Display Settings:

Format

Send to:

Choose Destination

SDC3 syndecan 3 [ Homo sapiens (human) ]

Gene ID: 9672, updated on 24-Aug-2015
Official Symbol
SDC3provided by HGNC
Official Full Name
syndecan 3provided by HGNC
Primary source
HGNC:HGNC:10660
See related
HPRD:01719; 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]
Orthologs
See SDC3 in Epigenomics, MapViewer
Location:
1p35.2
Exon count:
10
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 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 uncharacterized LOC102723832 Neighboring gene uncharacterized LOC400748 Neighboring gene small nucleolar RNA, C/D box 103A Neighboring gene pumilio RNA-binding family member 1 Neighboring gene small nucleolar RNA, C/D box 103B

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

  • A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystem (from REACTOME)
    A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystemThe biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence to the core protein. The ...
  • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
    Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
    Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystem (from REACTOME)
    Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystemChondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG). CS chains are unbranched polysaccharides of varying length containing two alternating monosaccharides: D-glucuronic acid (GlcA) and N-a...
  • Defective B3GAT3 causes JDSSDHD, organism-specific biosystem (from REACTOME)
    Defective B3GAT3 causes JDSSDHD, organism-specific biosystemGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferases1, 2 and 3 (B3GAT1-3) are involved in forming the linker tetrasaccharide present in heparan sulfate and chondroitin sulfate. Defects ...
  • Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystem (from REACTOME)
    Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystemEhlersDanlos syndrome (EDS) is a group of inherited connective tissue disorders, caused by a defect in the synthesis of collagen types I or III. Abnormal collagen renders connective tissues more elas...
  • Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystem (from REACTOME)
    Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Ex...
  • Defective EXT2 causes exostoses 2, organism-specific biosystem (from REACTOME)
    Defective EXT2 causes exostoses 2, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 ...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases associated with glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
    Diseases associated with glycosaminoglycan metabolism, organism-specific biosystemA number of genetic disorders are caused by mutations in the genes encoding glycosyltransferases and sulfotransferases, enzymes responsible for the synthesis of glycosaminoglycans (GAGs) as well as ...
  • Diseases of glycosylation, organism-specific biosystem (from REACTOME)
    Diseases of glycosylation, organism-specific biosystemDiseases of glycosylation, usually referred to as congenital disorders of glycosylation (CDG), are rare inherited disorders ascribing defects of nucleotide-sugar biosynthesis and transport, glycosylt...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
    Glycosaminoglycan metabolism, organism-specific biosystemGlycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)...
  • HS-GAG biosynthesis, organism-specific biosystem (from REACTOME)
    HS-GAG biosynthesis, organism-specific biosystemHeparan sulfate (HS) and heparin (sometimes collectively called HS-GAG) consist of the disaccharide unit GlcNAc-GlcA (N-acetylglucosamine-glucuronic acid) connected by a beta1,4 linkage. Heparin is e...
  • HS-GAG degradation, organism-specific biosystem (from REACTOME)
    HS-GAG degradation, organism-specific biosystemLysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of heparan sulfate/heparin. Complete d...
  • Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystem (from REACTOME)
    Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystemThe acronym HS-GAG is used to describe both heparin and heparan sulfate. HS-GAG is a member of the glycosaminoglycan family and consists of a variably sulfated repeating disaccharide unit, the most ...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of carbohydrates, organism-specific biosystem (from REACTOME)
    Metabolism of carbohydrates, organism-specific biosystemThese pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the b...
  • Non-integrin membrane-ECM interactions, organism-specific biosystem (from REACTOME)
    Non-integrin membrane-ECM interactions, organism-specific biosystemSeveral non-integrin membrane proteins interact with extracellular matrix proteins. Transmembrane proteoglycans may associate with integrins and growth factor receptors to influence their function, o...
  • Proteogylcan syndecan-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
    Proteogylcan syndecan-mediated signaling events, organism-specific biosystem
    Proteogylcan syndecan-mediated signaling events
  • Retinoid metabolism and transport, organism-specific biosystem (from REACTOME)
    Retinoid metabolism and transport, organism-specific biosystemVitamin A (all-trans-retinol) must be taken up, either as carotenes from plants, or as retinyl esters from animal food. The most prominent carotenes are alpha-carotene, lycopene, lutein, beta-cryptox...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Syndecan interactions, organism-specific biosystem (from REACTOME)
    Syndecan interactions, organism-specific biosystemSyndecans are type I transmembrane proteins, with an N-terminal ectodomain that contains several consensus sequences for glycosaminoglycan (GAG) attachment and a short C-terminal cytoplasmic domain. ...
  • Syndecan-3-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
    Syndecan-3-mediated signaling events, organism-specific biosystem
    Syndecan-3-mediated signaling events
  • Visual phototransduction, organism-specific biosystem (from REACTOME)
    Visual phototransduction, organism-specific biosystemVisual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are p...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
carbohydrate metabolic process TAS
Traceable Author Statement
more info
 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
chondroitin sulfate metabolic process TAS
Traceable Author Statement
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
glycosaminoglycan biosynthetic process TAS
Traceable Author Statement
more info
 
glycosaminoglycan catabolic process TAS
Traceable Author Statement
more info
 
glycosaminoglycan metabolic process TAS
Traceable Author Statement
more info
 
phototransduction, visible light TAS
Traceable Author Statement
more info
 
retinoid metabolic process TAS
Traceable Author Statement
more info
 
small molecule metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Golgi lumen TAS
Traceable Author Statement
more info
 
axon IEA
Inferred from Electronic Annotation
more info
 
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
plasma membrane TAS
Traceable Author Statement
more info
 
protein complex IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
syndecan-3
Names
N-syndecan
syndecan neural type
syndecan proteoglycan 3

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
    5001..44168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014654.3NP_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
    Conserved Domains (1) summary
    pfam01034
    Location:376440
    Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p2 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011542463.1XP_011540765.1  

    Conserved Domains (1) summary
    pfam01034
    Location:365429
    Syndecan; Syndecan domain
  2. XM_011542462.1XP_011540764.1  

    Conserved Domains (1) summary
    pfam01034
    Location:377441
    Syndecan; Syndecan domain
  3. XM_011542464.1XP_011540766.1  

    Conserved Domains (1) summary
    pfam01034
    Location:364428
    Syndecan; Syndecan domain
  4. XM_011542465.1XP_011540767.1  

    Conserved Domains (1) summary
    pfam01034
    Location:351415
    Syndecan; Syndecan domain
  5. XM_011542466.1XP_011540768.1  

    Conserved Domains (1) summary
    pfam01034
    Location:334398
    Syndecan; Syndecan domain

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 Alternate CHM1_1.1

    Range
    31458707..31467979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)