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

Gene ID: 20315, updated on 30-Nov-2021

Summary

Official Symbol
Cxcl12provided by MGI
Official Full Name
chemokine (C-X-C motif) ligand 12provided by MGI
Primary source
MGI:MGI:103556
See related
Ensembl:ENSMUSG00000061353
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
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Genomic context

See Cxcl12 in Genome Data Viewer
Location:
6 54.81 cM; 6 F1
Exon count:
4
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (117118553..117131386)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 53337 Neighboring gene RIKEN cDNA 2810048H02 gene Neighboring gene ribosomal protein L28, pseudogene 4 Neighboring gene VISTA enhancer mm247

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by MGI

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 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 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
 
acts_upstream_of_or_within ameboidal-type cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
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
PubMed 
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
PubMed 
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
PubMed 
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 other 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
PubMed 
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 protein kinase B signaling IGI
Inferred from Genetic Interaction
more info
PubMed 
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
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
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 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
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
stromal cell-derived factor 1
Names
12-O-tetradecanoylphorbol 13-acetate repressed protein 1
pre-B-cell growth-stimulating factor
thymic lymphoma cell-stimulating factor

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)

  1. NM_001012477.2NP_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:2788
    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 ...
  2. NM_013655.4NP_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
    Related
    ENSMUSP00000108492.2, ENSMUST00000112871.8
    Conserved Domains (1) summary
    cd00273
    Location:2788
    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 ...
  3. NM_021704.3NP_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:2788
    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 ...

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    117145496..117158329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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