL12 has therapeutic value in facial nerve injury and promotes Schwann cells autophagy and migration via PI3K-AKT-mTOR signal pathway.

Submit: New GeneRIF Correction See all GeneRIFs (145)

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: 328 organisms have orthologs with human gene Cxcl12
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
growth factor activity	IEA Inferred from Electronic Annotation more info
integrin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
T cell chemotaxis	ISO Inferred from Sequence Orthology more info
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
antimicrobial humoral immune response mediated by antimicrobial peptide	ISO Inferred from Sequence Orthology more info
axon guidance	IBA Inferred from Biological aspect of Ancestor 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	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
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	ISO Inferred from Sequence Orthology more info
killing of cells of other organism	ISO Inferred from Sequence Orthology more info
motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology 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 ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology 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	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 population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of chemotaxis	ISO Inferred from Sequence Orthology more info
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	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
positive regulation of protein kinase B signaling	ISO Inferred from Sequence Orthology more info
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; 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 contain an RCxC motif ...
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; 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 contain an RCxC motif ...
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; 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 contain an RCxC motif ...