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Aliases for XCL1 Gene

Aliases for XCL1 Gene

  • X-C Motif Chemokine Ligand 1 2 3 5
  • Small Inducible Cytokine Subfamily C, Member 1 (Lymphotactin) 2 3
  • Chemokine (C Motif) Ligand 1 2 3
  • Small-Inducible Cytokine C1 3 4
  • XC Chemokine Ligand 1 3 4
  • C Motif Chemokine 1 3 4
  • Cytokine SCM-1 3 4
  • Lymphotactin 2 3
  • Lymphotaxin 3 4
  • SCM-1-Alpha 3 4
  • SCYC1 3 4
  • ATAC 3 4
  • LTN 3 4
  • Single Cysteine Motif 1a 3
  • SCM-1a 3
  • SCM-1 3
  • SCM1A 3
  • LPTN 3
  • SCM1 3

External Ids for XCL1 Gene

Previous HGNC Symbols for XCL1 Gene

  • LTN
  • SCYC1

Previous GeneCards Identifiers for XCL1 Gene

  • GC01P166180
  • GC01P164196
  • GC01P165241
  • GC01P165733
  • GC01P165277
  • GC01P166812
  • GC01P139791

Summaries for XCL1 Gene

Entrez Gene Summary for XCL1 Gene

  • This antimicrobial 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, Sep 2014]

GeneCards Summary for XCL1 Gene

XCL1 (X-C Motif Chemokine Ligand 1) is a Protein Coding gene. Diseases associated with XCL1 include Renal Tuberculosis. Among its related pathways are Peptide ligand-binding receptors and RET signaling. GO annotations related to this gene include protein homodimerization activity and chemokine receptor binding. An important paralog of this gene is XCL2.

UniProtKB/Swiss-Prot for XCL1 Gene

  • Chemotactic activity for lymphocytes but not for monocytes or neutrophils. In thymus, mediates medullary accumulation of thymic dendritic cells and contributes to regulatoy T cell development, playing a role in self-tolerance establishment.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XCL1 Gene

Genomics for XCL1 Gene

Regulatory Elements for XCL1 Gene

Enhancers for XCL1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G168518 1.4 FANTOM5 ENCODE dbSUPER 33.6 -55.0 -54972 4.3 FOXA2 MXI1 PKNOX1 SAP130 MAX ZNF207 RELB IKZF2 CHD2 GATAD2A XCL1 XCL2 GC01P168543 ENSG00000228697
GH01G168509 1.4 FANTOM5 ENCODE dbSUPER 13.5 -65.8 -65842 2.0 HDGF PKNOX1 BMI1 NFXL1 CBX5 ZNF207 RELB IKZF2 CREM ZNF263 XCL1 XCL2 ENSG00000228697 GC01P168543
GH01G168553 1 ENCODE dbSUPER 16.7 -21.6 -21552 1.4 PKNOX1 ZNF133 BMI1 RELB IKZF2 HOMEZ MTA2 HLF NR2F1 BHLHE40 XCL2 XCL1 ATP1B1 LOC101928596
GH01G168540 0.9 dbSUPER 16.7 -33.3 -33303 4.6 HDGF PKNOX1 NFXL1 BMI1 CBX5 ZNF207 FOS RELB CREM IKZF2 XCL2 XCL1 RPL7AP19
GH01G169024 1.1 FANTOM5 ENCODE 13.3 +449.1 449110 0.5 TBP PKNOX1 TBL1XR1 EBF1 RELA ARID3A EED RELB IKZF2 CHD2 XCL1 XCL2 GC01M168993 RNA5SP66
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around XCL1 on UCSC Golden Path with GeneCards custom track

Genomic Location for XCL1 Gene

Chromosome:
1
Start:
168,576,061 bp from pter
End:
168,582,077 bp from pter
Size:
6,017 bases
Orientation:
Plus strand

Genomic View for XCL1 Gene

Genes around XCL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XCL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XCL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XCL1 Gene

Proteins for XCL1 Gene

  • Protein details for XCL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P47992-XCL1_HUMAN
    Recommended name:
    Lymphotactin
    Protein Accession:
    P47992
    Secondary Accessions:
    • Q52MA8

    Protein attributes for XCL1 Gene

    Size:
    114 amino acids
    Molecular mass:
    12517 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for XCL1 Gene

neXtProt entry for XCL1 Gene

Post-translational modifications for XCL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for XCL1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for XCL1 (XCL1/Lymphotactin)

Protein Products

Assay Products

  • Cloud-Clone Corp. Assay Kits for XCL1

No data available for DME Specific Peptides for XCL1 Gene

Domains & Families for XCL1 Gene

Gene Families for XCL1 Gene

Protein Domains for XCL1 Gene

Suggested Antigen Peptide Sequences for XCL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P47992

UniProtKB/Swiss-Prot:

XCL1_HUMAN :
  • Belongs to the intercrine gamma family.
Family:
  • Belongs to the intercrine gamma family.
genes like me logo Genes that share domains with XCL1: view

Function for XCL1 Gene

Molecular function for XCL1 Gene

UniProtKB/Swiss-Prot Function:
Chemotactic activity for lymphocytes but not for monocytes or neutrophils. In thymus, mediates medullary accumulation of thymic dendritic cells and contributes to regulatoy T cell development, playing a role in self-tolerance establishment.

Gene Ontology (GO) - Molecular Function for XCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA --
GO:0008009 chemokine activity IDA 7602097
GO:0042379 chemokine receptor binding NAS 7602097
GO:0042803 protein homodimerization activity IDA 11889129
GO:0048020 CCR chemokine receptor binding IBA --
genes like me logo Genes that share ontologies with XCL1: view
genes like me logo Genes that share phenotypes with XCL1: view

Animal Models for XCL1 Gene

MGI Knock Outs for XCL1:

Animal Model Products

  • Taconic Biosciences Mouse Models for XCL1

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for XCL1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for XCL1 Gene

Localization for XCL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XCL1 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 XCL1 gene
Compartment Confidence
extracellular 5
plasma membrane 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for XCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA,ISS --
GO:0005623 cell IEA --
genes like me logo Genes that share ontologies with XCL1: view

Pathways & Interactions for XCL1 Gene

genes like me logo Genes that share pathways with XCL1: view

SIGNOR curated interactions for XCL1 Gene

Activates:

Gene Ontology (GO) - Biological Process for XCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001916 positive regulation of T cell mediated cytotoxicity IDA 18832695
GO:0002548 monocyte chemotaxis IBA --
GO:0002690 positive regulation of leukocyte chemotaxis ISS --
GO:0002725 negative regulation of T cell cytokine production IDA 10887101
GO:0002726 positive regulation of T cell cytokine production ISS --
genes like me logo Genes that share ontologies with XCL1: view

Drugs & Compounds for XCL1 Gene

(9) Drugs for XCL1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for XCL1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with XCL1: view

Transcripts for XCL1 Gene

mRNA/cDNA for XCL1 Gene

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

Unigene Clusters for XCL1 Gene

Chemokine (C motif) ligand 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for XCL1

Alternative Splicing Database (ASD) splice patterns (SP) for XCL1 Gene

No ASD Table

Relevant External Links for XCL1 Gene

GeneLoc Exon Structure for
XCL1
ECgene alternative splicing isoforms for
XCL1

Expression for XCL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for XCL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for XCL1 Gene

This gene is overexpressed in Whole Blood (x9.5) and Spleen (x7.5).

NURSA nuclear receptor signaling pathways regulating expression of XCL1 Gene:

XCL1

SOURCE GeneReport for Unigene cluster for XCL1 Gene:

Hs.546295

mRNA Expression by UniProt/SwissProt for XCL1 Gene:

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

Evidence on tissue expression from TISSUES for XCL1 Gene

  • Blood(4.5)
  • Spleen(2)
genes like me logo Genes that share expression patterns with XCL1: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for XCL1 Gene

Orthologs for XCL1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for XCL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 35
  • 99 (a)
ManyToMany
XCL1 34
  • 98.83 (n)
-- 35
  • 96 (a)
ManyToMany
dog
(Canis familiaris)
Mammalia LOC490356 34
  • 80.48 (n)
-- 35
  • 71 (a)
OneToMany
cow
(Bos Taurus)
Mammalia XCL2 34
  • 79.17 (n)
-- 35
  • 71 (a)
ManyToMany
XCL1 35
  • 68 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Xcl1 34 16 35
  • 73.39 (n)
rat
(Rattus norvegicus)
Mammalia Xcl1 34
  • 71.64 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 49 (a)
ManyToMany
-- 35
  • 43 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 47 (a)
OneToMany
chicken
(Gallus gallus)
Aves IFNG 35
  • 29 (a)
OneToMany
Species where no ortholog for XCL1 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)
  • 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 XCL1 Gene

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

Paralogs for XCL1 Gene

Paralogs for XCL1 Gene

(15) SIMAP similar genes for XCL1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with XCL1: view

Variants for XCL1 Gene

Sequence variations from dbSNP and Humsavar for XCL1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000396385 -- 168,581,510(+) AAGAG(A/G)TTCTG downstream-variant-500B, utr-variant-3-prime
rs1000515705 -- 168,577,053(+) TCAGA(G/T)TTCCT intron-variant
rs1000994101 -- 168,576,815(+) CCTTA(A/C)ACTTC intron-variant
rs1001380428 -- 168,572,985(+) GTATG(C/T)TAAAT upstream-variant-2KB
rs1001868019 -- 168,581,415(+) GTTCC(C/T)TAGTC downstream-variant-500B, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for XCL1 Gene

Variant ID Type Subtype PubMed ID
esv2661292 CNV deletion 23128226
esv3575205 CNV gain 25503493
esv3587866 CNV loss 21293372
nsv1078878 OTHER inversion 25765185
nsv831836 CNV gain+loss 17160897
nsv946494 CNV duplication 23825009

Variation tolerance for XCL1 Gene

Residual Variation Intolerance Score: 78.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.52; 55.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for XCL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
XCL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XCL1 Gene

Disorders for XCL1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for XCL1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
renal tuberculosis
  • tuberculosis of kidney
- elite association - COSMIC cancer census association via MalaCards
Search XCL1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for XCL1

Genetic Association Database (GAD)
XCL1
Human Genome Epidemiology (HuGE) Navigator
XCL1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
XCL1
genes like me logo Genes that share disorders with XCL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for XCL1 Gene

Publications for XCL1 Gene

  1. Molecular cloning and functional characterization of human lymphotactin. (PMID: 7602097) Kennedy J. … Zlotnik A. (J. Immunol. 1995) 2 3 4 22 64
  2. Molecular cloning of a novel C or gamma type chemokine, SCM-1. (PMID: 7875320) Yoshida T. … Yoshie O. (FEBS Lett. 1995) 2 3 4 22 64
  3. Monomeric solution structure of the prototypical 'C' chemokine lymphotactin. (PMID: 11601972) Kuloglu E.S. … Volkman B.F. (Biochemistry 2001) 3 4 22 64
  4. Cloning of ATAC, an activation-induced, chemokine-related molecule exclusively expressed in CD8+ T lymphocytes. (PMID: 7615002) Mueller S. … Kroczek R.A. (Eur. J. Immunol. 1995) 3 4 22 64
  5. Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation. (PMID: 19064610) Cheung C.L. … Kung A.W. (Hum. Mol. Genet. 2009) 3 46 64

Products for XCL1 Gene

Sources for XCL1 Gene

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