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XCL2 Gene

protein-coding   GIFtS: 43

GC01M166776
chemokine (C motif) ligand 2
(Previous names: small inducible cytokine subfamily C, member 2 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: SCYC2)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
OTTHUMP00000032499 2
SCM-1b 1, 2
SCM1B 2, 5
SCYC2 2, 3, 5
Descriptions
C motif chemokine 2 3
XC chemokine ligand 2 3
chemokine (C motif) ligand 2 2
small inducible cytokine subfamily C, member 2 1, 2
External Ids
HGNC: 106461
Entrez Gene: 68462
UniProtKB: Q9UBD33
Ensembl: ENSG000001431857
Search outside databases for aliases for XCL2 gene

Previous GC identifers: GC01M166145 GC01M164161 GC01M165206 GC01M165697 GC01M165242

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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UniProtKB/Swiss-Prot: XCL2_HUMAN, Q9UBD3
Function: Chemotactic activity for lymphocytes but not for monocytes or neutrophils (By similarity)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the XCL2 gene  

Entrez Gene cytogenetic band: 1q23-q25   Ensembl cytogenetic band:  1q24.2   HGNC cytogenetic band: 1q24.2

XCL2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M166776:     (about GC identifiers)

Start:
166,776,626 bp from pter
End:
166,779,859 bp from pter
Size:
3,234 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004487.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: XCL2_HUMAN, Q9UBD3 (See protein sequence)
Recommended Name: Cytokine SCM-1 beta precursor  
Size: 114 amino acids; 12567 Da
Subcellular location: Secreted

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_003166.1  

    ENSEMBL proteins: 
    ENSP00000356793 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
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    Browse Abcam for Recombinant Proteins
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    2 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576 extracellular region IEA--
    GO:0005615 extracellular space IEA--
    About this table

    Antibodies for XCL2: 
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    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    Browse R&D Systems for Antibodies
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    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for XCL2

    Assays for XCL2: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    2 InterPro domains/families:
     IPR001811 Chemokine_IL8
     IPR008105 Lymphotactin


       GeneDecks  XCL2 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9UBD3

    ProtoNet protein and cluster: Q9UBD3

    1 Blocks protein family: IPB008105 Lymphotactin precursor signature

    UniProtKB/Swiss-Prot: XCL2_HUMAN, Q9UBD3
    Similarity: Belongs to the intercrine gamma family

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Browse Invitrogen for RNAi
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003175

                  Applied Biosystems Silencer® siRNAs for XCL2

                  Sigma-Aldrich siRNA for XCL2  
                         Sigma-Aldrich shRNA Panels and shRNA for XCL2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_003175
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_003175
                                     untagged cDNA clone in CMV expression vector: NM_003175 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_003175

    UniProtKB/Swiss-Prot: XCL2_HUMAN, Q9UBD3
    Function: Chemotactic activity for lymphocytes but not for monocytes or neutrophils (By similarity)

    1 Gene Ontology (GO) molecular function term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008009 chemokine activity TAS7875320
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    1 Kegg Pathway  (Kegg details for XCL2):
     hsa04060 Cytokine-cytokine receptor interaction

       GeneDecks  XCL2 for the pathways selected above  
    About GeneDecksing

    2 Interacting proteins for XCL2 (ENSP000003567933) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    XCR1ENSP000003104053STRING (score=.994)
    XCL1ENSP000003567923STRING (score=.902)
    About this table

    4 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006935 chemotaxis IEA--
    GO:0006955 immune response IEA--
    GO:0007165 signal transduction TAS7875320
    GO:0008015 blood circulation TAS7875320
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for XCL2

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Browse Invitrogen for RNAi
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003175

                  Sigma-Aldrich siRNA for XCL2  
                         Sigma-Aldrich shRNA Panels and shRNA for XCL2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_003175  

    REFSEQ mRNAs for XCL2 gene: 

    NM_003175.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_003175  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_003175
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_003175
                                     untagged cDNA clone in CMV expression vector: NM_003175 

    Additional cDNA sequence: 

    BC069360.1 BC070308.1 

    4 DOTS entries:

    DT.100735017  DT.305525  DT.109036  DT.91854396 

    14 AceView cDNA sequences:

    BC069360 NM_003175 AI057377 CD521967 U23772 BC070308 BE218461 AW050525 
    AW467190 AA650495 AI821666 AA420635 AA420679 AI915168 

    highest scoring ESTs for XCL2:

    AW467190 BC069360 BC070308 BE218461 CD521967 CD522040 AI057377 NM_003175 AA650495 AI915168 

    Unigene Cluster for XCL2:

    Chemokine (C motif) ligand 2
    Hs.458346  [show with all ESTs]
    Unigene Representative Sequence: BC070308


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000367819  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    XCL2 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for XCL2

    1 / 2 / 3

    6 probe-sets matching XCL2 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    31495_at2, 3 U95-A 3 1.00 0.61 0.94 1.11 D63789 0.20 0.50 0.38 1
    31496_g_at2, 3 U95-A 2 1.00 0.50 0.98 0.90 D63789 0.20 0.50 0.38 1

    214567_s_at2, 3 U133-A 2 1.00 0.50 -- -- NM_003175 0.60 0.83 0.73 1

    206366_x_at2, 3 U133-A 2 1.00 0.50 -- -- U23772 0.60 0.50 0.55 1

    214567_s_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --

    206366_x_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --
    GeneDecks  XCL2 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: --

    SOURCE GeneReport for Unigene cluster: Hs.458346
    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for XCL2 gene from 3 species
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    XCL21   -- chemokine (C motif) ligand 2 81.08(n)
    72.07(a)
    490356  XM_547477.2  XP_547477.2 
    chimpanzee
    (Pan troglodytes)
    XCL21   -- chemokine (C motif) ligand 2 98.25(n)
    94.74(a)
    735318  XM_001134638.1  XP_001134638.1 
    cow
    (Bos taurus)
    XCL21   -- chemokine (C motif) ligand 2 79.17(n)
    69.64(a)
    616569  XM_868619.2  XP_873712.2 
    About this table        Species with no ortholog for XCL2

    ENSEMBL Gene Tree for XCL2
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for XCL2 gene
    XCL12  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/62 NCBI SNPs in XCL2 are shown (see all 62 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 21)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 1 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    --
    rs4707331,2
    A,C,F166776746(-) CTGAGT/ATTATA 1 -- ut311Minor allele frequency- A:0.48MN 184
    --
    rs43016151,2
    A,F,H166777949(+) CCTATC/GTGAGA 1 H/D mis1 ese33Minor allele frequency- G:0.10EA WA 294
    --
    rs39165681,2
    A,C166781802(-) GTCATA/GGGTAT 1 -- ng310--------
    --
    rs107537741,2
    A,C166780632(+) ATCTGC/TATTGG 1 -- ng310--------
    --
    rs5973591,2
    A,C166781613(-) atcctA/Gtaggc 1 -- ng31 tfbs30--------
    --
    rs4744141,2
    C,F166779944(+) TGGGTA/GTAGGA 1 -- ng312Minor allele frequency- G:0.20MN 368
    --
    rs45018201,2
    A166777945(+) TCCTCC/TTATGT 1 R/K mis1 ese30--------
    --
    rs4752821,2
    F166780003(+) AAAAAT/AGTCCC 1 -- ng314Minor allele frequency- A:0.50NA 66
    --
    rs5973361,2
    A166781636(-) tcacaA/Gtgaaa 1 -- ng310--------
    --
    rs5973511,2
    A166781626(-) agattA/Tgaaat 1 -- ng310--------
    About this table

    HapMap Linkage Disequilibrium images for XCL2 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 604828

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    9 PubMed articles for XCL2 gene:
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    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, and/or H-InvDB)
    About This Section

    Entrez Gene: 6846 HGNC: 10646 AceView: XCL2 Ensembl:ENSG00000143185 euGenes: HUgn6846
    ECgene: XCL2 H-InvDB: XCL2
    (According to HUGE)
    About This Section

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

    NameDescription
    Wikipedia http://en.wikipedia.org/wiki/XCL2
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for XCL2:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
      Invitrogen Antibodies  Invitrogen Assays
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      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for XCL2-related products

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     Millipore Immunoassay Services
     Millipore Target Screening & Profiling Services


     Predesigned and custom siRNAs for XCL2 Browse antibodies at Sigma-Aldrich
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for XCL2 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
     Search Novus for antibodies for XCL2

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