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Aliases for XCL2 Gene

Aliases for XCL2 Gene

  • X-C Motif Chemokine Ligand 2 2 3 5
  • Small Inducible Cytokine Subfamily C, Member 2 2 3
  • Chemokine (C Motif) Ligand 2 2 3
  • XC Chemokine Ligand 2 3 4
  • C Motif Chemokine 2 3 4
  • SCYC2 3 4
  • Cytokine SCM-1 Beta 3
  • SCM-1b 3
  • SCM1B 3

External Ids for XCL2 Gene

Previous HGNC Symbols for XCL2 Gene

  • SCYC2

Previous GeneCards Identifiers for XCL2 Gene

  • GC01M166145
  • GC01M164161
  • GC01M165206
  • GC01M165697
  • GC01M165242
  • GC01M166776
  • GC01M139756

Summaries for XCL2 Gene

GeneCards Summary for XCL2 Gene

XCL2 (X-C Motif Chemokine Ligand 2) is a Protein Coding gene. Among its related pathways are Peptide ligand-binding receptors and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include chemokine activity. An important paralog of this gene is XCL1.

UniProtKB/Swiss-Prot for XCL2 Gene

  • Chemotactic activity for lymphocytes but not for monocytes or neutrophils.

Additional gene information for XCL2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XCL2 Gene

Genomics for XCL2 Gene

GeneHancer (GH) Regulatory Elements for XCL2 Gene

Promoters and enhancers for XCL2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I168543 Promoter/Enhancer 0.7 EPDnew dbSUPER 550.8 0.0 -20 0.1 GC01P168543 RPL7AP19 XCL2 XCL1
GH01I168518 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 17.2 +22.9 22907 4.3 PKNOX1 SMAD1 MAX KLF5 ZNF207 ATF7 RUNX3 IKZF2 ZNF362 NR2F1 XCL1 XCL2 GC01P168543 ENSG00000228697
GH01I168553 Enhancer 0.9 ENCODE dbSUPER 18.2 -10.5 -10512 1.4 PKNOX1 RB1 EBF1 BMI1 BATF IRF4 ATF7 HOMEZ IKZF2 SMARCA5 XCL2 XCL1 ATP1B1 LOC101928596 GC01P168543
GH01I168534 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 13.2 +8.1 8085 2.6 ZNF687 POLR2A IKZF1 REST DPF2 RUNX3 XCL2 XCL1 GC01P168543 ENSG00000228697
GH01I168509 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 12.3 +33.8 33777 2 HDGF PKNOX1 SMAD1 EBF1 BMI1 KLF5 E4F1 RELA ZNF207 ATF7 XCL1 XCL2 ENSG00000228697 GC01P168543
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around XCL2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the XCL2 gene promoter:

Genomic Locations for XCL2 Gene

Genomic Locations for XCL2 Gene
chr1:168,540,765-168,543,997
(GRCh38/hg38)
Size:
3,233 bases
Orientation:
Minus strand
chr1:168,510,003-168,513,235
(GRCh37/hg19)

Genomic View for XCL2 Gene

Genes around XCL2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XCL2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XCL2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XCL2 Gene

Proteins for XCL2 Gene

  • Protein details for XCL2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBD3-XCL2_HUMAN
    Recommended name:
    Cytokine SCM-1 beta
    Protein Accession:
    Q9UBD3

    Protein attributes for XCL2 Gene

    Size:
    114 amino acids
    Molecular mass:
    12567 Da
    Quaternary structure:
    No Data Available

neXtProt entry for XCL2 Gene

Post-translational modifications for XCL2 Gene

No Post-translational modifications

Other Protein References for XCL2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for XCL2 Gene

Domains & Families for XCL2 Gene

Gene Families for XCL2 Gene

Suggested Antigen Peptide Sequences for XCL2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UBD3

UniProtKB/Swiss-Prot:

XCL2_HUMAN :
  • Belongs to the intercrine gamma family.
Family:
  • Belongs to the intercrine gamma family.
genes like me logo Genes that share domains with XCL2: view

Function for XCL2 Gene

Molecular function for XCL2 Gene

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

Phenotypes From GWAS Catalog for XCL2 Gene

Gene Ontology (GO) - Molecular Function for XCL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0008009 chemokine activity IBA,TAS --
GO:0048020 CCR chemokine receptor binding IBA --
genes like me logo Genes that share ontologies with XCL2: view
genes like me logo Genes that share phenotypes with XCL2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for XCL2 Gene

Localization for XCL2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XCL2 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XCL2 gene
Compartment Confidence
extracellular 5

Gene Ontology (GO) - Cellular Components for XCL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IBA --
genes like me logo Genes that share ontologies with XCL2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for XCL2 Gene

Pathways & Interactions for XCL2 Gene

genes like me logo Genes that share pathways with XCL2: view

Gene Ontology (GO) - Biological Process for XCL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002548 monocyte chemotaxis IBA --
GO:0006935 chemotaxis IEA --
GO:0006954 inflammatory response IBA --
GO:0006955 immune response IEA --
GO:0007165 signal transduction TAS 7875320
genes like me logo Genes that share ontologies with XCL2: view

No data available for SIGNOR curated interactions for XCL2 Gene

Drugs & Compounds for XCL2 Gene

No Compound Related Data Available

Transcripts for XCL2 Gene

mRNA/cDNA for XCL2 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(14) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for XCL2 Gene

Chemokine (C motif) ligand 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for XCL2 Gene

No ASD Table

Relevant External Links for XCL2 Gene

GeneLoc Exon Structure for
XCL2
ECgene alternative splicing isoforms for
XCL2

Expression for XCL2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for XCL2 Gene

mRNA differential expression in normal tissues according to GTEx for XCL2 Gene

This gene is overexpressed in Whole Blood (x22.7) and Spleen (x10.7).

NURSA nuclear receptor signaling pathways regulating expression of XCL2 Gene:

XCL2

SOURCE GeneReport for Unigene cluster for XCL2 Gene:

Hs.458346

Evidence on tissue expression from TISSUES for XCL2 Gene

  • Blood(4.1)
genes like me logo Genes that share expression patterns with XCL2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for XCL2 Gene

Orthologs for XCL2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for XCL2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia XCL2 33
  • 98.25 (n)
-- 34
  • 97 (a)
ManyToMany
-- 34
  • 95 (a)
ManyToMany
dog
(Canis familiaris)
Mammalia -- 34
  • 71 (a)
OneToMany
cow
(Bos Taurus)
Mammalia -- 34
  • 70 (a)
ManyToMany
XCL1 34
  • 67 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Xcl1 34
  • 61 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 50 (a)
ManyToMany
-- 34
  • 44 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 46 (a)
OneToMany
chicken
(Gallus gallus)
Aves IFNG 34
  • 28 (a)
OneToMany
Species where no ortholog for XCL2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for XCL2 Gene

ENSEMBL:
Gene Tree for XCL2 (if available)
TreeFam:
Gene Tree for XCL2 (if available)

Paralogs for XCL2 Gene

Paralogs for XCL2 Gene

(14) SIMAP similar genes for XCL2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with XCL2: view

Variants for XCL2 Gene

Sequence variations from dbSNP and Humsavar for XCL2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000316518 -- 168,540,317(-) C/T downstream_transcript_variant
rs1000352527 -- 168,544,963(-) A/G upstream_transcript_variant
rs1000807092 -- 168,544,821(-) A/C upstream_transcript_variant
rs1001918384 -- 168,544,349(-) A/C upstream_transcript_variant
rs1001970622 -- 168,544,098(-) T/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for XCL2 Gene

Variant ID Type Subtype PubMed ID
nsv946493 CNV duplication 23825009
nsv1078878 OTHER inversion 25765185

Variation tolerance for XCL2 Gene

Residual Variation Intolerance Score: 69.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.74; 46.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for XCL2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
XCL2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XCL2 Gene

Disorders for XCL2 Gene

Additional Disease Information for XCL2

No disorders were found for XCL2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for XCL2 Gene

Publications for XCL2 Gene

  1. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  2. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z … Henzel WJ (Protein science : a publication of the Protein Society 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Structure and expression of two highly related genes encoding SCM-1/human lymphotactin. (PMID: 8849694) Yoshida T … Yoshie O (FEBS letters 1996) 3 4 58
  5. Molecular cloning of a novel C or gamma type chemokine, SCM-1. (PMID: 7875320) Yoshida T … Yoshie O (FEBS letters 1995) 2 3 58

Products for XCL2 Gene

Sources for XCL2 Gene

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