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XCL1 Gene

protein-coding   GIFtS: 56

GC01P166812
chemokine (C motif) ligand 1
(Previous names: small inducible cytokine subfamily C, member 1 (lymphotactin) )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: LTN, SCYC1)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
ATAC 1, 2, 3
LPTN 1, 2, 5
LTN 2, 3, 5
Lymphotaxin 3
OTTHUMP00000032498 2
OTTHUMP00000060404 2
SCM-1 1, 2
SCM-1-alpha 3
SCM-1a 1, 2
SCM1 2, 5
SCYC1 2, 3, 5
lymphotactin 1, 2
Descriptions
C motif chemokine 1 3
Cytokine SCM-1 3
Small-inducible cytokine C1 3
XC chemokine ligand 1 3
chemokine (C motif) ligand 1 2
small inducible cytokine subfamily C, member 1
(lymphotactin) 1, 2
External Ids
HGNC: 106451
Entrez Gene: 63752
UniProtKB: P479923
Ensembl: ENSG000001431847
Search outside databases for aliases for XCL1 gene

Previous GC identifers: GC01P166180 GC01P164196 GC01P165241 GC01P165733 GC01P165277

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the XCL1 gene  

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)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P166812:     (about GC identifiers)

Start:
166,812,480 bp from pter
End:
166,817,939 bp from pter
Size:
5,460 bases
Orientation:
plus 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: XCL1_HUMAN, P47992 (See protein sequence)
Recommended Name: Lymphotactin precursor  
Size: 114 amino acids; 12517 Da
Subcellular location: Secreted
PDB structures from and Proteopedia :
1J8I (3D)    1J9O (3D)    2HDM (3D)    2JP1 (3D)    2NYZ (3D)    
Secondary accessions: Q52MA8

REFSEQ proteins: NP_002986.1  

ENSEMBL proteins: 
ENSP00000356792 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Sigma-Aldrich Proteins for XCL1  
R&D Systems Recombinant & Natural Proteins for XCL1 (XCL1/Lymphotactin)
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Lymphotactin)
Human Recombinant Proteins from Abnova (XCL1)
                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--
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Antibodies for XCL1: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for XCL1
R&D Systems Antibodies for XCL1 (XCL1/Lymphotactin)
Antibodies from Abcam (Lymphotactin), each with their AbpromiseSM
Browse Abnova for Monoclonal and Polyclonal Antibodies
Novus Biologicals Antibodies for XCL1

Assays for XCL1: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
R&D Systems ELISAs for XCL1 (XCL1/Lymphotactin)         (see all)
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro domains/families:
 IPR001811 Chemokine_IL8
 IPR008105 Lymphotactin


   GeneDecks  XCL1 for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry P47992

ProtoNet protein and cluster: P47992

1 Blocks protein family: IPB008105 Lymphotactin precursor signature

UniProtKB/Swiss-Prot: XCL1_HUMAN, P47992
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:
Invitrogen RNAi Products for gene knock-down (XCL1)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (XCL1)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002995

              Applied Biosystems Silencer® siRNAs for XCL1

              Sigma-Aldrich siRNA for XCL1  
                     Sigma-Aldrich shRNA Panels and shRNA for XCL1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for XCL1
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_002995
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_002995
                                 untagged cDNA clone in CMV expression vector: NM_002995 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_002995

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

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

GO IDQualified GO termEvidencePubMed IDs
GO:0008009 chemokine activity TAS7602097
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 Invitrogen iPath™ Online BioAtlas - Pathway for XCL1 (Maps provided by GeneGo):
 Cell-matrix glycoconjugates

   GeneDecks  XCL1 for the pathways selected above  
About GeneDecksing

1 Millipore Pathway for XCL1
 Cell adhesion Cell-matrix glycoconjugates

   GeneDecks  XCL1 for the pathways selected above  
About GeneDecksing

1 Kegg Pathway  (Kegg details for XCL1):
 hsa04060 Cytokine-cytokine receptor interaction

   GeneDecks  XCL1 for the pathways selected above  
About GeneDecksing

5/36 Interacting proteins for XCL1 (ENSP000003567923) via UniProtKB, MINT, and/or STRING (see all 36 )
InteractantInteraction Details
GeneCardExternal ID(s)
XCR1ENSP000003104053STRING (score=.998)
CD28ENSP000003248903STRING (score=.924)
XCL2ENSP000003567933STRING (score=.902)
ATP2B1ENSP000003520543STRING (score=.899)
ATP2B3ENSP000003438863STRING (score=.899)
About this table

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

GO IDQualified GO termEvidencePubMed IDs
GO:0006874 cellular calcium ion homeostasis TAS7602097
GO:0006935 chemotaxis TAS7602097
GO:0006955 immune response IEA--
GO:0007165 signal transduction TAS7602097
GO:0007267 cell-cell signaling TAS7602097
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 XCL1
6 Novoseek chemical compound relationships for XCL1 gene
Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
rantes 84.78 33 9393669 (1), 10942204 (1), 14734774 (1), 19397398 (1) (see all 29)
ccl3 56.82 4 14734774 (1), 18179747 (1)
ccl4 30.82 5 14734774 (1), 12427307 (1), 18179747 (1)
wortmannin 17.11 2 10887101 (1), 10092776 (1)
nacl 0.00 1 17302442 (1)
calcium 0.00 5 9271361 (2), 7615002 (2), 7602097 (1)
About this table


(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:
Invitrogen RNAi Products for gene knock-down (XCL1)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (XCL1)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002995

              Sigma-Aldrich siRNA for XCL1  
                     Sigma-Aldrich shRNA Panels and shRNA for XCL1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_002995  

REFSEQ mRNAs for XCL1 gene: 

NM_002995.1   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_002995  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_002995
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_002995
                                 untagged cDNA clone in CMV expression vector: NM_002995 

Additional cDNA sequence: 

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

3 DOTS entries:

DT.109036  DT.100735017  DT.91854396 

23 AceView cDNA sequences:

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

highest scoring ESTs for XCL1:

BC069817 BG214157 BQ005208 AA864918 AI094359 AI929309 AL031736 BG057735 BG436992 AI298976 

Unigene Cluster for XCL1:

Chemokine (C motif) ligand 1
Hs.546295  [show with all ESTs]
Unigene Representative Sequence: NM_002995


GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:
ENST00000367818  
(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

XCL1 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for XCL1

1 / 2 / 3

8 probe-sets matching XCL1 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

39652_at2, 3 U95-A 1 1.00 1.00 -0.08 0.18 AL031736 0.20 1.00 0.72 1
31496_g_at2, 3 U95-A 2 1.00 0.50 1.00 1.00 D63789 0.20 0.50 0.38 1

206365_at2, 3 U133-A 1 1.00 1.00 -- -- NM_002995 0.40 0.67 0.55 1

214567_s_at2, 3 U133-A 2 1.00 0.50 -- -- NM_003175 0.20 0.17 0.18 2

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

206365_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

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

206366_x_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --
GeneDecks  XCL1 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.546295

Expression variation in blood from EXPOLDB for XCL1

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

(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 XCL1 gene from 3 species
Organism Gene Locus Description Human
Similarity
NCBI accessions
chimpanzee
(Pan troglodytes)
XCL11   -- chemokine (C motif) ligand 1 98.83(n)
99.12(a)
469572  XM_524955.2  XP_524955.2 
rat
(Rattus norvegicus)
Xcl11   -- chemokine (C motif) ligand 1 71.64(n)
57.02(a)
171371  NM_134361.1  NP_599188.1 
mouse
(Mus musculus)
Xcl11, 5 1 (87.00 cM)5
chemokine (C motif) ligand 11, 5 73.39(n)1
60.53(a)1
169631  NM_008510.11  NP_032536.11 
 AI6616825  AK0798205  (see all 11)
About this table        Species with no ortholog for XCL1

ENSEMBL Gene Tree for XCL1
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for XCL1 gene
XCL22  

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


10/75 NCBI SNPs in XCL1 are shown (see all 75 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 42)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 1 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs9821431,2
A,C,F,H166817860(+) GCTGAC/TCCATG 1 -- ut31 ese314Minor allele frequency- T:0.22EA NA MN EU WA 2476
--
rs120293701,2
A,F,H166811129(+) TTTGAA/GGTTTA 1 -- ng514Minor allele frequency- G:0.42EU EA WA 420
--
rs37539381,2
C,F,H166810855(+) TTGGCC/TTATGA 1 -- ng5111Minor allele frequency- T:0.41NA EU EA WA 978
--
rs6414961,2
A,C,F166817413(-) AAGAGA/TGATTG 1 -- ut311Minor allele frequency- T:0.10MN 184
--
rs6415001,2
A,C166817409(-) GAGATC/TGATAT 1 -- ut313Minor allele frequency- T:0.00EA NA 58
--
rs75416041,2
A,C166811095(+) TTGTGC/TAGTAA 1 -- ng510--------
--
rs109189271,2
A,C166811690(+) AATGCA/GGATTC 1 -- ng510--------
--
rs75416931,2
A,C166811206(+) TTTATC/GAAAAC 1 -- ng510--------
--
rs5525681,2
A166810707(+) catccC/Tatagg 1 -- ng510--------
--
rs120397571,2
A166810970(+) TCTAAC/GATGAT 1 -- ng510--------
About this table

HapMap Linkage Disequilibrium images for XCL1 (up to first 250kb)

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

OMIM: 600250

5 Novoseek disease relationships for XCL1 gene

Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
inflammation 27.19 2 9013979 (1), 11696436 (1)
rheumatoid arthritis 4.93 4 12847680 (2)
necrosis 0.00 1 15614041 (1)
cancer 0.00 2 15547752 (1)
tumors 0.00 4 12406881 (1), 17397028 (1), 15614041 (1), 17471169 (1)
About this table

Human Genome Epidemiology Navigator: XCL1 (2 documents)

(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

10/117 PubMed articles for XCL1 gene (see all 117 ):
(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: 6375 HGNC: 10645 AceView: XCL1 Ensembl:ENSG00000143184 euGenes: HUgn6375
ECgene: XCL1 H-InvDB: XCL1
(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/XCL1
(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 XCL1:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
  Invitrogen Clones  Invitrogen Q-PCR Products
  Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for XCL1-related products

 Millipore Custom Antibody & Bulk Services
 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for XCL1 Antibodies for XCL1
 Explore super-pooled esiRNAs Proteins for XCL1
 Lentivirus-delivered shRNAs for XCL1 Browse small molecules at Sigma-Aldrich
 "Your Favorite Gene" Pathwaysfeedback


  
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 Recombinant & Natural Proteins  

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 Recombinant Proteins
(Lymphotactin)
 Antibodies (Lymphotactin)
 Search OriGene for XCL1
 Search Tocris compounds for XCL1




 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Antibodies for XCL1

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