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XCL1 X-C motif chemokine ligand 1 [ Homo sapiens (human) ]

Gene ID: 6375, updated on 12-Oct-2019

Summary

Official Symbol
XCL1provided by HGNC
Official Full Name
X-C motif chemokine ligand 1provided by HGNC
Primary source
HGNC:HGNC:10645
See related
Ensembl:ENSG00000143184 MIM:600250
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LTN; ATAC; LPTN; SCM1; SCM-1; SCM1A; SCYC1; SCM-1a
Summary
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]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See XCL1 in Genome Data Viewer
Location:
1q24.2
Exon count:
4
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (168574128..168582069)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (168545711..168551315)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928565 Neighboring gene ribosomal protein L7a pseudogene 19 Neighboring gene X-C motif chemokine ligand 2 Neighboring gene ribosomal protein L7a pseudogene 21 Neighboring gene uncharacterized LOC105371604 Neighboring gene dermatopontin

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 interacts with XCL1 electrostatically; the K42R mutation in XCL1 maintained anti-HIV (IIIB and BAL) capacity whilst K42A mutation completely abrogates XCL1 anti-HIV-1 activity PubMed
env HIV-1 Env gp120 interacts with the basic residues (R18, R35, K42, R43 and K46) within XCL1 PubMed
env XCL1 inhibits a broad range of HIV-1 isolates irrespective of coreceptor-usage phenotype by blocking HIV-1 attachment and entry through its direct interaction with gp120 PubMed
env CXCR4-tropic HIV-1 gp120 augments the expression of RANTES, IP-10, MCP-1, and LTN in peripheral blood mononuclear cells (PBMCs), while CCR5-tropic HIV-1 gp120 also induces an increase in both IP-10 and MCP-1 production PubMed
Nef nef HIV-1 Nef-stimulated CD8+ T cells upregulate mRNAs expression for IFN-gamma, MIP-1alpha, MIP-1alphaP, MIP-1beta, TNFRSF9, XCL1, and GM-CSF compared to unstimulated cells PubMed
Tat tat Upregulation of XCL1 expression is induced by HIV-1 Tat in human astrocytes PubMed
tat SCYC1 is upregulated by HIV-1 Tat treatment in human epithelial cells PubMed
capsid gag HIV-1 CA-stimulated CD8+ T cells upregulate mRNAs expression for IFN-gamma, MIP-1alpha, MIP-1alphaP, MIP-1beta, TNFRSF9, XCL1, and GM-CSF compared to unstimulated cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Chemokine receptors bind chemokines, organism-specific biosystem (from REACTOME)
    Chemokine receptors bind chemokines, organism-specific biosystemChemokine receptors are cytokine receptors found on the surface of certain cells, which interact with a type of cytokine called a chemokine. Following interaction, these receptors trigger a flux of i...
  • Class A/1 (Rhodopsin-like receptors), organism-specific biosystem (from REACTOME)
    Class A/1 (Rhodopsin-like receptors), organism-specific biosystemRhodopsin-like receptors (class A/1) are the largest group of GPCRs and are the best studied group from a functional and structural point of view. They show great diversity at the sequence level and ...
  • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • G alpha (q) signalling events, organism-specific biosystem (from REACTOME)
    G alpha (q) signalling events, organism-specific biosystemThe classic signalling route for G alpha (q) is activation of phospholipase C beta thereby triggering phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides ...
  • GPCR downstream signaling, organism-specific biosystem (from REACTOME)
    GPCR downstream signaling, organism-specific biosystemG protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it h...
  • GPCR ligand binding, organism-specific biosystem (from REACTOME)
    GPCR ligand binding, organism-specific biosystemThere are more than 800 G-protein coupled receptor (GPCRs) in the human genome, making it the largest receptor superfamily. GPCRs are also the largest class of drug targets, involved in virtually all...
  • Gastrin-CREB signalling pathway via PKC and MAPK, organism-specific biosystem (from REACTOME)
    Gastrin-CREB signalling pathway via PKC and MAPK, organism-specific biosystemGastrin is a hormone whose main function is to stimulate secretion of hydrochloric acid by the gastric mucosa, which results in gastrin formation inhibition. This hormone also acts as a mitogenic fac...
  • Peptide ligand-binding receptors, organism-specific biosystem (from REACTOME)
    Peptide ligand-binding receptors, organism-specific biosystemThese receptors, a subset of the Class A/1 (Rhodopsin-like) family, all bind peptide ligands which include the chemokines, opioids and somatostatins.
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by GPCR, organism-specific biosystem (from REACTOME)
    Signaling by GPCR, organism-specific biosystemG protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors i...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
CCR chemokine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine activity IDA
Inferred from Direct Assay
more info
PubMed 
chemokine receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
chemokine receptor binding NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 
cell-cell signaling IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to interferon-gamma IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to interleukin-1 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to interleukin-4 ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to transforming growth factor beta stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to tumor necrosis factor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
eosinophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lymphocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mature natural killer cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
monocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of CD4-positive, alpha-beta T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of T cell cytokine production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of T-helper 1 cell activation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of T-helper 1 type immune response IC
Inferred by Curator
more info
PubMed 
negative regulation of interferon-gamma production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-2 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
neutrophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neutrophil chemotaxis TAS
Traceable Author Statement
more info
PubMed 
positive regulation of B cell chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of CD4-positive, alpha-beta T cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of CD8-positive, alpha-beta T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of T cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of T cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of T cell cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of T cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of T-helper 1 cell cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of T-helper 2 cell cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of granzyme A production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of granzyme B production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of immunoglobulin production in mucosal tissue ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-10 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of leukocyte chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of natural killer cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of neutrophil chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of release of sequestered calcium ion into cytosol IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of thymocyte migration ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transforming growth factor beta production IDA
Inferred from Direct Assay
more info
PubMed 
regulation of inflammatory response IDA
Inferred from Direct Assay
more info
PubMed 
release of sequestered calcium ion into cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
response to virus IDA
Inferred from Direct Assay
more info
PubMed 
signal transduction IC
Inferred by Curator
more info
PubMed 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
lymphotactin
Names
SCM-1-alpha
XC chemokine ligand 1
c motif chemokine 1
chemokine (C motif) ligand 1
cytokine SCM-1
lymphotaxin
single cysteine motif 1a
small inducible cytokine subfamily C, member 1 (lymphotactin)
small-inducible cytokine C1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_002995.3NP_002986.1  lymphotactin precursor

    See identical proteins and their annotated locations for NP_002986.1

    Status: REVIEWED

    Source sequence(s)
    BF433809, D43768
    Consensus CDS
    CCDS1274.1
    UniProtKB/Swiss-Prot
    P47992
    Related
    ENSP00000356792.3, ENST00000367818.4
    Conserved Domains (1) summary
    cd00271
    Location:2293
    Chemokine_C; Chemokine_C, C or lymphotactin subgroup, 1 of 4 subgroup designations of chemokines based on the arrangement of two N-terminal, conserved cysteine residues. Most of the known chemokines (cd00169) belong to either the CC (cd00272) or CXC (cd00273) ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    168574128..168582069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509865.2XP_011508167.1  lymphotactin isoform X1

    See identical proteins and their annotated locations for XP_011508167.1

    UniProtKB/Swiss-Prot
    P47992
    Conserved Domains (1) summary
    cd00271
    Location:2293
    Chemokine_C; Chemokine_C, C or lymphotactin subgroup, 1 of 4 subgroup designations of chemokines based on the arrangement of two N-terminal, conserved cysteine residues. Most of the known chemokines (cd00169) belong to either the CC (cd00272) or CXC (cd00273) ...
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