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

CXCL12 Gene

protein-coding   GIFtS: 66
GCID: GC10M044865

chemokine (C-X-C motif) ligand 12

(Previous name: stromal cell-derived factor 1 )
(Previous symbols: SDF1A, SDF1B, SDF1)
 Explore 222 diseases affiliated with
CXCL12 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for CXCL12    

Aliases
for CXCL12 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chemokine (C-X-C Motif) Ligand 121 2     IRH2 3
SDF11 2 3 5     SDF-1a1
PBSF1 2 3     SDF-1b1
SDF1A1 2 3     TLSF-A1
SDF1B1 2 3     TLSF-B1
SCYB121 2     TLSF2
TPAR11 2     SDF-13
Stromal Cell-Derived Factor 11 2     C-X-C Motif Chemokine 123
Intercrine Reduced In Hepatomas2 3     HIRH1
Pre-B Cell Growth-Stimulating Factor2 3     HSDF-11

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


Summaries
for CXCL12 gene

(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:
This gene encodes a stromal cell-derived alpha chemokine member of the intercrine family. This gene product and its
receptor CXCR4 can activate lymphocytes and have been implicated in the metastasis of some cancers such as breast
cancer. 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, Mar 2010)

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)


Genomic Views
for CXCL12 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.1  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

Proteins
for CXCL12 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

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
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P48061

    • CXCL12 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (4 alternative transcripts): 
    NP_000600.1  NP_001029058.1  NP_001171605.1  NP_954637.1  

    ENSEMBL proteins: 
     ENSP00000363551   ENSP00000379139   ENSP00000363548   ENSP00000339913   ENSP00000379140  
     ENSP00000379141  
    Reactome Protein details: P48061
    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 (see all 2): CXCL12
    OriGene Protein Over-expression Lysate: 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
    ProSpec Recombinant Protein for CXCL12
    Uscn Proteins for CXCL12

    Gene Ontology (GO): 4 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:0005886plasma membrane ----
    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 
    Uscn Antibodies for CXCL12
    ThermoFisher Antibodies for CXCL12

    Assay Products for CXCL12: 
    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Immunoassay Development
    Browse OriGene Fluorogenic Cell Assay Kits
    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
    Uscn ELISAs and CLIAs for CXCL12

    Protein Domains /
    Families
    for CXCL12 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    CXCL12 for domains           About GeneDecksing

    1 InterPro domain/family:
     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


    Function
    for CXCL12 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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

         Summary:  

    During embryonic development, CXCL12 as signaling molecule is secreted from the following cells: Dorsal Pancreatic Mesenchymal Cells in Dorsal Pancreatic Mesenchyme, Foregut Endoderm Cells in Foregut (see all 4).

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

    miRNA
    Products:            		miRTarBase miRNAs that target CXCL12:
    hsa-mir-31 (MIRT004980), hsa-mir-23a (MIRT001776)

    OriGene 3'-UTR Clone (see all 3): CXCL12
    Browse MicroRNA Expression Plasmids
    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 plasmid: CXCL12 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CXCL12 (see all 7)
    OriGene shRNA RFP: CXCL12
    OriGene siRNA: CXCL12
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CXCL12

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

    Clone
    Products:             		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CXCL12 (see all 10)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CXCL12 (see all 4)
    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 

    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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005102receptor binding TAS10438529
    GO:0008009chemokine activity IEA--
    GO:0008083growth factor activity IEA--
    GO:0045236CXCR chemokine receptor binding IDA--


    CXCL12 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Cxcl12tm1Tng for CXCL12
         9 MGI mutant phenotypes (inferred from 5 alleles) (MGI details for Cxcl12):
     cardiovascular system  cellular  hematopoietic system  immune system  liver/biliary system 
     mortality/aging  nervous system  no phenotypic analysis  reproductive system 

    CXCL12 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for CXCL12 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/36 super-pathways (see all 36) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Apoptotic Pathways in Synovial Fibroblasts
    8/14 pathways (see all 14)
    		Apoptotic Pathways in Synovial Fibroblasts1.00
    		ERK5 Signaling0.61
    		p53 Mediated Apoptosis0.84
    		eIF2 Pathway0.60
    		Mitochondrial Apoptosis0.73
    		Rac1 Pathway0.58
    		Telomerase Components in Cell Signaling0.72
    		Nuclear Receptor Activation by Vitamin-A0.57
    2PEDF Induced Signaling
    8/10 pathways (see all 10)
    		PEDF Induced Signaling1.00
    		RAR-Gamma-RXR-Alpha Degradation0.54
    		MIF Mediated Glucocorticoid Regulation0.73
    		STAT3 Pathway0.47
    		MIF Regulation of Innate Immune Cells0.71
    		Endothelin-1 Signaling Pathway0.44
    		IL-6 Pathway0.61
    		NFAT Signaling and Lymphocyte Interactions0.37
    3GPCR Pathway
    		GPCR Pathway1.00
    		Estrogen Pathway0.55
    		Ras Pathway0.62
    		Pancreatic Adenocarcinoma0.55
    		Breast Cancer Regulation by Stathmin10.58
    		Paxillin Interactions0.53
    		NFAT in Immune Response0.58
    4Rho Family GTPases
    		Rho Family GTPases1.00
    		MAPK Signaling0.51
    		ERK Signaling0.61
    		ILK Signaling0.45
    		Molecular Mechanisms of Cancer0.51
    5Class A/1 (Rhodopsin-like receptors)
    		Class A/1 (Rhodopsin-like receptors)1.00
    		Peptide ligand-binding receptors0.61
    		GPCR ligand binding0.75
    		G alpha (i) signalling events0.44

    Pathway sources
    See GeneCards unified pathways
    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 
        Syndecan-4-mediated signaling events
    CXCR4-mediated signaling events
    HIF-1-alpha transcription factor network

    5/11        Reactome Pathways for CXCL12 (see all 11)
        GPCR downstream signaling
    Peptide ligand-binding receptors
    Transcription of NR3C3 and CXCL12
    Signaling by GPCR
    GPCR ligand binding


    5/6         Kegg Pathways  (Kegg details for CXCL12) (see all 6):
        Cytokine-cytokine receptor interaction
    Chemokine signaling pathway
    Axon guidance
    Leukocyte transendothelial migration
    Intestinal immune network for IgA production


    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): 5/38 biological process terms (GO ID links to tree view) (see all 38):    About this table

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


    CXCL12 for ontologies           About GeneDecksing



    Drugs & Compounds
    for CXCL12 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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

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

    10/88 Novoseek 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 

    Transcripts
    for CXCL12 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for CXCL12 gene (4 alternative transcripts): 
    NM_000609.5  NM_001033886.2  NM_001178134.1  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
    Products:             		 OriGene 3'-UTR Clone (see all 3): CXCL12
    Browse OriGene MicroRNA Expression Plasmids
    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 plasmid: CXCL12 3' UTR sequence
    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CXCL12 (see all 7)
    OriGene shRNA RFP: CXCL12
    OriGene siRNA: CXCL12
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CXCL12
    Clone
    Products:             		 OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CXCL12 (see all 10)
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    GenScript: all cDNA clones in your preferred vector (see all 4): CXCL12 (NM_199168)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CXCL12 
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    Additional cDNA 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):

    BE677151 AA781695 AA321546 NM_000609 CA426017 BI711077 BU618033 BU735886 
    CA447400 AU118491 AU119967 C02038 CA413305 BM697738 CA426265 CA431576 
    CA426157 BU617163 AI655374 CR450283 AA055760 CA427573 BI770648 BX113123 

    GeneLoc Exon Structure


    Expression
    for CXCL12 gene

    (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)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    CXCL12 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/15 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 15) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BrainAnterior MeningesMeningeal CellsMeninges
    PancreasVentral Pancreatic MesenchymeVentral Pancreatic Mesenchymal CellsMesoderm
    BrainAnterior MeningesMeningeal Progenitor CellsMeninges
    OvaryPrimary FolliclePrimary OocyteFemale Gametocytes, Germ Cells
    OvaryPrimordial FolliclePrimary OocyteFemale Gametocytes, Germ Cells
    PancreasDorsal Pancreatic MesenchymeDorsal Pancreatic Mesenchymal CellsMesoderm
    BrainBlood Brain BarrierAdult Endothelial CellsBlood Brain Barrier, Endothelium
    BrainBlood Brain BarrierPostnatal Endothelial CellsBlood Brain Barrier, Endothelium
    Head MesenchymeBranchial Arch 1Paraxial Mesoderm CellsBone, Skeletal Muscle
    LimbZeugopodMesenchymal Condensate CellsBone, Cartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 10 LifeMap Cells 
    NameCategory
    Bone marrow-derived mesenchymal stem cells (Stempeucel) (Adult Stem / Progenitor Cell)Bone
    Mesenchymal Precursor Cells (STRO-3 selected) (Adult Stem / Progenitor Cell)Bone
    PureStem™ myogenic progenitor Z11 (Embryonic Progenitor Cell)Heart, Myocardium, Smooth Muscle
    PureStem™ progenitor EN2 (Embryonic Progenitor Cell)
    PureStem™ progenitor SM22 (Embryonic Progenitor Cell)
    PureStem™ progenitor W10 (Embryonic Progenitor Cell)
    ES04(HES-4) (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    Epiblast-like cells (Reconstitution of mo...)
    Primordial germ cell-like cells (Reconstitution of mo...)
    Beating cell clusters (Spontaneous differen...)

    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

    Primer
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    In Situ
    Assay Products:     
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    Orthologs
    for CXCL12 gene

    (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 Q6T7B9_CHICK6
    		 stromal cell derived factor 1
    		 52(a)
    		 1 ↔ 1
    		 6(20106470-20120158)
    lizard
    (Anolis carolinensis)    		 Reptilia CXCL126
    		 --
    		 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 cxcl12a6
    cxcl12b6
    		 chemokine (C-X-C motif) ligand 12a (stromal cell-d...
    chemokine (C-X-C motif) ligand 12b (stromal cell-d...
    		 43(a)
    42(a)
    		 many → 1
    many → 1
    		 13(31027969-31043317)
    22(27551657-27567596)


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

    Paralogs
    for CXCL12 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for CXCL12 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/365 NCBI SNPs in CXCL12 are shown (see all 365)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 10 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs112390231,2
    		C,--41391552(+) AGTGCT/CGGTCC 1 -- ds50012Minor allele frequency- C:0.05WA 120
    rs178804111,2
    		F--41391855(-) TACAGT/GGGTTC 1 -- ds50012Minor allele frequency- G:0.02NS 94
    rs77771,2
    		--41392081(-) CGCAGC/TGTGCT 1 -- ut31 ese31Minor allele frequency- T:0.00MN 184
    rs749307261,2
    		C,--41392086(+) GCTGCG/ATATAG 1 -- ut312Minor allele frequency- A:0.04CSA WA 120
    rs103471,2
    		--41392096(-) AGGNCA/GATTCC 1 -- ut31 ese31Minor allele frequency- G:0.00MN 184
    rs791605201,2
    		--41392275(+) TTTGGA/GAGTTT 1 -- ut311Minor allele frequency- G:0.01WA 118
    rs1133795351,2
    		C,--41392310(+) GGCTCC/TTTCAG 1 -- ut311Minor allele frequency- T:0.50WA 2
    rs178816041,2
    		C--41392365(-) AGCTGG/CATGAG 1 -- ut31 ese34Minor allele frequency- C:0.01NS NA 96
    rs1144820211,2
    		C,F,--41392445(+) CAGACG/AATCAC 1 -- ut311Minor allele frequency- A:0.02WA 118
    rs786579561,2
    		F,--41392467(+) GTCCAA/GTGAGA 1 -- ut311Minor allele frequency- G:0.03WA 118

    HapMap Linkage Disequilibrium report for CXCL12 (44793038 - 44881941 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for CXCL12: --
    Human Gene Mutation Database (HGMD): CXCL12

    SABiosciences Cancer Mutation PCR Assays
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    Disorders / Diseases
    for CXCL12 gene

    (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
    CXCL12 for disorders           About GeneDecksing

    OMIM gene information: 600835   
    OMIM disorders: 609423  
    20/222 diseases for CXCL12 (see all 222):    About MalaCards
    von hippel-lindau disease    breast cancer    wiskott-aldrich syndrome    immunodeficiency
    skeletal muscle regeneration    chronic inflammatory demyelinating polyradiculoneuropathy    aids dementia complex    diffuse large b-cell lymphoma
    guillain-barre syndrome    disseminated intravascular coagulation    human t-cell leukemia virus type 1    proliferative diabetic retinopathy
    cystoid macular edema    tropical spastic paraparesis    human immunodeficiency virus infectious disease    severe combined immunodeficiency
    usual interstitial pneumonia    central nervous system lymphoma    molluscum contagiosum    follicular dendritic cell tumor

    5 diseases from the University of Copenhagen DISEASES database for CXCL12:
    Human immunodeficiency virus infectious disease     Vascular disease     Myocardial infarction     Breast cancer
    Leukemia

    10/94 Novoseek 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

    Publications
    for CXCL12 gene

    (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 1620):
    (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. Identification and expression of novel isoforms of human stromal cell-derived factor 1. (PubMed id 16626895)1, 2, 9 Yu L.... Wang J. (2006)
    3. 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)
    4. 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)
    5. 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)
    6. Stromal cell-derived factor-1 (SDF-1) gene and susceptibility of Iranian patients with lung cancer. (PubMed id 15955592)1, 4, 9 Razmkhah M....Ghaderi A. (2005)
    7. Haplotype analysis of the SDF-1 (CXCL12) gene in a longitudinal HIV-1/AIDS cohort study. (PubMed id 16177829)1, 4, 9 Modi W.S....Winkler C. (2005)
    8. Risk for HIV-1 infection associated with a common CXCL12 (SDF1) polymorphism and CXCR4 variation in an African population. (PubMed id 16284526)1, 4, 9 Petersen D.C....Hayes V.M. (2005)
    9. Differential processing of stromal-derived factor-1alpha and beta explains functional diversity. (PubMed id 14525775)1, 2, 9 De La Luz Sierra M.... Tosato G. (2004)
    10. The impact of polymorphisms in chemokine and chemokine receptors on outcomes in liver transplantation. (PubMed id 12201365)1, 4, 9 Schroppel B....Murphy B. (2002)

    External Searches for CXCL12 gene

    (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)

    Genome Databases showing CXCL12 gene

    (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

    Other Databases showing CXCL12 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing CXCL12 gene

    (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/

    Intellectual Property
    for CXCL12 gene

    (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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