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CXCL12 Gene

protein-coding   GIFtS: 63
GCID: GC10M044865

Chemokine (C-X-C Motif) Ligand 12

(Previous name: stromal cell-derived factor 1)
(Previous symbols: SDF1A, SDF1B, SDF1)
  See CXCL12-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chemokine (C-X-C Motif) Ligand 121 2     PBSF2 3
SDF11 2 3 5     SCYB122
Stromal Cell-Derived Factor 11 2     TLSF2
SDF1A1 3     TPAR12
SDF1B1 3     SDF-13
Intercrine Reduced In Hepatomas2 3     C-X-C Motif Chemokine 123
Pre-B Cell Growth-Stimulating Factor2 3     hIRH3
IRH2 3     hSDF-13

External Ids:    HGNC: 106721   Entrez Gene: 63872   Ensembl: ENSG000001075627   OMIM: 6008355   UniProtKB: P480613   

Export aliases for CXCL12 gene to outside databases

Previous GC identifers: GC10M044154 GC10M044334 GC10M044640 GC10M044149 GC10M044185 GC10M041391


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CXCL12 Gene:
This gene encodes a stromal cell-derived alpha chemokine member of the intercrine family. The encoded protein
functions as the ligand for the G-protein coupled receptor, chemokine (C-X-C motif) receptor 4, and plays a role
in many diverse cellular functions, including embryogenesis, immune surveillance, inflammation response, tissue
homeostasis, and tumor growth and metastasis. Mutations in this gene are associated with resistance to human
immunodeficiency virus type 1 infections. Multiple transcript variants encoding different isoforms have been
found for this gene. (provided by RefSeq, May 2013)

GeneCards Summary for CXCL12 Gene:
CXCL12 (chemokine (C-X-C motif) ligand 12) is a protein-coding gene. Diseases associated with CXCL12 include retinal hemangioblastoma, and acquired immunodeficiency syndrome. GO annotations related to this gene include chemokine activity and receptor binding.

UniProtKB/Swiss-Prot: SDF1_HUMAN, P48061
Function: Chemoattractant active on T-lymphocytes, monocytes, but not neutrophils. Activates the C-X-C chemokine
receptor CXCR4 to induce a rapid and transient rise in the level of intracellular calcium ions and chemotaxis.
Also binds to atypical chemokine receptor ACKR3, which activates the beta-arrestin pathway and acts as a
scavenger receptor for SDF-1. SDF-1-beta(3-72) and SDF-1-alpha(3-67) show a reduced chemotactic activity. Binding
to cell surface proteoglycans seems to inhibit formation of SDF-1-alpha(3-67) and thus to preserve activity on
local sites. Acts as a positive regulator of monocyte migration and a negative regulator of monocyte adhesion via
the LYN kinase. Stimulates migration of monocytes and T-lymphocytes through its receptors, CXCR4 and ACKR3, and
decreases monocyte adherence to surfaces coated with ICAM-1, a ligand for beta-2 integrins. SDF1A/CXCR4 signaling
axis inhibits beta-2 integrin LFA-1 mediated adhesion of monocytes to ICAM-1 through LYN kinase. Inhibits
CXCR4-mediated infection by T-cell line-adapted HIV-1. Plays a protective role after myocardial infarction.
Induces down-regulation and internalization of ACKR3 expressed in various cells. Has several critical functions
during embryonic development; required for B-cell lymphopoiesis, myelopoiesis in bone marrow and heart
ventricular septum formation

Gene Wiki entry for CXCL12 (Stromal cell-derived factor-1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000010.10  NC_018921.2  NT_030059.14  
Regulatory elements:
   Regulatory transcription factor binding sites in the CXCL12 gene promoter:
         CREB   STAT1   deltaCREB   STAT5A   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CXCL12 promoter sequence
   Search Chromatin IP Primers for CXCL12

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CXCL12


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10q11.1   Ensembl cytogenetic band:  10q11.21   HGNC cytogenetic band: 10q11.1

CXCL12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CXCL12 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M044865:  view genomic region     (about GC identifiers)

Start:
44,793,038 bp from pter      End:
44,881,941 bp from pter
Size:
88,904 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SDF1_HUMAN, P48061 (See protein sequence)
Recommended Name: Stromal cell-derived factor 1 precursor  
Size: 93 amino acids; 10666 Da
Subunit: Monomer or homodimer; in equilibrium. Dimer formation is induced by non acidic pH and the presence of
multivalent anions, and by binding to CXCR4 or heparin. Monomeric form is required for full chemotactic activity
and resistance to ischemia/reperfusion injury, whereas the dimeric form acts as a partial agonist of CXCR4,
stimulating Ca2+ mobilization but with no chemotactic activity and instead acts as a selective antagonist that
blocks chemotaxis induced by the monomeric form. Interacts with the N-terminus of ACKR3
Developmental stage: Isoform Alpha is ubiquitously expressed in fetal tissues. Isoform Beta and isoform Delta have
more limited expression patterns, with highest levels detected in fetal spleen and fetal liver, respectively.
Isoform Gamma and isoform Theta are weakly detected in fetal kidney
Mass spectrometry: Mass=7959; Method=Electrospray; Range=22-89 (P48061-2); Source=PubMed:14525775;
Mass spectrometry: Mass=7606; Method=Electrospray; Range=24-88 (P48061-2); Source=PubMed:14525775;
Mass spectrometry: Mass=8522; Method=Electrospray; Range=22-93 (P48061-1); Source=PubMed:14525775;
Mass spectrometry: Mass=8297; Method=Electrospray; Range=24-93 (P48061-1); Source=PubMed:14525775;
Sequence caution: Sequence=CAC10202.1; Type=Erroneous gene model prediction;
Selected PDB 3D structures from and Proteopedia for CXCL12 (see all 18):
1A15 (3D)        1QG7 (3D)        1SDF (3D)        1VMC (3D)        2J7Z (3D)        2K01 (3D)    
Secondary accessions: B2R4G0 E7EVL0 Q2L985 Q2L986 Q2L988 Q5IT36 Q6ICW0 Q9H554
Alternative splicing: 6 isoforms:  P48061-1   P48061-2   P48061-3   P48061-4   P48061-5   P48061-6   

Explore the universe of human proteins at neXtProt for CXCL12: NX_P48061

Explore proteomics data for CXCL12 at MOPED

Post-translational modifications: 

  • Processed forms SDF-1-beta(3-72) and SDF-1-alpha(3-67) are produced after secretion by proteolytic cleavage of
    isoforms Beta and Alpha, respectively. The N-terminal processing is probably achieved by DPP4. Isoform Alpha is
    first cleaved at the C-terminus to yield a SDF-1-alpha(1-67) intermediate before being processed at the
    N-terminus. The C-terminal processing of isoform Alpha is reduced by binding to heparin and, probably, cell
    surface proteoglycans1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See CXCL12 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_000600.1  NP_001029058.1  NP_001171605.1  NP_001264919.1  NP_954637.1  

    ENSEMBL proteins: 
     ENSP00000363551   ENSP00000379139   ENSP00000363548   ENSP00000339913   ENSP00000379140  
     ENSP00000379141  
    Reactome Protein details: P48061

    CXCL12 Human Recombinant Protein Products:

    EMD Millipore Purified and/or Recombinant CXCL12 Protein
    R&D Systems Recombinant & Natural Proteins for CXCL12 (CXCL12/SDF-1 gamma, CXCL12/SDF-1, CXCL12/SDF-1 alpha, CXCL12/SDF-1 beta)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Proteins for CXCL12
    OriGene Protein Over-expression Lysate for CXCL12
    OriGene MassSpec for CXCL12
    OriGene Custom Protein Services for CXCL12
    GenScript Purified and Recombinant Proteins for CXCL12
    Novus Biologicals CXCL12 Proteins
    Novus Biologicals CXCL12 Lysates
    Sino Biological Recombinant Protein for CXCL12
    Sino Biological Cell Lysate for CXCL12
    ProSpec Recombinant Protein for CXCL12
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for CXCL12 

    CXCL12 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of CXCL12
    R&D Systems Antibodies for CXCL12 (CXCL12/SDF-1, CXCL12/SDF-1 beta)
    Cell Signaling Technology (CST) Antibodies for CXCL12 
    OriGene Antibodies for CXCL12
    OriGene Custom Antibody Services for CXCL12
    Novus Biologicals CXCL12 Antibodies
    Abcam antibodies for CXCL12
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibodies for CXCL12
    LSBio Antibodies in human, mouse, rat for CXCL12

    CXCL12 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for CXCL12
    R&D Systems Flow Cytometry Kits for CXCL12 (CXCL12/SDF-1, CXCL12/SDF-1 alpha)         (see all)
    GenScript Custom Assay Services for CXCL12
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for CXCL12 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ENDOLIG: Endogenous ligands

    1 InterPro protein domain:
     IPR001811 Chemokine_IL8-like_dom

    Graphical View of Domain Structure for InterPro Entry P48061

    ProtoNet protein and cluster: P48061

    UniProtKB/Swiss-Prot: SDF1_HUMAN, P48061
    Similarity: Belongs to the intercrine alpha (chemokine CxC) family


    Find genes that share domains with CXCL12           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SDF1_HUMAN, P48061
    Function: Chemoattractant active on T-lymphocytes, monocytes, but not neutrophils. Activates the C-X-C chemokine
    receptor CXCR4 to induce a rapid and transient rise in the level of intracellular calcium ions and chemotaxis.
    Also binds to atypical chemokine receptor ACKR3, which activates the beta-arrestin pathway and acts as a
    scavenger receptor for SDF-1. SDF-1-beta(3-72) and SDF-1-alpha(3-67) show a reduced chemotactic activity. Binding
    to cell surface proteoglycans seems to inhibit formation of SDF-1-alpha(3-67) and thus to preserve activity on
    local sites. Acts as a positive regulator of monocyte migration and a negative regulator of monocyte adhesion via
    the LYN kinase. Stimulates migration of monocytes and T-lymphocytes through its receptors, CXCR4 and ACKR3, and
    decreases monocyte adherence to surfaces coated with ICAM-1, a ligand for beta-2 integrins. SDF1A/CXCR4 signaling
    axis inhibits beta-2 integrin LFA-1 mediated adhesion of monocytes to ICAM-1 through LYN kinase. Inhibits
    CXCR4-mediated infection by T-cell line-adapted HIV-1. Plays a protective role after myocardial infarction.
    Induces down-regulation and internalization of ACKR3 expressed in various cells. Has several critical functions
    during embryonic development; required for B-cell lymphopoiesis, myelopoiesis in bone marrow and heart
    ventricular septum formation

         Summary: 

    During embryonic development, CXCL12 as signaling molecule is secreted from the following cells:
          selected tissues (see all 4)      
    Pancreas: Ventral Pancreatic Mesenchymal Cells (Dorsal Pancreatic Mesenchyme), Dorsal Pancreatic Mesenchymal Cells (Ventral Pancreatic Mesenchyme)
    Brain: Meningeal Cells (Anterior Meninges)

    It affects the following cells:
          selected tissues (see all 7)      fully expand
    Limb: Limb Muscle Progenitor Cells (Forelimb Myotome), Mononuclear Myocytes (Hindlimb Myotome)      fully expand to see all 6 cells
    Pancreas: Pancreatic Progenitor Cells (Ventral Pancreatic Bud), Pancreatic Progenitor Cells (Dorsal Pancreatic Bud)      fully expand to see all 2 cells

    CXCL12 as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells:
                
    Brain: Dopaminergic neuron-like cells, Dopaminergic neuron-like cells        to see all 2 cells
    Neurons: Dopaminergic neuron-like cells, Dopaminergic neuron-like cells        to see all 2 cells

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005102receptor binding TAS10358157
    GO:0008009chemokine activity TAS12782716
    GO:0008083growth factor activity IEA--
    GO:0042379chemokine receptor binding IMP--
    GO:0045236CXCR chemokine receptor binding IDA--
         
    Find genes that share ontologies with CXCL12           About GenesLikeMe


    Phenotypes:
         11 MGI mutant phenotypes (inferred from 9 alleles(MGI details for Cxcl12):
     cardiovascular system  cellular  hematopoietic system  immune system  liver/biliary system 
     mortality/aging  muscle  nervous system  no phenotypic analysis  normal 
     reproductive system 

    Find genes that share phenotypes with CXCL12           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for CXCL12: Cxcl12tm1Tng Cxcl12tm1.2Sjm

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CXCL12
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CXCL12

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CXCL12
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CXCL12

    miRNA
    Products:
        
    miRTarBase miRNAs that target CXCL12:
    hsa-mir-126-3p (MIRT007381), hsa-mir-31-5p (MIRT004980), hsa-mir-23a-3p (MIRT001776), hsa-mir-126-5p (MIRT007380), hsa-mir-886-3p (MIRT006598)

    Block miRNA regulation of human, mouse, rat CXCL12 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CXCL12 (see all 67):
    hsa-miR-520e hsa-miR-607 hsa-miR-199a-3p hsa-miR-200a hsa-miR-519a hsa-miR-3921 hsa-miR-1244 hsa-miR-29a*
    SwitchGear 3'UTR luciferase reporter plasmidCXCL12 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for CXCL12
    Predesigned siRNA for gene silencing in human, mouse, rat CXCL12

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for CXCL12

    Clone
    Products:
         
    OriGene clones in human, mouse for CXCL12 (see all 23)
    OriGene ORF clones in mouse, rat for CXCL12
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): CXCL12 (NM_199168)
    Sino Biological Human cDNA Clone for CXCL12
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CXCL12
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CXCL12
    Addgene plasmids for CXCL12 

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for CXCL12
    Browse ESI BIO Cell Lines and PureStem Progenitors for CXCL12 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CXCL12

    Flow Cytometry
    Products:
       

     
    eBioscience FlowRNA Probe Sets ( VA1-11035) for CXCL12 


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SDF1_HUMAN, P48061: Secreted
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    cytoskeleton2
    nucleus2
    plasma membrane2
    endosome1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005615extracellular space IEA--
    GO:0005886plasma membrane ----
    GO:0009897external side of plasma membrane IEA--

    Find genes that share ontologies with CXCL12           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for CXCL12 About   (see all 35)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1PEDF Induced Signaling
    MIF Regulation of Innate Immune Cells0.94
    IL-6 Pathway0.61
    MIF Mediated Glucocorticoid Regulation0.94
    NFAT Signaling and Lymphocyte Interactions0.57
    PEDF Induced Signaling0.73
    STAT3 Pathway0.47
    all-trans-Retinoic Acid Signaling in Brain0.71
    Endothelin-1 Signaling Pathway0.46
    2EphB-EphrinB Signaling
    EphB-EphrinB Signaling0.58
    Cytoskeleton remodeling Reverse signaling by ephrin B0.34
    Ephrin-Eph Signaling0.58
    3Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions
    Chemokine receptors bind chemokines0.81
    Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions0.81
    4LT-BetaR Pathway
    Apoptosis and survival Lymphotoxin beta receptor signaling0.46
    LT-BetaR Pathway0.46
    5Chemokine Signaling
    Chemokine signaling pathway0.33
    Chemokine Signaling0.33


    Find genes that share SuperPaths with CXCL12           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 R&D Systems Pathway for CXCL12
        Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CXCL12 (see all 70)
        Telomerase Components in Cell Signaling
    Molecular Mechanisms of Cancer
    eIF2 Pathway
    Intracellular Calcium Signaling
    JNK Pathway

    1 Cell Signaling Technology (CST) Pathway for CXCL12
        Lymphocyte Signaling

    4 GeneGo (Thomson Reuters) Pathways for CXCL12
        Cell adhesion Integrin inside-out signaling
    Cytoskeleton remodeling Reverse signaling by ephrin B
    Apoptosis and survival Lymphotoxin-beta receptor signaling
    Chemotaxis CXCR4 signaling pathway

    3 BioSystems Pathways for CXCL12
        Syndecan-4-mediated signaling events
    HIF-1-alpha transcription factor network
    CXCR4-mediated signaling events


    3 Reactome Pathways for CXCL12
        Chemokine receptors bind chemokines
    G alpha (i) signalling events
    Nuclear signaling by ERBB4


    Selected Kegg Pathways  (Kegg details for CXCL12) (see all 7):
        Cytokine-cytokine receptor interaction
    Chemokine signaling pathway
    NF-kappa B signaling pathway
    Axon guidance
    Leukocyte transendothelial migration

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CXCL12 (see all 15): 
              Lung Cancer in human mouse rat
              HIV Host Response in human mouse rat
              Growth Factors in human mouse rat
              Angiogenic Growth Factors in human mouse rat
              Tumor Metastasis in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CXCL12

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for CXCL12 (P480612, 3 ENSP000003635484) via UniProtKB, MINT, STRING, and/or I2D (see all 67)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DPP4P274872, 3, ENSP000003537314MINT-8091118 I2D: score=2 STRING: ENSP00000353731
    CXCR4P610733, ENSP000003868844I2D: score=4 STRING: ENSP00000386884
    FN1P027513, ENSP000003468394I2D: score=3 STRING: ENSP00000346839
    MMP2P082533, ENSP000002190704I2D: score=1 STRING: ENSP00000219070
    PF4P027763, ENSP000002960294I2D: score=1 STRING: ENSP00000296029
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 39):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001569patterning of blood vessels IEA--
    GO:0001666response to hypoxia IEA--
    GO:0001667ameboidal cell migration IEA--
    GO:0001764neuron migration IEA--
    GO:0001938positive regulation of endothelial cell proliferation IEA--

    Find genes that share ontologies with CXCL12           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
    About This Section

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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CXCL12 (SDF1)

    1 DrugBank Compound for CXCL12    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Tinzaparin-- 9041-08-1targetbinder18991783

    Selected Novoseek inferred chemical compound relationships for CXCL12 gene (see all 88)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sdf 1 95 255 10413364 (10), 15808852 (9), 18698020 (9), 8751377 (8) (see all 82)
    rantes 84.6 174 16011532 (11), 16343773 (4), 11064099 (4), 14717979 (3) (see all 99)
    bicyclam 79.1 10 9733901 (1), 16675573 (1), 17959712 (1), 12677165 (1) (see all 8)
    plerixafor 77.1 5 19834627 (1), 18940680 (1), 18691106 (1), 18847313 (1) (see all 5)
    teck 74.5 9 19362302 (1), 9886241 (1), 10449163 (1), 18501472 (1) (see all 6)
    vegf 69.4 316 19374809 (9), 19410951 (8), 12384916 (8), 18031819 (7) (see all 99)
    ccl3 68.9 20 20003942 (2), 15542651 (2), 16969502 (2), 12534281 (1) (see all 15)
    grobeta 67.4 1 19589793 (1)
    matrigel 55.6 24 15059909 (2), 15582259 (2), 11063876 (2), 16278822 (2) (see all 17)
    ly294002 54.6 11 16884765 (2), 12414810 (2), 20351091 (1), 18384792 (1) (see all 8)



    Find genes that share compounds with CXCL12           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CXCL12 gene (5 alternative transcripts): 
    NM_000609.6  NM_001033886.2  NM_001178134.1  NM_001277990.1  NM_199168.3  

    Unigene Cluster for CXCL12:

    Chemokine (C-X-C motif) ligand 12
    Hs.522891  [show with all ESTs]
    Unigene Representative Sequence: AK090482
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000374429(uc001jbf.3) ENST00000395793 ENST00000374426(uc001jbh.3)
    ENST00000343575(uc021ppm.1 uc001jbi.3) ENST00000395794 ENST00000496375
    ENST00000488591 ENST00000395795
    miRNA
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    Block miRNA regulation of human, mouse, rat CXCL12 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CXCL12 (see all 67):
    hsa-miR-520e hsa-miR-607 hsa-miR-199a-3p hsa-miR-200a hsa-miR-519a hsa-miR-3921 hsa-miR-1244 hsa-miR-29a*
    SwitchGear 3'UTR luciferase reporter plasmidCXCL12 3' UTR sequence
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    Predesigned siRNA for gene silencing in human, mouse, rat CXCL12
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    OriGene ORF clones in mouse, rat for CXCL12
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): CXCL12 (NM_199168)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CXCL12
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CXCL12
    Addgene plasmids for CXCL12 
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    eBioscience FlowRNA Probe Sets ( VA1-11035) for CXCL12 

    Additional mRNA sequence: 

    AJ227905.1 AK090482.1 AK124641.1 AK292628.1 AK311814.1 AL713778.1 AY644456.1 AY874118.1 
    BC031072.1 BC039893.1 CR450283.1 DQ345517.1 DQ345518.1 DQ345519.1 DQ345520.1 L36033.1 
    L36034.1 

    16 DOTS entries:

    DT.75167133  DT.95274185  DT.447215  DT.121284954  DT.121284964  DT.65284715  DT.100788017  DT.91803447 
    DT.92421328  DT.100788018  DT.95274178  DT.100788016  DT.100810713  DT.91749901  DT.95306903  DT.87016801 

    Selected AceView cDNA sequences (see all 323):

    AI539300 AL044635 BP377309 AA055761 AI521223 BU617923 BQ183301 BC039893 
    CA413305 AU118491 AA321546 CR450283 BU146385 BE328509 AI802430 CA426192 
    BU733387 BE645817 CA426265 AU119967 BQ708000 CA426157 C02038 BU617163 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CXCL12 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    CXCL12 Expression
    About this image


    CXCL12 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 39) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 10 entries
             Adventitial Reticular Cells Bone Marrow
             Zeugopod Long Bone
             Bone marrow-derived mesenchymal stem cells (Stemedyne-MSC)
     
     Mesenchymal Stem Cells
             Adventitial Reticular Cells Bone Marrow
             Bone marrow-derived mesenchymal stem cells (Stemedyne-MSC)
     
     Brain (Nervous System)    fully expand to see all 7 entries
             Meningeal Cells Anterior Meninges
             Striatum
             Caudal astroglia-like cells
     
     Kidney (Urinary System)    fully expand to see all 3 entries
             Metanephric Mesenchyme Cells Metanephric Mesenchyme
             S-shaped Body
     
     Umbilical Cord (Extraembryonic Tissues)    fully expand to see all 4 entries
             Umbilical Arteries
             Umbilical tissue-derived cells (CNTO2476)
    CXCL12 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CXCL12 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.522891

    UniProtKB/Swiss-Prot: SDF1_HUMAN, P48061
    Tissue specificity: Isoform Alpha and isoform Beta are ubiquitously expressed, with highest levels detected in
    liver, pancreas and spleen. Isoform Gamma is mainly expressed in heart, with weak expression detected in several
    other tissues. Isoform Delta, isoform Epsilon and isoform Theta have highest expression levels in pancreas, with
    lower levels detected in heart, kidney, liver and spleen

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CXCL12 (see all 15): 
              Lung Cancer in human mouse rat
              HIV Host Response in human mouse rat
              Growth Factors in human mouse rat
              Angiogenic Growth Factors in human mouse rat
              Tumor Metastasis in human mouse rat

    Primer
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CXCL12

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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    This gene was present in the common ancestor of chordates.

    Orthologs for CXCL12 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cxcl121 , 5 chemokine (C-X-C motif) ligand 121, 5 82.22(n)1
    80.95(a)1
      6 (54.81 cM)5
    203151  NM_001012477.21  NP_001012495.11 
     1171685355 
    chicken
    (Gallus gallus)
    Aves CXCL121 chemokine (C-X-C motif) ligand 12 79.45(n)
    83.56(a)
      395180  NM_204510.1  NP_989841.1 
    lizard
    (Anolis carolinensis)
    Reptilia CXCL126
    chemokine (C-X-C motif) ligand 12
    69(a)
    1 ↔ 1
    GL343297.1(1122807-1129487)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC687702 hypothetical protein MGC68770 72.98(n)    AJ278857.1 
    zebrafish
    (Danio rerio)
    Actinopterygii cxcl12b6
    cxcl12a6
    chemokine (C-X-C motif) ligand 12b (stromal cell-d...
    chemokine (C-X-C motif) ligand 12a (stromal cell-d...
    42(a)
    42(a)
    many → 1
    many → 1
    22(27551657-27567596) ENSDARG00000055100
    13(31027969-31043317) ENSDARG00000037116


    ENSEMBL Gene Tree for CXCL12 (if available)
    TreeFam Gene Tree for CXCL12 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CXCL12 gene
    10 SIMAP similar genes for CXCL12 using alignment to 2 protein entries:     SDF1_HUMAN (see all proteins):
    IL8    CXCL6    CCL5    CXCL10    CXCL2    CCL13
    CXCL1    CXCL3    CCL7    MCP-3

    Find genes that share paralogs with CXCL12           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CXCL12 (see all 454)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs578725411,2
    C--41397283(+) CTGCTGGGCT/
            
    AGCAG
    3 -- ds5001 int11Minor allele frequency- -:0.00NA 2
    rs1821005321,2
    --41406906(+) GTGGGA/GGGCGC 5 -- us2k10--------
    rs178795291,2
    C,F--41407739(-) CTTACTTAC/-  
            
    AGCTA
    1 -- us2k12Minor allele frequency- -:0.10NS 92
    rs362321631,2
    C--41407745(+) TAAGT-/AAGT  
            
    CCTTT
    5 -- us2k10--------
    rs178828491,2
    C,F--44870932(-) CTAGCCCAGC/
            
    AGAGG
    2 -- int13Minor allele frequency- -:0.20NS CSA 96
    rs710203331,2
    C--44872362(+) AAAAG-/A/AA  
            
    ATCCA
    5 -- int1 ds50011NA 2
    rs178842041,2
    C--44872845(-) TTTTTT/-TACGT 5 -- int1 ut312Minor allele frequency- -:0.01NS 88
    rs93265141,2
    C--44879058(+) GGGGG-/G/GC  
     
    /GG/GGG
    TCAGT
    10 -- int1 cds10--------
    rs1403872041,2
    --44981456(+) TCCTAC/TGCCCC 2 -- ds50010--------
    rs178833391,2
    C,F--44981501(-) CGATTC/TTCTCA 2 -- ds50016Minor allele frequency- T:0.10NS NA EA 334

    HapMap Linkage Disequilibrium report for CXCL12 (44793038 - 44881941 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for CXCL12:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv646n71CNV Loss21882294
    nsv895098CNV Loss21882294
    dgv647n71CNV Loss21882294
    dgv648n71CNV Loss21882294
    dgv645n71CNV Gain21882294
    nsv895089CNV Gain21882294
    nsv825357CNV Gain20364138
    nsv895095CNV Gain+Loss21882294

    Human Gene Mutation Database (HGMD): CXCL12
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CXCL12
    DNA2.0 Custom Variant and Variant Library Synthesis for CXCL12

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 600835   
    OMIM disorders: 609423  
    15 diseases for CXCL12:    
    About MalaCards
    retinal hemangioblastoma    acquired immunodeficiency syndrome    whim syndrome    bursitis
    cystoid macular edema    cytomegalovirus retinitis    follicular dendritic cell tumor    usual interstitial pneumonia
    polyradiculoneuropathy    chronic inflammatory demyelinating polyradiculoneuropathy    intraocular lymphoma    cervical adenocarcinoma
    diabetic retinopathy    tuberculosis    breast cancer

    6 diseases from the University of Copenhagen DISEASES database for CXCL12:
    Acquired immunodeficiency syndrome     Vascular disease     Myocardial infarction     Breast cancer
    Leukemia     Multiple myeloma

    Find genes that share disorders with CXCL12           About GenesLikeMe

    Selected Novoseek inferred disease relationships for CXCL12 gene (see all 94)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    whim syndrome 80.4 2 15781337 (1), 18556651 (1)
    neovascularization 66.6 42 19595531 (3), 19215683 (3), 12628955 (2), 12680875 (1) (see all 24)
    immunodeficiency 65.3 48 12232832 (2), 9108384 (1), 10413364 (1), 16306611 (1) (see all 43)
    metastasis 62.8 252 18558091 (5), 18176915 (5), 20032431 (4), 18223219 (4) (see all 99)
    tumors 51 295 19350687 (6), 17355795 (5), 16982747 (4), 18558091 (4) (see all 99)
    hiv infections 49.5 39 20104779 (3), 12215924 (2), 9108384 (1), 10413364 (1) (see all 27)
    cancer 47.6 125 20032431 (4), 14749473 (4), 15854291 (3), 19825996 (2) (see all 81)
    inflammation 42.1 34 11095335 (3), 18383856 (2), 12444153 (1), 15339043 (1) (see all 28)
    myeloma 37.6 22 16278822 (4), 15023543 (3), 11154207 (3), 14688392 (2) (see all 11)
    hypogammaglobulinemia 37.1 1 18556651 (1)

    Genetic Association Database (GAD): CXCL12
    Human Genome Epidemiology (HuGE) Navigator: CXCL12 (156 documents)

    Export disorders for CXCL12 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CXCL12 gene, integrated from 10 sources (see all 1722):
    (articles sorted by number of sources associating them with CXCL12)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Structure and chromosomal localization of the human stromal cell- derived factor 1 (SDF1) gene. (PubMed id 7490086)1, 2, 3, 9 Shirozu M....Honjo T. (Genomics 1995)
    2. Plasma stromal cell-derived factor-1: host derived marker predictive of distant metastasis in breast cancer. (PubMed id 18223219)1, 4, 9 Hassan S....Basik M. (Clin. Cancer Res. 2008)
    3. Identification and expression of novel isoforms of human stromal cell-derived factor 1. (PubMed id 16626895)1, 2, 9 Yu L.... Wang J. (Gene 2006)
    4. SDF1 gene variation is associated with circulating SDF1alpha level and endothelial progenitor cell number: the Bruneck Study. (PubMed id 19115008)1, 4, 9 Xiao Q....Xu Q. (PLoS ONE 2008)
    5. Structural and functional basis of CXCL12 (stromal cell-derived factor-1 alpha) binding to heparin. (PubMed id 17264079)1, 2, 9 Murphy J.W.... Lolis E. (J. Biol. Chem. 2007)
    6. Stromal cell-derived factor 1 (SDF1) genetic polymorphism in a sample of healthy individuals, seronegative individuals exposed to human immunodeficiency virus type 1 (HIV-1) and patients infected with HIV-1 from the Brazilian population. (PubMed id 16611258)1, 4, 9 Reiche E.M....Oliveira K.B. (Int. J. Immunogenet. 2006)
    7. Role of CCR5, CCR2 and SDF-1 gene polymorphisms in a population of HIV-1 infected individuals. (PubMed id 11693435)1, 4, 9 Mazzucchelli R....Balotta C. (J. Biol. Regul. Homeost. Agents 2001)
    8. Solution structure and basis for functional activity of stromal cell- derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1. (PubMed id 9384579)1, 2, 9 Crump M.P....Clark-Lewis I. (EMBO J. 1997)
    9. The effect of stromal cell-derived factor 1 (SDF1/CXCL12) genetic polymorphism on HIV-1 disease progression. (PubMed id 16964435)1, 4, 9 Reiche E.M....Siscar A.R. (Int. J. Mol. Med. 2006)
    10. Contribution of genetic polymorphisms of stromal cell-derived factor-1 and its receptor, CXCR4, to the susceptibility and clinicopathologic development of oral cancer. (PubMed id 19373784)1, 4, 9 Teng Y.H....Yang S.F. (amp 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6387 HGNC: 10672 AceView: CXCL12 Ensembl:ENSG00000107562 euGenes: HUgn6387
    ECgene: CXCL12 Kegg: 6387 H-InvDB: CXCL12

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for CXCL12 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for CXCL12 Genetics and Cytogenetics in Oncology and Haematology
    Wikipedia http://en.wikipedia.org/wiki/SDF-1_%28biology%29
    SeattleSNPshttp://pga.gs.washington.edu/data/cxcl12/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CXCL12 gene:
    Search GeneIP for patents involving CXCL12

    Licensable Technologies for CXCL12 gene:
    Weizmann Institute:Enrichment of Repopulating Stem Cells For Clinical Protocols
    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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