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SDC3 syndecan 3 [ Homo sapiens (human) ]

Gene ID: 9672, updated on 2-Nov-2024

Summary

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Official Symbol
SDC3provided by HGNC
Official Full Name
syndecan 3provided by HGNC
Primary source
HGNC:HGNC:10660
See related
Ensembl:ENSG00000162512 MIM:186357; AllianceGenome:HGNC:10660
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
mouse all
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Genomic context

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See SDC3 in Genome Data Viewer
Location:
1p35.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (30869466..30909735, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (30721742..30761962, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31342313..31381605, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31317155-31317674 Neighboring gene Sharpr-MPRA regulatory region 1191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31320286-31321089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31322620-31323120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31323121-31323621 Neighboring gene Sharpr-MPRA regulatory region 1173 Neighboring gene RN7SK pseudogene 91 Neighboring gene uncharacterized LOC400748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31343383-31344254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31358623-31359123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31363707-31364422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31368603-31369362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:31392155-31393153 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A genome-wide association study identifies a novel association between SDC3 and apparent treatment-resistant hypertension.
    Title: A genome-wide association study identifies a novel association between SDC3 and apparent treatment-resistant hypertension.
  2. The Cell Surface Heparan Sulfate Proteoglycan Syndecan-3 Promotes Ovarian Cancer Pathogenesis.
    Title: The Cell Surface Heparan Sulfate Proteoglycan Syndecan-3 Promotes Ovarian Cancer Pathogenesis.
  3. Syndecan Family Gene and Protein Expression and Their Prognostic Values for Prostate Cancer.
    Title: Syndecan Family Gene and Protein Expression and Their Prognostic Values for Prostate Cancer.
  4. LncRNA TRPM2-AS promotes ovarian cancer progression and cisplatin resistance by sponging miR-138-5p to release SDC3 mRNA.
    Title: LncRNA TRPM2-AS promotes ovarian cancer progression and cisplatin resistance by sponging miR-138-5p to release SDC3 mRNA.
  5. The Interplay of Apoes with Syndecans in Influencing Key Cellular Events of Amyloid Pathology.
    Title: The Interplay of Apoes with Syndecans in Influencing Key Cellular Events of Amyloid Pathology.
  6. Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment.
    Title: Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment.
  7. Contribution of syndecans to cellular uptake and fibrillation of alpha-synuclein and tau.
    Title: Contribution of syndecans to cellular uptake and fibrillation of α-synuclein and tau.
  8. Data show that soluble syndecan-3 occurred naturally in the sera of patients with rheumatoid arthritis.
    Title: Soluble syndecan-3 binds chemokines, reduces leukocyte migration in vitro and ameliorates disease severity in models of rheumatoid arthritis.
  9. High PTN and N-syndecan expression was closely associated with metastasis and poor prognosis, suggesting that they may promote tumor progression and perineural invasion in the orthotopic mouse model of pancreatic cancer.
    Title: Pleiotrophin and N-syndecan promote perineural invasion and tumor progression in an orthotopic mouse model of pancreatic cancer.
  10. Syndecan-3 and TFPI colocalize on the surface of endothelial-, smooth muscle-, and cancer cells
    Title: Syndecan-3 and TFPI colocalize on the surface of endothelial-, smooth muscle-, and cancer cells.
Submit: New GeneRIF Correction See all GeneRIFs (27)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Inherited obesity
MedGen: C4054476 OMIM: 601665 GeneReviews: Not available
Compare labs

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
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 collagen-containing extracellular matrix HDA PubMed 
located_in lysosomal lumen TAS
Traceable Author Statement
more info
  
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in microspike ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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

NCBI Reference Sequences (RefSeq)

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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_014654.4 → NP_055469.3  syndecan-3

    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, Q5T1Z6, Q5T1Z7, Q96CT3, Q96PR8
    UniProtKB/TrEMBL
    A0A0S2Z540, A0A9K3Y886, F8W8E9
    Related
    ENSP00000344468.6, ENST00000339394.7
    Conserved Domains (1) summary
    pfam01034
    Location:399 → 440
    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_000001.11 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B4DIN4
    Conserved Domains (1) summary
    pfam01034
    Location:388 → 429
    Syndecan; Syndecan domain

  2. XM_011542464.3 → XP_011540766.1  syndecan-3 isoform X2

    UniProtKB/TrEMBL
    B4DIN4
    Conserved Domains (1) summary
    pfam01034
    Location:387 → 428
    Syndecan; Syndecan domain

  3. XM_011542466.2 → XP_011540768.1  syndecan-3 isoform X3

    UniProtKB/TrEMBL
    B4DIN4
    Conserved Domains (1) summary
    pfam01034
    Location:357 → 398
    Syndecan; Syndecan domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    30721742..30761962 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339740.1 → XP_054195715.1  syndecan-3 isoform X1

  2. XM_054339741.1 → XP_054195716.1  syndecan-3 isoform X2

  3. XM_054339742.1 → XP_054195717.1  syndecan-3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75056.2 GenPept UniProtKB/Swiss-Prot:O75056

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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