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    SDC4 syndecan 4 [ Homo sapiens (human) ]

    Gene ID: 6385, updated on 28-Oct-2024

    Summary

    Official Symbol
    SDC4provided by HGNC
    Official Full Name
    syndecan 4provided by HGNC
    Primary source
    HGNC:HGNC:10661
    See related
    Ensembl:ENSG00000124145 MIM:600017; AllianceGenome:HGNC:10661
    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
    SYND4
    Summary
    The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan that functions as a receptor in intracellular signaling. The encoded protein is found as a homodimer and is a member of the syndecan proteoglycan family. This gene is found on chromosome 20, while a pseudogene has been found on chromosome 22. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in liver (RPKM 189.5), lung (RPKM 100.6) and 23 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SDC4 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45325288..45348424, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47061165..47084301, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (43953928..43977064, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene matrilin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12956 Neighboring gene recombination signal binding protein for immunoglobulin kappa J region like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17946 Neighboring gene tRNA-Val (anticodon CAC) 14-1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43971073-43971967 Neighboring gene uncharacterized LOC124904914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17947 Neighboring gene SYS1-DBNDD2 readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17950 Neighboring gene SYS1 golgi trafficking protein Neighboring gene TP53 target 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies three psoriasis susceptibility loci.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env The V3 region (amino acids 298-329) of HIV-1 gp120 contains the syndecan-binding site for HIV-1 via 6-O sulfated motifs; a single conserved arginine (Arg-298) in the V3 region of gp120 governs HIV-1 binding to syndecans PubMed
    Nef nef HIV-1 Nef enhances the expression of syndecan 4 in human podocyte PubMed
    Tat tat Binding of HIV-1 Tat to heparan sulfate proteoglycans is competed out by the heparin-binding factor bFGF PubMed
    tat Cell membrane heparin sulfate proteoglycans bind to the basic region of HIV-1 Tat (amino acids 49-57) and act as receptors for extracellular Tat uptake, an effect that may contribute to the angiogenic properties of Tat in promoting Kaposi's sarcoma PubMed
    matrix gag HIV-1 matrix protein co-localizes with syndecan-2, syndecan-4, and CD44v3 on activated CD4+ T cells to modulate TNF-alpha and IL2 production 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

    Clone Names

    • MGC22217

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables fibronectin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase C binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables thrombospondin receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in inner ear receptor cell stereocilium organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neural tube closure IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of extracellular exosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of focal adhesion assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of stress fiber assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of fibroblast migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ureteric bud development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in wound healing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in costamere IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in focal adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    syndecan-4
    Names
    amphiglycan
    ryudocan amphiglycan
    ryudocan core protein
    syndecan 4 (amphiglycan, ryudocan)
    syndecan proteoglycan 4

    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_002999.4NP_002990.2  syndecan-4 precursor

      See identical proteins and their annotated locations for NP_002990.2

      Status: REVIEWED

      Source sequence(s)
      AL021578, D13292
      Consensus CDS
      CCDS13350.1
      UniProtKB/Swiss-Prot
      O00773, P31431, Q16833, Q53FN9, Q6FGN3
      Related
      ENSP00000361818.3, ENST00000372733.3
      Conserved Domains (1) summary
      pfam01034
      Location:139196
      Syndecan; Syndecan domain

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      45325288..45348424 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528977.3XP_011527279.1  syndecan-4 isoform X1

      See identical proteins and their annotated locations for XP_011527279.1

      UniProtKB/TrEMBL
      B4E1S6
      Conserved Domains (1) summary
      pfam01034
      Location:67124
      Syndecan; Syndecan domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      47061165..47084301 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323804.1XP_054179779.1  syndecan-4 isoform X1

      UniProtKB/TrEMBL
      B4E1S6