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SDC4 syndecan 4 [ Homo sapiens (human) ]

Gene ID: 6385, updated on 24-Nov-2020

Summary

Official Symbol
SDC4provided by HGNC
Official Full Name
syndecan 4provided by HGNC
Primary source
HGNC:HGNC:10661
See related
Ensembl:ENSG00000124145 MIM:600017
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

Genomic context

See SDC4 in Genome Data Viewer
Location:
20q13.12
Exon count:
5
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (45325288..45348424, complement)
105 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 recombination signal binding protein for immunoglobulin kappa J region like Neighboring gene tRNA-Val (anticodon CAC) 14-1 Neighboring gene SYS1-DBNDD2 readthrough (NMD candidate) Neighboring gene SYS1 golgi trafficking protein Neighboring gene TP53 target 5 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 10

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?

Phenotypes

Associated conditions

Description Tests
Genome-wide association analysis identifies three psoriasis susceptibility loci.
GeneReviews: Not available

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

Homology

Clone Names

  • MGC22217

Gene Ontology Provided by GOA

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

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
    P31431
    Related
    ENSP00000361818.3, ENST00000372733.3
    Conserved Domains (1) summary
    pfam01034
    Location:139196
    Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011528977.2XP_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
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