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 AllianceGenome:RGD:3651
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: Predicted to enable CXCR chemokine receptor binding activity; chemokine activity; and integrin binding activity. Involved in several processes, including detection of stimulus involved in sensory perception of pain; nervous system development; and regulation of ion transport. Located in several cellular components, including extracellular space; nucleus; and plasma membrane. Used to study myocardial infarction. Biomarker of anti-basement membrane glomerulonephritis; brain ischemia; myocardial infarction; status epilepticus; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in breast carcinoma; diabetic angiopathy; human immunodeficiency virus infectious disease; and type 1 diabetes mellitus. Orthologous to human CXCL12 (C-X-C motif chemokine ligand 12). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 358.2), Liver (RPKM 284.3) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 4q42

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
108	current	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (150388326..150401173)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (149261044..149273891)

Chromosome 4 - NC_051339.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Inflammation down regulates stromal cell-derived factor 1alpha in the early phase of pulpitis.
Title: Inflammation down regulates stromal cell-derived factor 1α in the early phase of pulpitis.
Schwann cell-derived EVs facilitate dental pulp regeneration through endogenous stem cell recruitment via SDF-1/CXCR4 axis.
Title: Schwann cell-derived EVs facilitate dental pulp regeneration through endogenous stem cell recruitment via SDF-1/CXCR4 axis.
CXCL12 promotes spinal nerve regeneration and functional recovery after spinal cord injury.
Title: CXCL12 promotes spinal nerve regeneration and functional recovery after spinal cord injury.
CXCL12 and its receptors regulate granulosa cell apoptosis in PCOS rats and human KGN tumor cells.
Title: CXCL12 and its receptors regulate granulosa cell apoptosis in PCOS rats and human KGN tumor cells.
Stromal cell-derived factor-1alpha predominantly mediates the ameliorative effect of linagliptin against cisplatin-induced testicular injury in adult male rats.
Title: Stromal cell-derived factor-1α predominantly mediates the ameliorative effect of linagliptin against cisplatin-induced testicular injury in adult male rats.
Electroacupuncture Alleviates Mechanical Allodynia in a Rat Model of Complex Regional Pain Syndrome Type-I via Suppressing Spinal CXCL12/CXCR4 Signaling.
Title: Electroacupuncture Alleviates Mechanical Allodynia in a Rat Model of Complex Regional Pain Syndrome Type-I via Suppressing Spinal CXCL12/CXCR4 Signaling.
CXCL12 promotes proliferation of radial glia like cells after traumatic brain injury in rats.
Title: CXCL12 promotes proliferation of radial glia like cells after traumatic brain injury in rats.
SDF-1 mediates mesenchymal stem cell recruitment and migration via the SDF-1/CXCR4 axis in bone defect.
Title: SDF-1 mediates mesenchymal stem cell recruitment and migration via the SDF-1/CXCR4 axis in bone defect.
Foam cells promote atherosclerosis progression by releasing CXCL12.
Title: Foam cells promote atherosclerosis progression by releasing CXCL12.
Intra-Articular Injection of Stromal Cell-Derived Factor 1alpha Promotes Meniscal Healing via Macrophage and Mesenchymal Stem Cell Accumulation in a Rat Meniscal Defect Model.
Title: Intra-Articular Injection of Stromal Cell-Derived Factor 1α Promotes Meniscal Healing via Macrophage and Mesenchymal Stem Cell Accumulation in a Rat Meniscal Defect Model.

Submit: New GeneRIF Correction See all GeneRIFs (155)

General gene information

Go to the top of the page Help

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: 449 organisms have orthologs with human gene Cxcl12
Orthologs

Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
involved_in T cell chemotaxis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in adult locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ameboidal-type cell migration	ISO Inferred from Sequence Orthology more info
involved_in animal organ regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within blood vessel endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in brain development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within branching involved in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in cell migration	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within cell-cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to chemokine	ISO Inferred from Sequence Orthology more info
involved_in chemokine (C-X-C motif) ligand 12 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in chemokine-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in defense response	IEA Inferred from Electronic Annotation more info
involved_in detection of mechanical stimulus involved in sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in detection of temperature stimulus involved in sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within germ cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within germ cell migration	ISO Inferred from Sequence Orthology more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in induction of positive chemotaxis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within induction of positive chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in integrin activation	ISO Inferred from Sequence Orthology more info
involved_in killing of cells of another organism	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dendritic cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of leukocyte tethering or rolling	ISO Inferred from Sequence Orthology more info
involved_in neuron migration	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of T cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of axon extension involved in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of calcium ion import	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dopamine secretion	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of endothelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of monocyte chemotaxis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of myoblast fusion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of protein kinase B signaling	ISO Inferred from Sequence Orthology more info
involved_in regulation of calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in response to heat	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to peptide hormone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to radiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to ultrasound	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within signal transduction	ISO Inferred from Sequence Orthology more info
involved_in telencephalon cell migration	IMP Inferred from Mutant Phenotype more info	PubMed

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

General protein information

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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)

CK475409, CV081127, JACYVU010000149

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)

AF217564, CK475409, JACYVU010000149

UniProtKB/TrEMBL

Q80YV8

Related

ENSRNOP00000059574.1, ENSRNOT00000066670.4

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 ...