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    SPN sialophorin [ Homo sapiens (human) ]

    Gene ID: 6693, updated on 7-Oct-2018

    Summary

    Official Symbol
    SPNprovided by HGNC
    Official Full Name
    sialophorinprovided by HGNC
    Primary source
    HGNC:HGNC:11249
    See related
    Ensembl:ENSG00000197471 MIM:182160; Vega:OTTHUMG00000097765
    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
    LSN; CD43; GALGP; GPL115
    Summary
    This gene encodes a highly sialylated glycoprotein that functions in antigen-specific activation of T cells, and is found on the surface of thymocytes, T lymphocytes, monocytes, granulocytes, and some B lymphocytes. It contains a mucin-like extracellular domain, a transmembrane region and a carboxy-terminal intracellular region. The extracellular domain has a high proportion of serine and threonine residues, allowing extensive O-glycosylation, and has one potential N-glycosylation site, while the carboxy-terminal region has potential phosphorylation sites that may mediate transduction of activation signals. Different glycoforms of this protein have been described. In stimulated immune cells, proteolytic cleavage of the extracellular domain occurs in some cell types, releasing a soluble extracellular fragment. Defects in expression of this gene are associated with Wiskott-Aldrich syndrome. [provided by RefSeq, Sep 2017]
    Expression
    Biased expression in bone marrow (RPKM 10.2), lymph node (RPKM 6.8) and 13 other tissues See more
    Orthologs

    Genomic context

    See SPN in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (29662950..29670876)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29674271..29681828)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene SMG1 pseudogene 2 Neighboring gene solute carrier family 7 member 5 pseudogene 1 Neighboring gene carbonic anhydrase 5A pseudogene 1 Neighboring gene quinolinate phosphoribosyltransferase Neighboring gene RNA, 7SK small nuclear pseudogene 127 Neighboring gene chromosome 16 open reading frame 54

    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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CD3/CD28-activated primary CD4+ T cells downregulates plasma membrane expression of SPN PubMed
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SPN PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120-treated vaginal epithelial cells show downregulation of sialophorin (SPN) expression as compared to untreated control PubMed
    env Elimination of CD43 expression by gene targeting in the CEM T cell line results in its increased homotypic adhesion and binding to HIV-1 gp120 PubMed
    Nef nef Production of infectious triple deletion vpr/vpu/nef HIV-1 mutant is suppressed, indicating that Nef may antagonize restriction activity of SPN against production of infectious wild-type HIV-1 PubMed
    Pr55(Gag) gag Basic sequences in the cytoplasmic domains of PSGL-1, CD43, and CD44 are required for efficient association with HIV-1 Gag in HeLa cells PubMed
    gag The highly basic region (HBR) of HIV-1 MA promotes Gag association with specific UDMs containing PSGL-1, CD43, and CD59 PubMed
    gag HIV-1 Gag multimers associate with a specific subset of uropod-directed microdomains (UDMs) containing PSGL-1, CD43, and CD44 PubMed
    gag HIV-1 Gag co-localizes with both uropod markers PSGL-1 and CD43 on the plasma membrane PubMed
    Vpr vpr Production of infectious triple deletion vpr/vpu/nef HIV-1 mutant is suppressed, indicating that Vpr may antagonize restriction activity of SPN against production of infectious wild-type HIV-1 PubMed
    Vpu vpu Production of infectious triple deletion vpr/vpu/nef HIV-1 mutant is suppressed, indicating that Vpu may antagonize restriction activity of SPN against production of infectious wild-type HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Basigin interactions, organism-specific biosystem (from REACTOME)
      Basigin interactions, organism-specific biosystemBasigin is a widely expressed transmembrane glycoprotein that belongs to the Ig superfamily and is highly enriched on the surface of epithelial cells. Basigin is involved in intercellular interaction...
    • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
      Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
      Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell surface interactions at the vascular wall, organism-specific biosystem (from REACTOME)
      Cell surface interactions at the vascular wall, organism-specific biosystemLeukocyte extravasation is a rigorously controlled process that guides white cell movement from the vascular lumen to sites of tissue inflammation. The powerful adhesive interactions that are require...
    • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
      Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Epstein-Barr virus infection, conserved biosystem (from KEGG)
      Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Hemostasis, organism-specific biosystem (from REACTOME)
      Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    Hsp70 protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    heat shock protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transmembrane signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    T-helper 1 cell lineage commitment IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular defense response TAS
    Traceable Author Statement
    more info
    PubMed 
    chemotaxis TAS
    Traceable Author Statement
    more info
    PubMed 
    defense response to bacterium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    establishment or maintenance of cell polarity TAS
    Traceable Author Statement
    more info
    PubMed 
    immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    interferon-gamma production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    leukocyte migration TAS
    Traceable Author Statement
    more info
     
    leukocyte tethering or rolling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of T cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of T cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of tumor necrosis factor biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of T cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    PML body IEA
    Inferred from Electronic Annotation
    more info
     
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome HDA PubMed 
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    membrane HDA PubMed 
    microvillus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    uropod ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    leukosialin
    Names
    galactoglycoprotein
    leukocyte sialoglycoprotein
    sialophorin (gpL115, leukosialin, CD43)

    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_001030288.3NP_001025459.1  leukosialin precursor

      See identical proteins and their annotated locations for NP_001025459.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC009086, BQ774811, DA951208, X60502
      Consensus CDS
      CCDS10650.1
      UniProtKB/Swiss-Prot
      P16150
      UniProtKB/TrEMBL
      A0A024R629
      Related
      ENSP00000378787.2, OTTHUMP00000123397, ENST00000395389.2
      Conserved Domains (1) summary
      pfam15782
      Location:80224
      GREB1; Gene regulated by oestrogen in breast cancer
    2. NM_003123.5NP_003114.1  leukosialin precursor

      See identical proteins and their annotated locations for NP_003114.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC009086, AK292626, BQ774811, DB108930
      Consensus CDS
      CCDS10650.1
      UniProtKB/Swiss-Prot
      P16150
      UniProtKB/TrEMBL
      A0A024R629
      Related
      ENSP00000353238.3, ENST00000360121.4
      Conserved Domains (1) summary
      pfam15782
      Location:80224
      GREB1; Gene regulated by oestrogen in breast cancer

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

      Range
      29662950..29670876
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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