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SPN sialophorin [ Homo sapiens (human) ]

Gene ID: 6693, updated on 27-Nov-2024

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
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Genomic context

See SPN in Genome Data Viewer
Location:
16p11.2
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29662963..29670876)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29945006..29952917)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29674284..29682197)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene SMG1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7327 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7328 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29625406-29626091 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29626092-29626776 Neighboring gene solute carrier family 7 member 5 pseudogene 1 Neighboring gene carbonic anhydrase 5A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10660 Neighboring gene Sharpr-MPRA regulatory region 12377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7330 Neighboring gene Sharpr-MPRA regulatory region 12104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29688005-29688506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29688507-29689006 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29690545-29691046 Neighboring gene Sharpr-MPRA regulatory region 8247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29706317-29706848 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:29710774-29710948 Neighboring gene quinolinate phosphoribosyltransferase Neighboring gene CRISPRi-validated cis-regulatory element chr16.2261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7331 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29720469-29721050 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29721051-29721632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29723379-29723960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29731775-29732277 Neighboring gene RN7SK pseudogene 127

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

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
 
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 cell costimulation IEA
Inferred from Electronic Annotation
more info
 
involved_in T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in T-helper 1 cell lineage commitment IDA
Inferred from Direct Assay
more info
PubMed 
involved_in apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in cell surface receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
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 negative regulation of type IV hypersensitivity IEA
Inferred from Electronic Annotation
more info
 
involved_in negative thymic T cell selection IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of T cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of T cell proliferation IEA
Inferred from Electronic Annotation
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 defense response to virus IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of immune response IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in response to protozoan IEA
Inferred from Electronic Annotation
more info
 
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 basement membrane 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
 
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
    C9JUK7
    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
    C9JUK7
    Related
    ENSP00000498852.1, ENST00000652691.1
    Conserved Domains (1) summary
    pfam15782
    Location:80224
    GREB1; Gene regulated by oestrogen in breast cancer

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_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)