Cxcl12 C-X-C motif chemokine ligand 12 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cxcl12provided by MGI
Official Full Name: C-X-C motif chemokine ligand 12provided by MGI
Primary source: MGI:MGI:103556
See related: Ensembl:ENSMUSG00000061353 AllianceGenome:MGI:103556
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Pbsf; Sdf1; Tlsf; Tpar1; Scyb12
Summary: This gene encodes a member of the alpha chemokine protein family. The encoded protein is secreted and functions as the ligand for the G-protein coupled receptor, chemokine (C-X-C motif) receptor 4. The encoded protein plays a role in many diverse cellular functions, including embryogenesis, immune surveillance, inflammation response, tissue homeostasis, and tumor growth and metastasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
Expression: Ubiquitous expression in spleen adult (RPKM 77.0), liver adult (RPKM 50.9) and 27 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 6 54.81 cM; 6 F1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (117145496..117158329)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (117168535..117181368)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[Stromal Cell-Derived Factor 1alpha Inhibits Chondrocyte Apoptosis and Promotes Autophagy Through the Akt Signaling Pathway].
Title: [Stromal Cell-Derived Factor 1α Inhibits Chondrocyte Apoptosis and Promotes Autophagy Through the Akt Signaling Pathway].
FOXC1 Promotes Osteoblastic Differentiation of Bone Marrow Mesenchymal Stem Cells via the Dnmt3b/CXCL12 Axis.
Title: FOXC1 Promotes Osteoblastic Differentiation of Bone Marrow Mesenchymal Stem Cells via the Dnmt3b/CXCL12 Axis.
The bone-liver interaction modulates immune and hematopoietic function through Pinch-Cxcl12-Mbl2 pathway.
Title: The bone-liver interaction modulates immune and hematopoietic function through Pinch-Cxcl12-Mbl2 pathway.
CXCL12 promotes the crossing of retinal ganglion cell axons at the optic chiasm.
Title: CXCL12 promotes the crossing of retinal ganglion cell axons at the optic chiasm.
Hedgehog signalling in Foxd1+ embryonic kidney stromal progenitors controls nephron formation via Cxcl12 and Wnt5a.
Title: Hedgehog signalling in Foxd1+ embryonic kidney stromal progenitors controls nephron formation via Cxcl12 and Wnt5a.
Ebf3[+] niche-derived CXCL12 is required for the localization and maintenance of hematopoietic stem cells.
Title: Ebf3(+) niche-derived CXCL12 is required for the localization and maintenance of hematopoietic stem cells.
Impairment of HIF-2alpha Expression Induced the Compensatory Overexpression of the HIF-1alpha/SDF-1 Axis to Promote Wound Healing.
Title: Impairment of HIF-2α Expression Induced the Compensatory Overexpression of the HIF-1α/SDF-1 Axis to Promote Wound Healing.
SDF-1 and NOTCH signaling in myogenic cell differentiation: the role of miRNA10a, 425, and 5100.
Title: SDF-1 and NOTCH signaling in myogenic cell differentiation: the role of miRNA10a, 425, and 5100.
Early Angiogenesis-Dependent CXCL12 Attracts Adipose-Derived Stem Cells to Promote the Repair of Fat Grafting in a Mouse Model.
Title: Early Angiogenesis-Dependent CXCL12 Attracts Adipose-Derived Stem Cells to Promote the Repair of Fat Grafting in a Mouse Model.
Increased SPRY1 expression activates NF-kappaB signaling and promotes pancreatic cancer progression by recruiting neutrophils and macrophages through CXCL12-CXCR4 axis.
Title: Increased SPRY1 expression activates NF-κB signaling and promotes pancreatic cancer progression by recruiting neutrophils and macrophages through CXCL12-CXCR4 axis.

Submit: New GeneRIF Correction See all GeneRIFs (433)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (23) 1 citation
Endonuclease-mediated (5)

General gene information

Go to the top of the page Help

Markers

Sdf1 (e-PCR), detects polymorphism
- UniSTS:144384

Sdf1 (e-PCR), detects polymorphism
- UniSTS:144385

NoName (e-PCR)
- UniSTS:235532

L12030 (e-PCR)
- UniSTS:159562

Cxcl12 (e-PCR), detects polymorphism
- UniSTS:470615

Cxcl12 (e-PCR), detects polymorphism
- UniSTS:525662

Cxcl12 (e-PCR), detects polymorphism
- UniSTS:525663

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

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

AI174028 (e-PCR)
- UniSTS:179445

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables CXCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables CXCR chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables chemokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	IDA Inferred from Direct Assay more info	PubMed
enables chemokine activity	ISO Inferred from Sequence Orthology more info
enables chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables cytokine activity	IEA Inferred from Electronic Annotation 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 CXCL12-activated CXCR4 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in T cell chemotaxis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in adult locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in animal organ regeneration	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within blood vessel endothelial cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within brain development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within branching involved in blood vessel morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell chemotaxis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell-cell adhesion	IDA Inferred from Direct Assay more info	PubMed
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
involved_in chemokine-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in chemotaxis	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
involved_in detection of temperature stimulus involved in sensory perception of pain	ISO Inferred from Sequence Orthology more info
involved_in dopaminergic neuron differentiation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within germ cell development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within germ cell migration	IDA Inferred from Direct Assay more info	PubMed
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
acts_upstream_of_or_within induction of positive chemotaxis	IDA Inferred from Direct Assay more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cell population proliferation	IGI Inferred from Genetic Interaction more info	PubMed
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of ERK1 and ERK2 cascade	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of T cell migration	ISO Inferred from Sequence Orthology more info	PubMed
involved_in positive regulation of axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of calcium ion import	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of cell adhesion	ISO Inferred from Sequence Orthology more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of chemotaxis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of dopamine secretion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of monocyte chemotaxis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of myoblast fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of vasculature development	ISO Inferred from Sequence Orthology more info
involved_in regulation of calcium ion transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of cell migration	IGI Inferred from Genetic Interaction more info	PubMed
involved_in telencephalon cell migration	ISO Inferred from Sequence Orthology more info

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

General protein information

Go to the top of the page Help

Preferred Names: stromal cell-derived factor 1

Names: 12-O-tetradecanoylphorbol 13-acetate repressed protein 1; chemokine (C-X-C motif) ligand 12; pre-B-cell growth-stimulating factor; thymic lymphoma cell-stimulating factor

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_001012477.2 → NP_001012495.1 stromal cell-derived factor 1 isoform gamma precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (gamma).

Source sequence(s)

AC155646, BC046827

Consensus CDS

CCDS20463.1

UniProtKB/TrEMBL

H7BX38

Related

ENSMUSP00000072800.5, ENSMUST00000073043.5

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_013655.4 → NP_038683.1 stromal cell-derived factor 1 isoform beta precursor

See identical proteins and their annotated locations for NP_038683.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region compared to variant 3. The resulting isoform (beta) is shorter and has a distinct C-terminus compared to isoform gamma.

Source sequence(s)

AC155646, BB840704

Consensus CDS

CCDS39605.1

UniProtKB/Swiss-Prot

P40224, Q4FJL5, Q543V6

Related

ENSMUSP00000108492.2, ENSMUST00000112871.8

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_021704.3 → NP_068350.1 stromal cell-derived factor 1 isoform alpha precursor

See identical proteins and their annotated locations for NP_068350.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs in the 3' UTR and 3' coding region compared to variant 3. The resulting isoform (alpha) is shorter at the C-terminus, compared to isoform gamma.

Source sequence(s)

AC155646, AK045092

Consensus CDS

CCDS39606.1

UniProtKB/Swiss-Prot

P40224

Related

ENSMUSP00000108487.2, ENSMUST00000112866.8

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 ...