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    SPN sialophorin [ Homo sapiens (human) ]

    Gene ID: 6693, updated on 22-Sep-2022

    Summary

    Official Symbol
    SPNprovided by HGNC
    Official Full Name
    sialophorinprovided by HGNC
    Primary source
    HGNC:HGNC:11249
    See related
    Ensembl:ENSG00000197471 MIM:182160; AllianceGenome:HGNC:11249
    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; LEU-22
    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
    NEW
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    Genomic context

    See SPN in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29662963..29670876)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29945006..29952917)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29674284..29682197)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene carbonic anhydrase 5A pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 12377 Neighboring gene quinolinate phosphoribosyltransferase Neighboring gene Sharpr-MPRA regulatory region 8247 Neighboring gene CRISPRi-validated cis-regulatory element chr16.2261

    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

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

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

    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_001030288.4NP_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
      A8K9B1, P16150
      UniProtKB/TrEMBL
      A0A024R629
      Related
      ENSP00000378787.2, ENST00000395389.2
      Conserved Domains (1) summary
      pfam15782
      Location:80224
      GREB1; Gene regulated by oestrogen in breast cancer
    2. NM_003123.6NP_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
      Consensus CDS
      CCDS10650.1
      UniProtKB/Swiss-Prot
      A8K9B1, P16150
      UniProtKB/TrEMBL
      A0A024R629
      Related
      ENSP00000498852.1, ENST00000652691.1
      Conserved Domains (1) summary
      pfam15782
      Location:80224
      GREB1; Gene regulated by oestrogen in breast cancer

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      29662963..29670876
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      29945006..29952917
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)