XCL2 X-C motif chemokine ligand 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: XCL2provided by HGNC
Official Full Name: X-C motif chemokine ligand 2provided by HGNC
Primary source: HGNC:HGNC:10646
See related: Ensembl:ENSG00000143185 MIM:604828; AllianceGenome:HGNC:10646
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SCM1B; SCYC2; SCM-1b
Summary: Predicted to enable CCR chemokine receptor binding activity and chemokine activity. Predicted to be involved in several processes, including antimicrobial humoral immune response mediated by antimicrobial peptide; chemokine-mediated signaling pathway; and eosinophil chemotaxis. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in spleen (RPKM 4.0), bone marrow (RPKM 3.8) and 18 other tissues See more
Orthologs: all
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Genomic context

Location:: 1q24.2

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (168540768..168543997, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (167895859..167899089, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (168510006..168513235, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Comprehensive analysis reveals XCL2 as a cancer prognosis and immune infiltration-related biomarker.
Title: Comprehensive analysis reveals XCL2 as a cancer prognosis and immune infiltration-related biomarker.
The effect of ITLN1, XCL2 and DOT1L variants on knee osteoarthritis risk in the Han population.
Title: The effect of ITLN1, XCL2 and DOT1L variants on knee osteoarthritis risk in the Han population.
Upregulated X-C motif chemokine ligand 2 (XCL2) is associated with poor prognosis and increased immune infiltration in clear cell renal cell carcinoma.
Title: Upregulated X-C motif chemokine ligand 2 (XCL2) is associated with poor prognosis and increased immune infiltration in clear cell renal cell carcinoma.
XCL2 and CX3CL1 expression in lung cancers and adjacent non-cancerous tissues was detected by quantitative PCR and ELISA. The expression of XCL2 and CX3CL1 increases with increasing degree of malignancy, indicating that both chemokines might be important targets in gene therapy for lung cancer.
Title: Expression of Chemokine XCL2 and CX3CL1 in Lung Cancer.
analysis of XCL1 and XCL2, members of the C-chemokine subfamily, in the immune system
Title: Structural and agonist properties of XCL2, the other member of the C-chemokine subfamily.
identified 13 ADCC-activated genes. Six gene expression assays including 8 of the 13 genes (CCL3, CCL4/CCL4L1/CCL4L2, CD160, IFNG, NR4A3 and XCL1/XCL2) were analyzed in 127 kidney biopsies
Title: Genes associated with antibody-dependent cell activation are overexpressed in renal biopsies from patients with antibody-mediated rejection.
S1P induced the macrophage-recruiting factor CCL2 expression in NB cells via S1P2, providing new insights into the complicated functions of S1P2 in cancer.
Title: Induction of chemokine (C-C motif) ligand 2 by sphingosine-1-phosphate signaling in neuroblastoma.
Wag31 was found to specifically stimulate XCL2 expression in macrophages
Title: Mycobacterium tuberculosis antigen Wag31 induces expression of C-chemokine XCL2 in macrophages.
The G carrier of the -2510A/G promoter polymorphism was found to be associated with primary knee knee osteoarthritis among Koreans.
Title: Association of the -2510A/G chemokine (C-C motif) ligand 2 polymorphism with knee osteoarthritis in a Korean population.

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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)

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

NoName (e-PCR)
- UniSTS:481425

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

NoName (e-PCR)
- UniSTS:481472

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 protein binding	IPI Inferred from Physical Interaction 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 blood circulation	TAS Traceable Author Statement more info	PubMed
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	TAS Traceable Author Statement 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

General protein information

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Preferred Names: cytokine SCM-1 beta

Names: XC chemokine ligand 2; c motif chemokine 2; chemokine (C motif) ligand 2; small inducible cytokine subfamily C, member 2

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_003175.4 → NP_003166.1 cytokine SCM-1 beta precursor

See identical proteins and their annotated locations for NP_003166.1

Status: VALIDATED

Source sequence(s)

BC070308, BE218461

Consensus CDS

CCDS1273.1

UniProtKB/Swiss-Prot

Q9UBD3

Related

ENSP00000356793.2, ENST00000367819.3

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) ...