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

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; AllianceGenome:HGNC:10645
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: all
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Genomic context

Location:: 1q24.2

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (168576605..168582069)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (167929278..167937161)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (168545843..168551307)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Thermodynamic Evolution of a Metamorphic Protein: A Theoretical-Computational Study of Human Lymphotactin.
Title: Thermodynamic Evolution of a Metamorphic Protein: A Theoretical-Computational Study of Human Lymphotactin.
XCL1, a serum biomarker in neurological diseases; HTLV-1-associated myelopathy and multiple sclerosis.
Title: XCL1, a serum biomarker in neurological diseases; HTLV-1-associated myelopathy and multiple sclerosis.
XCL1 Aggravates Diabetic Nephropathy-Mediated Renal Glomerular Endothelial Cell Apoptosis and Inflammatory Response via Regulating p53/Nuclear Factor-Kappa B Pathway.
Title: XCL1 Aggravates Diabetic Nephropathy-Mediated Renal Glomerular Endothelial Cell Apoptosis and Inflammatory Response via Regulating p53/Nuclear Factor-Kappa B Pathway.
Specific binding-induced modulation of the XCL1 metamorphic equilibrium.
Title: Specific binding-induced modulation of the XCL1 metamorphic equilibrium.
Involvement of the ERK/HIF-1alpha/EMT Pathway in XCL1-Induced Migration of MDA-MB-231 and SK-BR-3 Breast Cancer Cells.
Title: Involvement of the ERK/HIF-1α/EMT Pathway in XCL1-Induced Migration of MDA-MB-231 and SK-BR-3 Breast Cancer Cells.
Evolution of fold switching in a metamorphic protein.
Title: Evolution of fold switching in a metamorphic protein.
XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary.
Title: XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary.
The systemic exercise-released chemokine lymphotactin/XCL1 modulates in vitro adult hippocampal precursor cell proliferation and neuronal differentiation.
Title: The systemic exercise-released chemokine lymphotactin/XCL1 modulates in vitro adult hippocampal precursor cell proliferation and neuronal differentiation.
Diepoxybutane induces the expression of a novel p53-target gene XCL1 that mediates apoptosis in exposed human lymphoblasts.
Title: Diepoxybutane induces the expression of a novel p53-target gene XCL1 that mediates apoptosis in exposed human lymphoblasts.
Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1.
Title: Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1.

Submit: New GeneRIF Correction See all GeneRIFs (37)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH91674 (e-PCR)
- UniSTS:86631

XCL1_1110 (e-PCR)
- UniSTS:277865

NoName (e-PCR)
- UniSTS:481425

SHGC-35495 (e-PCR)
- UniSTS:36531

NoName (e-PCR)
- UniSTS:481472

SHGC-80982 (e-PCR)
- UniSTS:102607

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables CCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	IDA Inferred from Direct Assay more info	PubMed
enables chemokine receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables chemokine receptor binding	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to interleukin-4	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to transforming growth factor beta stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in eosinophil chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in mature natural killer cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of CD4-positive, alpha-beta T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of T cell cytokine production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of T-helper 1 cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of T-helper 1 type immune response	IC Inferred by Curator more info	PubMed
involved_in negative regulation of interleukin-2 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of type II interferon production	IDA Inferred from Direct Assay more info	PubMed
involved_in neutrophil chemotaxis	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of B cell chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of CD4-positive, alpha-beta T cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of CD8-positive, alpha-beta T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of T cell cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of T-helper 1 cell cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T-helper 2 cell cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of granzyme A production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of granzyme B production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of immunoglobulin production in mucosal tissue	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-10 production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of leukocyte chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of natural killer cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of neutrophil chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of release of sequestered calcium ion into cytosol	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of thymocyte migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transforming growth factor beta production	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in release of sequestered calcium ion into cytosol	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to virus	IDA Inferred from Direct Assay more info	PubMed
involved_in signal transduction	IC Inferred by Curator more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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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)

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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)

NM_002995.3 → NP_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, Q52MA8

Related

ENSP00000356792.3, ENST00000367818.4

Conserved Domains (1) summary

cd00271
Location:22 → 93

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) ...