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CX3CL1 Gene

protein-coding   GIFtS: 62
GCID: GC16P057406

Chemokine (C-X3-C Motif) Ligand 1

(Previous names: small inducible cytokine subfamily D (Cys-X3-Cys), member...)
(Previous symbol: SCYD1)
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Aliases
for CX3CL1 gene

(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-X3-C Motif) Ligand 11 2     C3Xkine2
SCYD11 2 3 5     CXC32
NTT2 3 5     CXC3C2
Small Inducible Cytokine Subfamily D (Cys-X3-Cys), Member 1 (Fractalkine,
Neurotactin)1 2
     fractalkine2
Small-Inducible Cytokine D12 3     neurotactin2
C-X3-C Motif Chemokine 12 3     Small Inducible Cytokine Subfamily D (Cys-X3-Cys), Member-12
CX3C Membrane-Anchored Chemokine2 3     FKN3
NTN2 5     Neurotactin3
ABCD-32     

External Ids:    HGNC: 106471   Entrez Gene: 63762   Ensembl: ENSG000000062107   OMIM: 6018805   UniProtKB: P784233   

Export aliases for CX3CL1 gene to outside databases

Previous GC identifers: GC16P047801 GC16P057466 GC16P057140 GC16P057181 GC16P057162 GC16P055963 GC16P043274


Summaries
for CX3CL1 gene

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CX3CL1 Gene:
CX3CL1 (chemokine (C-X3-C motif) ligand 1) is a protein-coding gene. Diseases associated with CX3CL1 include pityriasis rosea, and rheumatoid vasculitis. GO annotations related to this gene include chemokine activity and receptor binding.

UniProtKB/Swiss-Prot: X3CL1_HUMAN, P78423
Function: The soluble form is chemotactic for T-cells and monocytes, but not for neutrophils. The membrane-bound
form promotes adhesion of those leukocytes to endothelial cells. May play a role in regulating leukocyte adhesion
and migration processes at the endothelium. Binds to CX3CR1

Gene Wiki entry for CX3CL1 Gene


Genomic Views
for CX3CL1 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:
NC_000016.10  NC_018927.2  NT_010498.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the CX3CL1 gene promoter:
         AP-1   ATF-2   c-Jun   NF-kappaB   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CX3CL1 promoter sequence
   Search Chromatin IP Primers for CX3CL1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CX3CL1


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

Entrez Gene cytogenetic band: 16q13   Ensembl cytogenetic band:  16q21   HGNC cytogenetic band: 16q13

CX3CL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CX3CL1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P057406:  view genomic region     (about GC identifiers)

Start:
 57,406,370 bp from pter      End:
 57,418,960 bp from pter
Size:
 12,591 bases      Orientation:
 plus strand

Proteins
for CX3CL1 gene

(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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: X3CL1_HUMAN, P78423 (See protein sequence)
Recommended Name: Fractalkine precursor  
Size: 397 amino acids; 42203 Da
Subunit: Monomer. Interacts with pox virus crmD; this inhibits cell migration mediated by CX3CL1
3 PDB 3D structures from and Proteopedia for CX3CL1:
1B2T (3D)        1F2L (3D)        3ONA (3D)    
Secondary accessions: O00672

Explore the universe of human proteins at neXtProt for CX3CL1: NX_P78423

Explore proteomics data for CX3CL1 at MOPED

Post-translational modifications: 

  • A soluble short 95 kDa form may be released by proteolytic cleavage from the long membrane-anchored form (By
    similarity)1
  • O-glycosylated with core 1 or possibly core 8 glycans1
  • Glycosylation2 at Asn33, Thr183, Ser253, Thr318, Thr329
  • Modification sites at PhosphoSitePlus

    • See CX3CL1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002987.1  
    ENSEMBL proteins: 
     ENSP00000006053   ENSP00000456830   ENSP00000457996   ENSP00000464114  
    Reactome Protein details: P78423

    CX3CL1 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for CX3CL1 (CX3CL1/Fractalkine)
    Enzo Life Sciences proteins for CX3CL1
    OriGene Purified Protein for CX3CL1
    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec
    OriGene Custom Protein Services for CX3CL1
    GenScript Purified and Recombinant Proteins for CX3CL1
    Novus Biologicals CX3CL1 Proteins
    Sino Biological Recombinant Protein for CX3CL1
    Sino Biological Cell Lysate for CX3CL1
    ProSpec Recombinant Protein for CX3CL1
    Cloud-Clone Corp. Proteins for CX3CL1

    CX3CL1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of CX3CL1
    R&D Systems Antibodies for CX3CL1 (CX3CL1/Fractalkine)
    OriGene Antibodies for CX3CL1
    OriGene Custom Antibody Services for CX3CL1
    Novus Biologicals CX3CL1 Antibodies
    Abcam antibodies for CX3CL1
    Cloud-Clone Corp. Antibodies for CX3CL1
    ThermoFisher Antibody for CX3CL1
    LSBio Antibodies in human, mouse, rat for CX3CL1

    CX3CL1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for CX3CL1
    R&D Systems Flow Cytometry Kits for CX3CL1 (CX3CL1/Fractalkine)         (see all)
    GenScript Custom Assay Services for CX3CL1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for CX3CL1
    Cloud-Clone Corp. CLIAs for CX3CL1

    Domains /
    Families
    for CX3CL1 gene

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

    TryGeneCards Plus    		 HGNC Gene Families:
    ENDOLIG: Endogenous ligands

    2 InterPro protein domains:
     IPR008097 Chemokine_CX3CL1
     IPR001811 Chemokine_IL8-like_dom

    Graphical View of Domain Structure for InterPro Entry P78423

    ProtoNet protein and cluster: P78423

    1 Blocks protein domain: IPB008097 Fractalkine/neurotactin precursor signature

    UniProtKB/Swiss-Prot: X3CL1_HUMAN, P78423
    Similarity: Belongs to the intercrine delta family


    CX3CL1 for domains           About GeneDecksing


    Function
    for CX3CL1 gene

    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
    About This Section

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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: X3CL1_HUMAN, P78423
    Function: The soluble form is chemotactic for T-cells and monocytes, but not for neutrophils. The membrane-bound
    form promotes adhesion of those leukocytes to endothelial cells. May play a role in regulating leukocyte adhesion
    and migration processes at the endothelium. Binds to CX3CR1
    Induction: By TNF and IL1/interleukin-1 in pulmonary endothelial cells and umbilical vein endothelial cells

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005102receptor binding TAS12714508
    GO:0005515protein binding IPI9931005
    GO:0008009chemokine activity TAS12714508
         
    CX3CL1 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for CX3CL1:
     Decreased viability of wild-ty  Increased circadian period len 

         7 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Cx3cl1):
     behavior/neurological  cardiovascular system  cellular  hematopoietic system  homeostasis/metabolism 
     immune system  nervous system 

    CX3CL1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for CX3CL1: Cx3cl1tm1Sgs Cx3cl1tm1Lira

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CX3CL1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CX3CL1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CX3CL1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CX3CL1

    miRNA
    Products:            		Block miRNA regulation of human, mouse, rat CX3CL1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CX3CL1 (see all 35):
    hsa-miR-21* hsa-miR-185* hsa-miR-106a hsa-miR-509-5p hsa-miR-15a hsa-miR-29a hsa-miR-29c hsa-let-7a-2*
    SwitchGear 3'UTR luciferase reporter plasmid: CX3CL1 3' UTR sequence
    Inhib. RNA
    Products:            		OriGene RNAi products in human, mouse, rat for CX3CL1
    Predesigned siRNA for gene silencing in human, mouse, rat CX3CL1

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for CX3CL1

    Clone
    Products:             		 OriGene clones in human, mouse for CX3CL1 (see all 6)
    OriGene ORF clones in mouse, rat for CX3CL1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CX3CL1 (NM_002996)
    Sino Biological Human cDNA Clone for CX3CL1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CX3CL1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CX3CL1

    Cell Line
    Products:             		GenScript Custom overexpressing Cell Line Services for CX3CL1
    Browse ESI BIO Cell Lines and PureStem Progenitors for CX3CL1 
    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CX3CL1


    Localization
    for CX3CL1 gene

    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
    About This Section

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    Subcellular locations from UniProtKB/Swiss-Prot
    X3CL1_HUMAN, P78423: Cell membrane; Single-pass type I membrane protein
    X3CL1_HUMAN, P78423: Processed fractalkine: Secreted
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    plasma membrane5
    nucleus2
    cytoskeleton1
    lysosome1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 6 cellular component terms (see first 5):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IDA12714508
    GO:0005615extracellular space IEA--
    GO:0005886plasma membrane TAS--
    GO:0009986cell surface IDA12714508
    GO:0016020membrane ----
    GO:0016021integral component of membrane IDA12714508

    CX3CL1 for ontologies           About GeneDecksing


    Pathways & Interactions
    for CX3CL1 gene

    (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 CX3CL1 About   (see all 12)  
    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
    		STAT3 Pathway0.47
    		PEDF Induced Signaling0.73
    		Endothelin-1 Signaling Pathway0.46
    		all-trans-Retinoic Acid Signaling in Brain0.71
    		Cytokine-cytokine receptor interaction0.43
    2Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions
    		Chemokine receptors bind chemokines0.81
    		Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions0.81
    3Chemokine Signaling
    		Chemokine signaling pathway0.33
    		Chemokine Signaling0.33
    4Peptide ligand-binding receptors
    		Class A/1 (Rhodopsin-like receptors)0.71
    		Peptide ligand-binding receptors0.60
    		GPCR ligand binding0.71
    5ERK Signaling
    		Rho Family GTPases0.61
    		Molecular Mechanisms of Cancer0.51
    		ERK Signaling0.61

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 R&D Systems Pathways for CX3CL1
        A-beta Uptake & Degradation
    Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CX3CL1 (see all 17)
        Endothelin-1 Signaling Pathway
    Molecular Mechanisms of Cancer
    Antioxidant Action of Vitamin-C
    Transendothelial Migration of Leukocytes
    MIF Mediated Glucocorticoid Regulation

    1 BioSystems Pathway for CX3CL1
        Direct p53 effectors


    1 Reactome Pathway for CX3CL1
        Chemokine receptors bind chemokines


    3 Kegg Pathways  (Kegg details for CX3CL1):
        Cytokine-cytokine receptor interaction
    Chemokine signaling pathway
    TNF signaling pathway


    CX3CL1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CX3CL1 (see all 9): 
              HIV Host Response in human mouse rat
              T-cell & B-cell Activation in human mouse rat
              Inflammatory Response & Autoimmunity 384HT in human mouse rat
              Notch Signaling Targets in human mouse rat
              Th17 Response in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CX3CL1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    Selected Interacting proteins for CX3CL1 (P784233 ENSP000000060534) via UniProtKB, MINT, STRING, and/or I2D (see all 19)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CX3CR1P492383, ENSP000003821664I2D: score=3 STRING: ENSP00000382166
    TP53ENSP000002693054STRING: ENSP00000269305
    CCR1ENSP000002961404STRING: ENSP00000296140
    CCR10ENSP000003325044STRING: ENSP00000332504
    CCR2ENSP000002923014STRING: ENSP00000292301
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 18):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006935chemotaxis IDA--
    GO:0006952defense response TAS12714508
    GO:0006955immune response TAS12714508
    GO:0007155cell adhesion IEA--
    GO:0019221cytokine-mediated signaling pathway TAS11777952

    CX3CL1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for CX3CL1 gene

    (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 CX3CL1 (X3CL1)

    7 Novoseek inferred chemical compound relationships for CX3CL1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tarc 60.3 3 11397698 (1), 9691168 (1), 10372118 (1)
    ccl4 26.1 4 16452465 (3), 18565769 (1)
    forskolin 0 9 11163337 (3), 1360635 (3)
    calcium 0 1 16166268 (1)
    glutamate 0 1 10640747 (1)
    serine 0 4 2100266 (2), 2120047 (1), 18436581 (1)
    cysteine 0 3 15361546 (1), 9177350 (1)



    CX3CL1 for compounds           About GeneDecksing



    Transcripts
    for CX3CL1 gene

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
    About This Section

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    REFSEQ mRNAs for CX3CL1 gene: 
    NM_002996.3  

    Unigene Cluster for CX3CL1:

    Chemokine (C-X3-C motif) ligand 1
    Hs.531668  [show with all ESTs]
    Unigene Representative Sequence: AB209037
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000006053(uc002eli.3) ENST00000563383 ENST00000564948 ENST00000565912

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

    miRNA
    Products:             		 Block miRNA regulation of human, mouse, rat CX3CL1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CX3CL1 (see all 35):
    hsa-miR-21* hsa-miR-185* hsa-miR-106a hsa-miR-509-5p hsa-miR-15a hsa-miR-29a hsa-miR-29c hsa-let-7a-2*
    SwitchGear 3'UTR luciferase reporter plasmid: CX3CL1 3' UTR sequence
    Inhib. RNA
    Products:             		OriGene RNAi products in human, mouse, rat for CX3CL1
    Predesigned siRNA for gene silencing in human, mouse, rat CX3CL1
    Clone
    Products:             		 OriGene clones in human, mouse for CX3CL1 (see all 6)
    OriGene ORF clones in mouse, rat for CX3CL1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CX3CL1 (NM_002996)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CX3CL1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CX3CL1
    Primer
    Products:            		OriGene qPCR primer pairs and template standards for CX3CL1
    OriGene qSTAR qPCR primer pairs in human, mouse for CX3CL1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CX3CL1
      QuantiTect SYBR Green Assays in human, mouse, rat CX3CL1
      QuantiFast Probe-based Assays in human, mouse, rat CX3CL1

    Additional mRNA sequence: 

    AB209037.1 AK222692.1 AK223351.1 AK313806.1 BC001163.1 BC016164.1 CR457426.1 GU047346.1 
    U84487.1 U91835.1 

    7 DOTS entries:

    DT.445170  DT.100754639  DT.100027835  DT.100663663  DT.92430608  DT.100027838  DT.100677031 

    Selected AceView cDNA sequences (see all 192):

    BI765277 BI766891 BI822306 AI560343 AA595197 BI754355 CA395409 AL536123 
    BQ878197 BC001163 BQ893231 BM709856 AA349609 AA349491 BI752894 BI914377 
    CR595915 BQ045219 BE263269 T31247 CB960463 AI369215 BI769456 CA396869 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for CX3CL1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b
    SP1:                              
    SP2:              -               


    ECgene alternative splicing isoforms for CX3CL1

    Expression
    for CX3CL1 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™, 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)
    About This Section

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    CX3CL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GACAAGGATG
    CX3CL1 Expression
    About this image


    CX3CL1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 11) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebellum
     
     Bone (Muscoskeletal System)
             Mesenchymal Condensate Cells Zeugopod
     
     Cartilage (Muscoskeletal System)
             Mesenchymal Condensate Cells Zeugopod
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
    CX3CL1 Protein expression data from MOPED1, PaxDb2 and MaxQB3:     About this image

    CX3CL1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.531668

    UniProtKB/Swiss-Prot: X3CL1_HUMAN, P78423
    Tissue specificity: Small intestine, colon, testis, prostate, heart, brain, lung, skeletal muscle, kidney and
    pancreas

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CX3CL1 (see all 9): 
              HIV Host Response in human mouse rat
              T-cell & B-cell Activation in human mouse rat
              Inflammatory Response & Autoimmunity 384HT in human mouse rat
              Notch Signaling Targets in human mouse rat
              Th17 Response in human mouse rat

    Primer
    Products:    		OriGene qPCR primer pairs and template standards for CX3CL1
    OriGene qSTAR qPCR primer pairs in human, mouse for CX3CL1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CX3CL1
    QuantiTect SYBR Green Assays in human, mouse, rat CX3CL1
    QuantiFast Probe-based Assays in human, mouse, rat CX3CL1
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CX3CL1

    Orthologs
    for CX3CL1 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

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    This gene was present in the common ancestor of human and mouse.

    Orthologs for CX3CL1 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Cx3cl11 , 5 chemokine (C-X3-C motif) ligand 11, 5 73.33(n)1
    66.92(a)1    		   8 (46.79 cM)5
    203121  NM_009142.31  NP_033168.21 
     947720095 


    ENSEMBL Gene Tree for CX3CL1 (if available)
    TreeFam Gene Tree for CX3CL1 (if available)

    Paralogs
    for CX3CL1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CX3CL1 gene
    17 SIMAP similar genes for CX3CL1 using alignment to 6 protein entries:     X3CL1_HUMAN (see all proteins):
    CCL11    CCL8    CCL2    CCL7    MCP-3    LOC728835
    CCL18    CCL3    CCL3L1    CCL3L3    CCL4L2    CCL14
    CCL4L1    CCL4    CCL13    CCL17    CCL26

    CX3CL1 for paralogs           About GeneDecksing



    Genomic Variants
    for CX3CL1 gene

    (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 CX3CL1 (see all 404)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 16 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1127113411,2
    		C--57413239(+) AACTC-/AAAAAA 1 -- int11Minor allele frequency- A:0.50CSA 2
    rs1148475501,2
    		C,F--58417566(+) TATGGA/GCATAA 1 -- us2k11Minor allele frequency- G:0.04WA 118
    rs1477329091,2
    		--58417596(+) TGGTCC/TTCGCA 1 -- us2k10--------
    rs1425537151,2
    		C--58417601(+) CTCGCA/GGTGAG 1 -- us2k10--------
    rs1448602201,2
    		C--58417671(+) GGGACA/GAATCC 1 -- us2k10--------
    rs1458018911,2
    		--58417761(+) TCACCC/GAGGCT 1 -- us2k10--------
    rs1488627481,2
    		--58417779(+) AGTGGC/TGTGAT 1 -- us2k10--------
    rs71967071,2
    		C--58417800(+) tgcaaC/Tcctct 1 -- us2k10--------
    rs1911364121,2
    		--58417827(+) CGATTC/TTCCTG 1 -- us2k10--------
    rs1434945261,2
    		C--58417896(+) ATTTTC/TAGTAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CX3CL1 (57406370 - 57418960 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for CX3CL1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CX3CL1
    DNA2.0 Custom Variant and Variant Library Synthesis for CX3CL1

    Disorders / Diseases
    for CX3CL1 gene

    (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.)
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    OMIM gene information: 601880    OMIM disorders: --

    Selected diseases for CX3CL1 (see all 78):    
    About MalaCards
    pityriasis rosea    rheumatoid vasculitis    chorioretinitis    aneurysm disease
    head injury    anterior uveitis    adult-onset still's disease    microscopic polyangiitis
    traumatic brain injury    hemolytic-uremic syndrome    brain disease    vasculitis
    angina pectoris    brain injury    common variable immunodeficiency    wegener's granulomatosis
    allergic asthma    uveitis    abdominal aortic aneurysm    eye disease


    CX3CL1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014

    Selected Novoseek inferred disease relationships for CX3CL1 gene (see all 16)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chorioretinitis 40.5 1 12657599 (1)
    atherosclerosis 30.1 2 17679613 (1), 17885215 (1)
    rheumatoid arthritis 29.6 1 11465708 (1)
    inflammation 29 10 20512991 (1), 15131578 (1), 17804530 (1), 17616549 (1) (see all 11)
    necrosis 18.9 11 17679613 (1), 12824004 (1), 17665439 (1), 15013759 (1) (see all 8)
    encephalitis 17.8 3 9177350 (2), 10640747 (1)
    atherosclerotic plaque 15.4 2 14581400 (1), 15886814 (1)
    brain diseases 15.4 2 12742664 (1), 12476352 (1)
    inflammatory bowel diseases 6.56 3 17241867 (1), 12940913 (1), 17285595 (1)
    tumors 4.09 16 16391873 (4), 17679613 (1), 12824004 (1), 17665439 (1) (see all 9)

    Genetic Association Database (GAD): CX3CL1
    Human Genome Epidemiology (HuGE) Navigator: CX3CL1 (153 documents)

    Export disorders for CX3CL1 gene to outside databases

    Publications
    for CX3CL1 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)
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    PubMed articles for CX3CL1 gene, integrated from 10 sources (see all 253):
    (articles sorted by number of sources associating them with CX3CL1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. A new class of membrane-bound chemokine with a CX3C motif. (PubMed id 9024663)1, 2, 3, 9 Bazan J.F.... Schall T.J. (Nature 1997)
    2. Neurotactin, a membrane-anchored chemokine upregulated in brain inflammation. (PubMed id 9177350)1, 3, 9 Pan Y....Gearing D. (Nature 1997)
    3. Polymorphisms of Fractalkine receptor CX3CR1 and plasma levels of its ligand CX3CL1 in colorectal cancer patients. (PubMed id 17611763)1, 4, 9 Dimberg J....WAYgsAoter D. (Int J Colorectal Dis 2007)
    4. Fractalkine receptor/ligand genetic variants and carotid intima-media thickness. (PubMed id 19372452)1, 4, 9 Debette S....Markus H.S. ( a journal of cerebral circulation 2009)
    5. Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1. (PubMed id 9931005)1, 2, 9 Mizoue L.S.... Handel T.M. (Biochemistry 1999)
    6. Common polymorphisms in ITGA2, PON1 and THBS2 are associated with coronary atherosclerosis in a candidate gene association study of the Chinese Han population. (PubMed id 20485444)1, 4 Wang Y....Huang W. (J. Hum. Genet. 2010)
    7. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    8. Candidate gene polymorphisms for ischemic stroke. (PubMed id 19729601)1, 4 Matarin M....Meschia J.F. ( a journal of cerebral circulation 2009)
    9. CX3CR1 polymorphisms are associated with atopy but not asthma in German children. (PubMed id 17505143)1, 4 Depner M....Kabesch M. (Int. Arch. Allergy Immunol. 2007)
    10. Polymorphisms in the 3' untranslated region of the fractalkine (CX3CL1) gene and the risk of HIV-1 infection and disease progression. (PubMed id 17415055)1, 4 Peraire J....Broch M. (AIDS 2007)

    External Searches for CX3CL1 gene

    (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)

    Genome Databases showing CX3CL1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6376 HGNC: 10647 AceView: CX3CL1 Ensembl:ENSG00000006210 euGenes: HUgn6376
    ECgene: CX3CL1 Kegg: 6376 H-InvDB: CX3CL1

    Other Databases showing CX3CL1 gene

    (According to HUGE)
    About This Section

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    Specialized Databases showing CX3CL1 gene

    (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 CX3CL1 Pharmacogenomics, SNPs, Pathways
    Wikipedia http://en.wikipedia.org/wiki/CX3CL1

    Intellectual Property
    for CX3CL1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

    TryGeneCards Plus    		Patent Information for CX3CL1 gene:
    Search GeneIP for patents involving CX3CL1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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