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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CXCL12 Gene

protein-coding   GIFtS: 64
GCID: GC10M044865

Chemokine (C-X-C Motif) Ligand 12

(Previous name: stromal cell-derived factor 1)
(Previous symbols: SDF1A, SDF1B, SDF1)
Microbiology & Infectious Diseases Congress
  See 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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 whim syndrome, and retinal hemangioblastoma, and among its related super-pathways are MIF Mediated Glucocorticoid Regulation and LT-BetaR Pathway. 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 another C-X-C chemokine receptor CXCR7, 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 CXCR7, 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 CXCR7 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.2  NT_033985.7  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for CXCL12

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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 CXCR7
Subcellular location: Secreted
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;
6/17 PDB 3D structures from and Proteopedia for CXCL12 (see all 17):
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:

  • UniProtKB: 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 proteoglycans
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P48061

  • CXCL12 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CXCL12 Protein Expression
    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
    Human Recombinant Protein Products for CXCL12: 
    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. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

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

    CXCL12 for ontologies           About GeneDecksing



    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 
    Browse OriGene Antibodies
    OriGene Custom Antibody Services for CXCL12
    GenScript Custom Superior Antibodies 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 

    Assay Products for CXCL12: 
    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.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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


    CXCL12 for domains           About GeneDecksing


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    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 another C-X-C chemokine receptor CXCR7, 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 CXCR7, 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 CXCR7 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: Adventitial Reticular Cells in Bone Marrow, Dorsal Pancreatic Mesenchymal Cells in Dorsal Pancreatic Mesenchyme (see all 5).

    It affects the following cells: Angioblasts in Embryonic Capillary Plexus, Limb Muscle Progenitor Cells in Forelimb Myotome (see all 14).

    CXCL12 as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells: Dopaminergic neuron-like cells from Brain, Dopaminergic neuron-like cells from Brain (see all).

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005102receptor binding TAS10358157
    GO:0008009chemokine activity IEA--
    GO:0008083growth factor activity IEA--
    GO:0045236CXCR chemokine receptor binding IDA--
         
    CXCL12 for ontologies           About GeneDecksing


    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 

    CXCL12 for phenotypes           About GeneDecksing

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

       inGenious Targeting Laboratory - Custom generated mouse model solutions for CXCL12 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions 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-31 (MIRT004980), hsa-mir-23a (MIRT001776)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CXCL12
    8/67 QIAGEN miScript miRNA 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:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for CXCL12
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CXCL12

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for CXCL12
    Sirion Biotech Customized adenovirus for overexpression of CXCL12

    Clone
    Products:
         
    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene clones in human, mouse for CXCL12 (see all 20)
    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
    Sirion Biotech Customized lentivirus for stable overexpression of CXCL12 
                         Customized lentivirus expression plasmids for stable overexpression of CXCL12 

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for CXCL12
    Search LifeMap BioReagents cell lines for CXCL12
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CXCL12


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for CXCL12 About   (see all 36)                                                                                              See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1PEDF Induced Signaling
    MIF Mediated Glucocorticoid Regulation0.94
    IL-6 Pathway0.61
    MIF Regulation of Innate Immune Cells0.94
    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
    2Apoptosis and survival Lymphotoxin-beta receptor signaling
    Apoptosis and survival Lymphotoxin-beta receptor signaling0.46
    LT-BetaR Pathway0.46
    3Chemokine Signaling
    Chemokine Signaling0.33
    Chemokine signaling pathway0.33
    4Apoptotic Pathways in Synovial Fibroblasts
    Mitochondrial Apoptosis0.85
    Rac1 Pathway0.65
    Cellular Apoptosis Pathway0.85
    Glioma Invasiveness0.64
    Apoptotic Pathways in Synovial Fibroblasts0.84
    Actin-Based Motility by Rho Family GTPases0.62
    p53 Mediated Apoptosis0.84
    ERK5 Signaling0.61
    5GPCR Pathway
    Ras Pathway0.73
    Breast Cancer Regulation by Stathmin10.58
    Paxillin Interactions0.73
    NFAT in Immune Response0.58
    GPCR Pathway0.62
    Estrogen Pathway0.55
    Pancreatic Adenocarcinoma0.59

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    4 EMD Millipore Pathways for CXCL12
        Chemotaxis CXCR4 signaling pathway
    Cell adhesion Integrin inside-out signaling
    Cytoskeleton remodeling Reverse signaling by ephrin B
    Apoptosis and survival Lymphotoxin-beta receptor signaling

    5/70 Downloadable PowerPoint Slides of QIAGEN 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
        HIF-1-alpha transcription factor network
    Syndecan-4-mediated signaling events
    CXCR4-mediated signaling events


    5/10        Reactome Pathways for CXCL12 (see all 10)
        GPCR downstream signaling
    Peptide ligand-binding receptors
    Signaling by GPCR
    GPCR ligand binding
    Class A/1 (Rhodopsin-like receptors)


    5/7         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


    CXCL12 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CXCL12

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

    5/67 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): 5/23 biological process terms (GO ID links to tree view) (see all 23):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001569patterning of blood vessels IEA--
    GO:0001667ameboidal cell migration IEA--
    GO:0006874cellular calcium ion homeostasis TAS10772939
    GO:0006935chemotaxis TAS10620615
    GO:0006955immune response IEA--

    CXCL12 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    CXCL12 for compounds           About GeneDecksing

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

    Browse Tocris compounds for CXCL12 (SDF1)

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

    10/88 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)

    Search CenterWatch for drugs/clinical trials and news about CXCL12 / SDF1

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CXCL12
    8/67 QIAGEN miScript miRNA 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
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    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 

    24/323 AceView cDNA sequences (see all 323):

    F02492 BQ183301 NM_199168 BM697738 AU118491 AA055761 AI539300 BU618117 
    AI857805 BU146332 BI760697 BU146385 CA447990 AA978287 AI094025 CA427573 
    CA426017 BU733387 CA447400 BX113123 BU617923 CA431576 T92785 BE464692 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CXCL12 expression in normal human tissues (normalized intensities)      CXCL12 embryonic expression: see
    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 
     5/49 selected tissues (see all 49) fully expand
     
     Brain (Nervous System)    fully expand to see all 20 entries
             Meningeal Cells Anterior Meninges
             Globus Pallidus
             Human Brain Vascular Pericyte (HBVP)   
             Olfactory Bulb   
     
     Bone (Muscoskeletal System)    fully expand to see all 12 entries
             Adventitial Reticular Cells Bone Marrow
             Thoracic Rib
             Bone marrow-derived lineage-negative cells
             Normal Human osteoblasts (NHOST)   
             sensory organ/ear/inner ear   
     
     Mesenchymal Stem Cells
             Decidua-derived mesenchymal stem cells
             Human Mesenchymal Stem Cells (hMSC)-1   
     
     Fibroblast
             Human Prostate Fibroblasts (HPrF)   
     
     Heart (Cardiovascular System)    fully expand to see all 6 entries
             Coronary Artery Smooth Muscle Cells (CASMC)   
             heart/atrium   

    See CXCL12 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CXCL12

    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

        SABiosciences Expression via Pathway-Focused 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

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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

    This gene was present in the common ancestor of chordates.

    Orthologs for CXCL12 gene from 5/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cxcl125 chemokine (C-X-C motif) ligand 12   --   6 (54.81 cM) 117168535 
    chicken
    (Gallus gallus)
    Aves CXCL126
    stromal cell-derived factor 1 precursor
    51(a)
    1 ↔ 1
    6(18559508-18577315)
    lizard
    (Anolis carolinensis)
    Reptilia CXCL126
    Uncharacterized protein
    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)
    13(31027969-31043317)


    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)
    About This Section
    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

    CXCL12 for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/454 SNPs in CXCL12 are shown (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
    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 600835   
    OMIM disorders: 609423  
    20/207 diseases for CXCL12 (see all 207):    About MalaCards
    whim syndrome    retinal hemangioblastoma    aids, resistance to    hiv-1, resistance to
    bursitis    cystoid macular edema    polyradiculoneuropathy    chronic inflammatory demyelinating polyradiculoneuropathy
    intraocular lymphoma    cytomegalovirus retinitis    coronary arteriosclerosis    follicular dendritic cell tumor
    retinal ischemia    aids dementia complex    cervical adenocarcinoma    skeletal muscle regeneration
    usual interstitial pneumonia    pelvic inflammatory disease    corneal neovascularization    diabetic retinopathy

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

    CXCL12 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10/94 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)
    About This Section

    PubMed articles for CXCL12 gene, integrated from 9 sources (see all 1687):
    (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. (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. (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. (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. (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. (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. (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. (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. (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. (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. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 6387 HGNC: 10672 AceView: CXCL12 Ensembl:ENSG00000107562 euGenes: HUgn6387
    ECgene: CXCL12 Kegg: 6387 H-InvDB: CXCL12

    (According to HUGE)
    About This Section
      --

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



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    About This Section

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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