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

    Gene ID: 20315, updated on 21-Oct-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
    NEW
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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)

    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)

    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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