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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)

(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)
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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

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	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 ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005615	extracellular space	IEA	--

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Antibodies for XCL2:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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	Browse R&D Systems for Antibodies
	Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
	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)
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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.)
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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 ID	Qualified GO term	Evidence	PubMed IDs
GO:0008009	chemokine activity	TAS	7875320

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(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.)
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2 Interacting proteins for XCL2 (ENSP00000356793³) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
XCR1	ENSP00000310405³	STRING (score=.994)
XCL1	ENSP00000356792³	STRING (score=.902)

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006935	chemotaxis	IEA	--
GO:0006955	immune response	IEA	--
GO:0007165	signal transduction	TAS	7875320
GO:0008015	blood circulation	TAS	7875320

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

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Data from

(Publications) and GNF BioGPS
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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)

AB	SNP ID	Valid	Chr 1 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
--	rs470733^1,2	A,C,F	166776746(-)	`CTGAGT/ATTATA`	1	--	ut3¹		1		MN	184
--	rs4301615^1,2	A,F,H	166777949(+)	`CCTATC/GTGAGA`	1	H/D	mis¹ ese³		3		EA WA	294
--	rs3916568^1,2	A,C	166781802(-)	`GTCATA/GGGTAT`	1	--	ng3¹		0	--	--	--	--
--	rs10753774^1,2	A,C	166780632(+)	`ATCTGC/TATTGG`	1	--	ng3¹		0	--	--	--	--
--	rs597359^1,2	A,C	166781613(-)	`atcctA/Gtaggc`	1	--	ng3¹ tfbs³		0	--	--	--	--
--	rs474414^1,2	C,F	166779944(+)	`TGGGTA/GTAGGA`	1	--	ng3¹		2		MN	368
--	rs4501820^1,2	A	166777945(+)	`TCCTCC/TTATGT`	1	R/K	mis¹ ese³		0	--	--	--	--
--	rs475282^1,2	F	166780003(+)	`AAAAAT/AGTCCC`	1	--	ng3¹		4		NA	66
--	rs597336^1,2	A	166781636(-)	`tcacaA/Gtgaaa`	1	--	ng3¹		0	--	--	--	--
--	rs597351^1,2	A	166781626(-)	`agattA/Tgaaat`	1	--	ng3¹		0	--	--	--	--

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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:

The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)^{3, 4} Gregory S.G.... Bentley D.R. (2006)
Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PubMed id 15340161)^{3, 4} Zhang Z. and Henzel W.J. (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{3, 4} Gerhard D.S....Malek J. (2004)
Structure and expression of two highly related genes encoding SCM- 1/human lymphotactin. (PubMed id 8849694)^{3, 4} Yoshida T....Yoshie O. (1996)
Molecular cloning of a novel C or gamma type chemokine, SCM-1. (PubMed id 7875320)^{2, 3} Yoshida T....Yoshie O. (1995)
Mycobacterium tuberculosis antigen Wag31 induces expression of C-chemokine XCL2 in macrophages. (PubMed id 18618175)³ Cao W....Lu H. (2008)
Association of the -2510A/G chemokine (C-C motif) ligand 2 polymorphism with knee osteoarthritis in a Korean population. (PubMed id 17763208)³ Park H.J....Hong S.J. (2007)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)³ Strausberg R.L....Marra M.A. (2002)
Identification of single C motif-1/lymphotactin receptor XCR1. (PubMed id 9632725)³ Yoshida T.... Yoshie O. (1998)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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)
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Name	Description
Wikipedia	http://en.wikipedia.org/wiki/XCL2

Licensable Technologies for XCL2
(Available from WIS Yeda, Salk, Tufts)

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(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)
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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
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 XCL2-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 XCL2		Browse antibodies at Sigma-Aldrich
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	Recombinant & Natural Proteins

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XCL2 Gene

protein-coding GIFtS: 43

Aliases &
Descriptions
for XCL2

Summaries
for XCL2

Genomic Location
for XCL2

Proteins
for XCL2

Protein Domains/
Families
for XCL2

Gene Function
for XCL2

Pathways & Interactions
for XCL2

Drugs & Compounds
for XCL2

Transcripts
for XCL2

Expression
for XCL2

Orthologs
for XCL2

Paralogs
for XCL2

SNPs/Variants
for XCL2

Disorders & Mutations
for XCL2

Medical News
for XCL2

Publications
for XCL2

Search for XCL2

Genome Databases showing XCL2

Other Databases showing XCL2

Specialized Databases showing XCL2

Licensable Technologies
for XCL2

Services
for XCL2

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

XCL2 Gene

protein-coding GIFtS: 43

Aliases & Descriptionsfor XCL2

Summariesfor XCL2

Genomic Locationfor XCL2

Proteinsfor XCL2

Protein Domains/Familiesfor XCL2

Gene Functionfor XCL2

Pathways & Interactionsfor XCL2

Drugs & Compoundsfor XCL2

Transcriptsfor XCL2

Expression for XCL2

Orthologsfor XCL2

Paralogsfor XCL2

SNPs/Variantsfor XCL2

Disorders & Mutationsfor XCL2

Medical Newsfor XCL2

Publicationsfor XCL2

Search for XCL2

Genome Databases showing XCL2

Other Databases showing XCL2

Specialized Databases showing XCL2

Licensable Technologiesfor XCL2

Servicesfor XCL2

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for XCL2

Summaries
for XCL2

Genomic Location
for XCL2

Proteins
for XCL2

Protein Domains/
Families
for XCL2

Gene Function
for XCL2

Pathways & Interactions
for XCL2

Drugs & Compounds
for XCL2

Transcripts
for XCL2

Expression
for XCL2

Orthologs
for XCL2

Paralogs
for XCL2

SNPs/Variants
for XCL2

Disorders & Mutations
for XCL2

Medical News
for XCL2

Publications
for XCL2

Licensable Technologies
for XCL2

Services
for XCL2