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XCL1 Gene

protein-coding   GIFtS: 58
GCID: GC01P168545

Chemokine (C Motif) Ligand 1

(Previous names: small inducible cytokine subfamily C, member 1 (lymphotactin))
(Previous symbols: LTN, SCYC1)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chemokine (C Motif) Ligand 11 2     LPTN2 5
LTN1 2 3 5     SCM12 5
SCYC11 2 3 5     SCM-12
Small Inducible Cytokine Subfamily C, Member 1 (Lymphotactin)1 2     SCM-1a2
C Motif Chemokine 12 3     SCM1A2
Cytokine SCM-12 3     lymphotactin2
Small-Inducible Cytokine C12 3     lymphotaxin2
ATAC2 3     Single Cysteine Motif 1a2
SCM-1-alpha2 3     Lymphotaxin3
XC Chemokine Ligand 12 3     

External Ids:    HGNC: 106451   Entrez Gene: 63752   Ensembl: ENSG000001431847   OMIM: 6002505   UniProtKB: P479923   

Export aliases for XCL1 gene to outside databases

Previous GC identifers: GC01P166180 GC01P164196 GC01P165241 GC01P165733 GC01P165277 GC01P166812 GC01P139791


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for XCL1 Gene:
This gene encodes a member of the chemokine superfamily. Chemokines function in inflammatory and immunological
responses, inducing leukocyte migration and activation. The encoded protein is a member of the C-chemokine
subfamily, retaining only two of four cysteines conserved in other chemokines, and is thought to be specifically
chemotactic for T cells. This gene and a closely related family member are located on the long arm of chromosome
1. (provided by RefSeq, Nov 2010)

GeneCards Summary for XCL1 Gene:
XCL1 (chemokine (C motif) ligand 1) is a protein-coding gene. Diseases associated with XCL1 include renal tuberculosis, and dacryoadenitis. GO annotations related to this gene include chemokine receptor binding and protein homodimerization activity. An important paralog of this gene is XCL2.

UniProtKB/Swiss-Prot: XCL1_HUMAN, P47992
Function: Chemotactic activity for lymphocytes but not for monocytes or neutrophils




(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_000001.11  NC_018912.2  NT_004487.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the XCL1 gene promoter:
         FOXI1   HFH-3   C/EBPbeta   AML1a   NRSF form 1   STAT3   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   NRSF form 2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidXCL1 promoter sequence
   Search Chromatin IP Primers for XCL1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat XCL1


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

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

XCL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
XCL1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P168545:  view genomic region     (about GC identifiers)

Start:
168,545,711 bp from pter      End:
168,551,315 bp from pter
Size:
5,605 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, 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: XCL1_HUMAN, P47992 (See protein sequence)
Recommended Name: Lymphotactin precursor  
Size: 114 amino acids; 12517 Da
5 PDB 3D structures from and Proteopedia for XCL1:
1J8I (3D)        1J9O (3D)        2HDM (3D)        2JP1 (3D)        2NYZ (3D)    
Secondary accessions: Q52MA8

Explore the universe of human proteins at neXtProt for XCL1: NX_P47992

Explore proteomics data for XCL1 at MOPED


See XCL1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_002986.1  
ENSEMBL proteins: 
 ENSP00000356792  
Reactome Protein details: P47992

XCL1 Human Recombinant Protein Products:

Browse Purified and Recombinant Proteins at EMD Millipore
R&D Systems Recombinant & Natural Proteins for XCL1 (XCL1/Lymphotactin)
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OriGene Protein Over-expression Lysate for XCL1
OriGene Custom MassSpec
OriGene Custom Protein Services for XCL1
GenScript Purified and Recombinant Proteins for XCL1
Novus Biologicals XCL1 Proteins
Novus Biologicals XCL1 Lysate
Sino Biological Recombinant Protein for XCL1
Sino Biological Cell Lysate for XCL1
ProSpec Recombinant Protein for XCL1
Browse Proteins at Cloud-Clone Corp.

XCL1 Antibody Products:

Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
R&D Systems Antibodies for XCL1 (XCL1/Lymphotactin)
OriGene Antibodies for XCL1
OriGene Custom Antibody Services for XCL1
Novus Biologicals XCL1 Antibodies
Abcam antibodies for XCL1
Browse Antibodies at Cloud-Clone Corp.
ThermoFisher Antibodies for XCL1
LSBio Antibodies in human, mouse, rat for XCL1

XCL1 Assay Products:

Browse Kits and Assays available from EMD Millipore
OriGene Custom Assay Services for XCL1
R&D Systems ELISAs for XCL1 (XCL1/Lymphotactin)         (see all)
GenScript Custom Assay Services for XCL1
Browse Enzo Life Sciences for kits & assays
Browse ELISAs at Cloud-Clone Corp.
Browse CLIAs at Cloud-Clone Corp.


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

2 InterPro protein domains:
 IPR001811 Chemokine_IL8-like_dom
 IPR008105 Chemokine_XCL1

Graphical View of Domain Structure for InterPro Entry P47992

ProtoNet protein and cluster: P47992

1 Blocks protein domain: IPB008105 Lymphotactin precursor signature

UniProtKB/Swiss-Prot: XCL1_HUMAN, P47992
Similarity: Belongs to the intercrine gamma family


XCL1 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
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.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: XCL1_HUMAN, P47992
Function: Chemotactic activity for lymphocytes but not for monocytes or neutrophils

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

GO IDQualified GO termEvidencePubMed IDs
GO:0008009chemokine activity IDA7602097
GO:0042379chemokine receptor binding NAS7602097
GO:0042803protein homodimerization activity IDA11889129
     
XCL1 for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for XCL1:
 Decreased viability 

     7 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Xcl1):
 cardiovascular system  digestive/alimentary  endocrine/exocrine gland  hematopoietic system  immune system 
 liver/biliary system  vision/eye 

XCL1 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-outs for XCL1: Xcl1tm1.1Dnax Xcl1tm1Rakr

   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for XCL1
   inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for XCL1

   genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for XCL1
   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for XCL1

miRNA
Products:
    
Block miRNA regulation of human, mouse, rat XCL1 using miScript Target Protectors
Search for qRT-PCR Assays for microRNAs that regulate XCL1
SwitchGear 3'UTR luciferase reporter plasmidXCL1 3' UTR sequence
Inhib. RNA
Products:
    
OriGene RNAi products in human, mouse, rat for XCL1
Predesigned siRNA for gene silencing in human, mouse, rat XCL1

Gene Editing
Products:
DNA2.0 Custom Protein Engineering Service for XCL1

Clone
Products:
     
OriGene clones in human, mouse for XCL1 (see all 6)
OriGene ORF clones in mouse, rat for XCL1
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector: XCL1 (NM_001511)
Sino Biological Human cDNA Clone for XCL1
DNA2.0 Custom Codon Optimized Gene Synthesis Service for XCL1
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat XCL1

Cell Line
Products:
     
GenScript Custom overexpressing Cell Line Services for XCL1
Browse ESI BIO Cell Lines and PureStem Progenitors for XCL1 
In Situ Assay
Products:
   

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for XCL1


(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
XCL1_HUMAN, P47992: Secreted
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region TAS--
GO:0005615extracellular space ISS--

XCL1 for ontologies           About GeneDecksing


(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 XCL1 About   (see all 8)                                                                                              See pathways by source

SuperPathContained pathways About
1Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions
Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions0.81
Chemokine receptors bind chemokines0.81
2Chemokine Signaling
Chemokine signaling pathway0.33
Chemokine Signaling0.33
3Signaling by GPCR
Signaling by GPCR0.90
Signal Transduction0.58
GPCR downstream signaling0.90
4Peptide ligand-binding receptors
Class A/1 (Rhodopsin-like receptors)0.71
Peptide ligand-binding receptors0.60
GPCR ligand binding0.71
5Gastrin-CREB signalling pathway via PKC and MAPK
Gastrin-CREB signalling pathway via PKC and MAPK0.90
G alpha (q) signalling events0.90

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways

1 R&D Systems Pathway for XCL1
    Chemokine Superfamily: Human/Mouse Ligand-Receptor Interactions

2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for XCL1
    Chemokine Signaling
Transendothelial Migration of Leukocytes

1 GeneGo (Thomson Reuters) Pathway for XCL1
    Cell adhesion Cell-matrix glycoconjugates


2 Reactome Pathways for XCL1
    Chemokine receptors bind chemokines
G alpha (q) signalling events


2 Kegg Pathways  (Kegg details for XCL1):
    Cytokine-cytokine receptor interaction
Chemokine signaling pathway


XCL1 for pathways           About GeneDecksing

    Pathway & Disease-focused RT2 Profiler PCR Arrays including XCL1: 
          HIV Host Response in human mouse rat
          Cytokines & Chemokines in human mouse rat
          Inflammatory Response & Autoimmunity 384HT in human mouse rat
          Chemokines & Receptors in human mouse rat

Interactions:

    Search GeneGlobe Interaction Network for XCL1

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

Selected Interacting proteins for XCL1 (P479923 ENSP000003567924) via UniProtKB, MINT, STRING, and/or I2D (see all 19)
InteractantInteraction Details
GeneCardExternal ID(s)
VCANP136113, ENSP000002650774I2D: score=1 STRING: ENSP00000265077
XCR1P460943, ENSP000003104054I2D: score=1 STRING: ENSP00000310405
CCR1ENSP000002961404STRING: ENSP00000296140
CCR10ENSP000003325044STRING: ENSP00000332504
CCR2ENSP000002923014STRING: ENSP00000292301
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Gene Ontology (GO): Selected biological process terms (see all 36):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0001916positive regulation of T cell mediated cytotoxicity IDA18832695
GO:0002690positive regulation of leukocyte chemotaxis ISS--
GO:0002725negative regulation of T cell cytokine production IDA10887101
GO:0002726positive regulation of T cell cytokine production ISS--
GO:0002826negative regulation of T-helper 1 type immune response IC10887101

XCL1 for ontologies           About GeneDecksing



(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)
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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 XCL1

Selected Novoseek inferred chemical compound relationships for XCL1 gene (see all 11)    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
rantes 84.4 33 9393669 (1), 10942204 (1), 14734774 (1), 19397398 (1) (see all 29)
ccl3 54.3 4 14734774 (1), 18179747 (1)
ccl4 28.9 5 14734774 (1), 12427307 (1), 18179747 (1)
cysteine 19.3 7 9393669 (1), 9632725 (1), 8977329 (1), 7602097 (1) (see all 5)
wortmannin 15.4 2 10887101 (1), 10092776 (1)
cyclosporin a 14.6 4 12393716 (1), 7615002 (1), 11696436 (1)
heparin 6.63 4 14707146 (2), 19480914 (1), 9079718 (1)
tacrolimus 3.26 1 11696436 (1)
nacl 0 1 17302442 (1)
calcium 0 5 9271361 (2), 7615002 (2), 7602097 (1)



XCL1 for compounds           About GeneDecksing



(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 )
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REFSEQ mRNAs for XCL1 gene: 
NM_002995.2  

Unigene Cluster for XCL1:

Chemokine (C motif) ligand 1
Hs.546295  [show with all ESTs]
Unigene Representative Sequence: NM_002995
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000367818(uc001gfo.2)
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 XCL1 using miScript Target Protectors
Search for qRT-PCR Assays for microRNAs that regulate XCL1
SwitchGear 3'UTR luciferase reporter plasmidXCL1 3' UTR sequence
Inhib. RNA
Products:
     
OriGene RNAi products in human, mouse, rat for XCL1
Predesigned siRNA for gene silencing in human, mouse, rat XCL1
Clone
Products:
     
OriGene clones in human, mouse for XCL1 (see all 6)
OriGene ORF clones in mouse, rat for XCL1
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector: XCL1 (NM_001511)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for XCL1
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat XCL1
Primer
Products:
    
OriGene qSTAR qPCR primer pairs in human, mouse for XCL1
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat XCL1
  QuantiTect SYBR Green Assays in human, mouse, rat XCL1
  QuantiFast Probe-based Assays in human, mouse, rat XCL1

Additional mRNA sequence: 

BC069817.1 BC070309.1 D43768.1 U23772.1 X86474.1 

3 DOTS entries:

DT.109036  DT.100735017  DT.91854396 

23 AceView cDNA sequences:

BX282187 AI969003 NM_002995 D43768 BE348632 AI669817 AW134570 BF433809 
BQ005208 AW050650 CD522000 X86474 BE466930 BV198119 BC070309 U23772 
AI651995 AI298976 AW050525 CB120610 CD639746 AA650495 BG214157 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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XCL1 expression in normal human tissues (normalized intensities)      XCL1 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
XCL1 Expression
About this image


XCL1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Thymus (Hematopoietic System)
         T-Cytotoxic Cells Thymus
 
 Bone (Muscoskeletal System)    fully expand to see all 3 entries
         Bone marrow-derived mesenchymal stem cells (Stempeucel)
 
 Blood (Cardiovascular System)
         T-Cytotoxic Cells Thymus
 
 Mesenchymal Stem Cells
         Bone marrow-derived mesenchymal stem cells (Stempeucel)
XCL1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

XCL1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.546295

UniProtKB/Swiss-Prot: XCL1_HUMAN, P47992
Tissue specificity: Highest level in spleen, lower in peripheral leukocytes and very low levels in lung, colon and
small intestine

    Pathway & Disease-focused RT2 Profiler PCR Arrays including XCL1: 
          HIV Host Response in human mouse rat
          Cytokines & Chemokines in human mouse rat
          Inflammatory Response & Autoimmunity 384HT in human mouse rat
          Chemokines & Receptors in human mouse rat

Primer
Products:
OriGene qSTAR qPCR primer pairs in human, mouse for XCL1
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat XCL1
QuantiTect SYBR Green Assays in human, mouse, rat XCL1
QuantiFast Probe-based Assays in human, mouse, rat XCL1
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for XCL1

(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)
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This gene was present in the common ancestor of chordates.

Orthologs for XCL1 gene from Selected species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Xcl11 , 5 chemokine (C motif) ligand 11, 5 73.39(n)1
60.53(a)1
  1 (72.26 cM)5
169631  NM_008510.11  NP_032536.11 
 1649316445 
chicken
(Gallus gallus)
Aves IFNG6
Gallus gallus Interferon-gamma level (IFNG), mRNA....
29(a)
1 → many
1(83400070-83404445)


ENSEMBL Gene Tree for XCL1 (if available)
TreeFam Gene Tree for XCL1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for XCL1 gene
XCL22  
15 SIMAP similar genes for XCL1 using alignment to 1 protein entry:     XCL1_HUMAN:
XCL2    CCL8    CCL13    CCL11    CCL14    CCL3L1
CCL3L3    CCL26    CCL24    CCL4L1    CCL4L2    LOC728835
CCL5    CCL7    MCP-3

XCL1 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), 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 XCL1 (see all 254)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1877520811,2
--168543718(+) GGAGAA/CGCAGG 1 -- us2k10--------
rs4707391,2
C,F,O,A--168543747(-) CTCATG/TGTGTT 1 -- us2k12Minor allele frequency- T:0.47WA NA 238
rs43045521,2
C,F,A,H--168543756(+) AGATTC/AGTTGC 1 -- us2k112Minor allele frequency- A:0.44NS EA NA 1476
rs2018630061,2
C--168543846(+) GGAAA-/CTTATA 1 -- us2k10--------
rs1931413261,2
--168543907(+) CCAGTC/TAAAGG 1 -- us2k10--------
rs1406355811,2
C--168544060(+) ATCACA/TGTGAA 1 -- us2k10--------
rs1827723881,2
--168544062(+) CACAGC/TGAAAG 1 -- us2k10--------
rs5525681,2
A--168544083(+) catccC/Tatagg 1 -- us2k12Minor allele frequency- T:0.00NA 4
rs340384451,2
C--168544084(+) ATCCCG/ATAGGC 1 -- us2k17Minor allele frequency- A:0.37NA WA CSA EA 365
rs1875077971,2
--168544144(+) GAGGCA/TTTACA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for XCL1 (168545711 - 168551315 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for XCL1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2661292CNV Deletion23128226
nsv831836CNV Gain+Loss17160897

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing XCL1
DNA2.0 Custom Variant and Variant Library Synthesis for XCL1

(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: 600250    OMIM disorders: --

Selected diseases for XCL1 (see all 28):    About MalaCards
renal tuberculosis    dacryoadenitis    t-lymphocytopenia    allergic asthma
wegener's granulomatosis    myocarditis    pertussis    tuberculosis
essential hypertension    crohn's disease    asthma    sepsis
rheumatoid arthritis    hypertension    neuroblastoma    chronic lymphocytic leukemia
arthritis    hiv-1    multiple sclerosis    t-cell leukemia

1 disease from the University of Copenhagen DISEASES database for XCL1:
Renal tuberculosis

XCL1 for disorders           About GeneDecksing

5 Novoseek inferred disease relationships for XCL1 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
inflammation 26.7 3 19797511 (1), 9013979 (1), 11696436 (1)
rheumatoid arthritis 2.62 4 12847680 (2)
necrosis 0 1 15614041 (1)
tumors 0 4 12406881 (1), 17397028 (1), 15614041 (1), 17471169 (1)
cancer 0 3 15547752 (1), 20225245 (1)

Genetic Association Database (GAD): XCL1
Human Genome Epidemiology (HuGE) Navigator: XCL1 (5 documents)

Export disorders for XCL1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for XCL1 gene, integrated from 10 sources (see all 126):
(articles sorted by number of sources associating them with XCL1)
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  1. Molecular cloning of a novel C or gamma type chemokine, SCM-1. (PubMed id 7875320)1, 2, 3, 9 Yoshida T.... Yoshie O. (FEBS Lett. 1995)
  2. Molecular cloning and functional characterization of human lymphotactin. (PubMed id 7602097)1, 2, 3, 9 Kennedy J.... Zlotnik A. (J. Immunol. 1995)
  3. Cloning of ATAC, an activation-induced, chemokine-related molecule exclusively expressed in CD8+ T lymphocytes. (PubMed id 7615002)1, 2, 9 Mueller S.... Kroczek R.A. (Eur. J. Immunol. 1995)
  4. Monomeric solution structure of the prototypical 'C' chemokine lymphotactin. (PubMed id 11601972)1, 2, 9 Kuloglu E.S....Volkman B.F. (Biochemistry 2001)
  5. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. (PubMed id 19536175)1, 4 Ehret G.B....Chakravarti A. (Eur. J. Hum. Genet. 2009)
  6. Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation. (PubMed id 19064610)1, 4 Cheung C.L....Kung A.W. (Hum. Mol. Genet. 2009)
  7. Genetic variants in apoptosis and immunoregulation-related genes are associated with risk of chronic lymphocytic leukemia. (PubMed id 19074885)1, 4 Enjuanes A....Campo E. (Cancer Res. 2008)
  8. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
  9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  10. Structure and expression of two highly related genes encoding SCM- 1/human lymphotactin. (PubMed id 8849694)1, 2 Yoshida T....Yoshie O. (FEBS Lett. 1996)

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

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

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 6375 HGNC: 10645 AceView: XCL1 Ensembl:ENSG00000143184 euGenes: HUgn6375
ECgene: XCL1 Kegg: 6375 H-InvDB: XCL1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for XCL1 Pharmacogenomics, SNPs, Pathways
Wikipedia http://en.wikipedia.org/wiki/XCL1

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for XCL1 gene:
Search GeneIP for patents involving XCL1

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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