U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 6375, updated on 10-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See XCL1 in Genome Data Viewer
    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 (168576605..168582069)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (167929278..167937161)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (168545843..168551307)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC125312414 Neighboring gene uncharacterized LOC101928565 Neighboring gene MPRA-validated peak443 silencer Neighboring gene MPRA-validated peak444 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:168479196-168480395 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:168481645-168482844 Neighboring gene ribosomal protein L7a pseudogene 19 Neighboring gene X-C motif chemokine ligand 2 Neighboring gene ribosomal protein L7a pseudogene 21 Neighboring gene NANOG hESC enhancer GRCh37_chr1:168594433-168594934 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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 antimicrobial humoral immune response mediated by antimicrobial peptide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell chemotaxis 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 inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in killing of cells of another organism IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 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

    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)

    NEW Try the new Transcript table

    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, Q52MA8
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      168576605..168582069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      167929278..167937161
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338141.1XP_054194116.1  lymphotactin isoform X1

      UniProtKB/Swiss-Prot
      P47992, Q52MA8