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SDC3 syndecan 3 [ Homo sapiens (human) ]

Gene ID: 9672, updated on 1-Jun-2020

Summary

Official Symbol
SDC3provided by HGNC
Official Full Name
syndecan 3provided by HGNC
Primary source
HGNC:HGNC:10660
See related
Ensembl:ENSG00000162512 MIM:186357
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
SDCN; SYND3
Summary
The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]
Expression
Broad expression in brain (RPKM 64.6), spleen (RPKM 56.5) and 21 other tissues See more
Orthologs

Genomic context

See SDC3 in Genome Data Viewer
Location:
1p35.2
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (30869466..30909735, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31342313..31381480, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 91 Neighboring gene uncharacterized LOC400748 Neighboring gene RNA, 7SL, cytoplasmic 371, pseudogene Neighboring gene small nucleolar RNA, C/D box 103A Neighboring gene pumilio RNA binding family member 1

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

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
Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of syndecan 3 (SDC3) in peptide-treated PBMCs PubMed
Nef nef HIV-1 Nef inhibits the expression of syndecan 3 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

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
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
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
 
leukocyte migration TAS
Traceable Author Statement
more info
 
retinoid metabolic process TAS
Traceable Author Statement
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 
collagen-containing extracellular matrix HDA PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
lysosomal lumen TAS
Traceable Author Statement
more info
 
membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
microspike ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
syndecan-3
Names
N-syndecan
syndecan neural type
syndecan proteoglycan 3

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.

Genomic

  1. NG_013371.1 RefSeqGene

    Range
    4876..44168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014654.4NP_055469.3  syndecan-3 precursor

    See identical proteins and their annotated locations for NP_055469.3

    Status: REVIEWED

    Source sequence(s)
    AF248634, AL445235, BQ887307
    Consensus CDS
    CCDS30661.1
    UniProtKB/Swiss-Prot
    O75056
    Related
    ENSP00000344468.6, ENST00000339394.7
    Conserved Domains (1) summary
    pfam01034
    Location:399440
    Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    30869466..30909735 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542463.1XP_011540765.1  syndecan-3 isoform X1

    Conserved Domains (1) summary
    pfam01034
    Location:388429
    Syndecan; Syndecan domain
  2. XM_011542464.2XP_011540766.1  syndecan-3 isoform X2

    Conserved Domains (1) summary
    pfam01034
    Location:387428
    Syndecan; Syndecan domain
  3. XM_011542466.1XP_011540768.1  syndecan-3 isoform X3

    Conserved Domains (1) summary
    pfam01034
    Location:357398
    Syndecan; Syndecan domain
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