Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SDC3 Gene

Aliases for SDC3 Gene

  • Syndecan 3 2 3 5
  • Syndecan Proteoglycan 3 2 3
  • SYND3 3 4
  • Syndecan 3 (N-Syndecan) 2
  • Syndecan Neural Type 3
  • N-Syndecan 3
  • Syndecan-3 3
  • KIAA0468 4
  • SDCN 3

External Ids for SDC3 Gene

Previous GeneCards Identifiers for SDC3 Gene

  • GC01M031136
  • GC01M030326
  • GC01M030768
  • GC01M030844
  • GC01M031011
  • GC01M031342
  • GC01M029448

Summaries for SDC3 Gene

Entrez Gene Summary for SDC3 Gene

  • 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]

GeneCards Summary for SDC3 Gene

SDC3 (Syndecan 3) is a Protein Coding gene. Diseases associated with SDC3 include Body Mass Index Quantitative Trait Locus 11 and Charcot-Marie-Tooth Disease, Dominant Intermediate C. Among its related pathways are Development Slit-Robo signaling and Glycosaminoglycan metabolism. Gene Ontology (GO) annotations related to this gene include cytoskeletal protein binding. An important paralog of this gene is SDC1.

UniProtKB/Swiss-Prot for SDC3 Gene

  • Cell surface proteoglycan that may bear heparan sulfate (By similarity). May have 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.

Gene Wiki entry for SDC3 Gene

Additional gene information for SDC3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDC3 Gene

Genomics for SDC3 Gene

GeneHancer (GH) Regulatory Elements for SDC3 Gene

Promoters and enhancers for SDC3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I030908 Promoter/Enhancer 1.8 EPDnew Ensembl dbSUPER 550.8 +1.2 1234 1 HDAC1 MXI1 RB1 ZBTB40 E2F1 ZFHX2 GLIS2 MTA3 EGR1 POLR2A SDC3 LOC400748
GH01I030909 Enhancer 1.2 Ensembl ENCODE 550.8 -0.8 -776 3 HDGF ARNT SIN3A ZNF2 GLIS2 ZNF213 ARID2 ZNF143 ATF7 KLF13 SDC3 LOC400748 MATN1 MATN1-AS1 RN7SL371P
GH01I030823 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 28.2 +85.6 85558 2.3 HDGF FOXA2 PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A FEZF1 ZNF2 LINC01778 SNRNP40 SDC3 LOC400748 ENSG00000229447 COL16A1 MATN1 MATN1-AS1 ENSG00000235790 RN7SKP91
GH01I030797 Enhancer 1.1 Ensembl ENCODE dbSUPER 36.1 +111.3 111312 2.6 BCOR MEIS2 CTCF ATF1 NFATC3 JUN MZF1 ZMYM3 ZIC2 RAD21 SDC3 MATN1 LOC400748 MATN1-AS1 GC01P030805 LOC105378621
GH01I030815 Enhancer 0.9 Ensembl ENCODE 40.6 +92.7 92676 2.3 BCOR ZSCAN4 MAX SIN3A ZMYM3 BMI1 ZIC2 ZFHX2 CTBP1 POLR2A ENSG00000229607 SDC3 LOC400748 MATN1 MATN1-AS1 LINC01778
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SDC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SDC3 gene promoter:

Genomic Locations for SDC3 Gene

Genomic Locations for SDC3 Gene
chr1:30,869,466-30,909,735
(GRCh38/hg38)
Size:
40,270 bases
Orientation:
Minus strand
chr1:31,342,313-31,381,608
(GRCh37/hg19)

Genomic View for SDC3 Gene

Genes around SDC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDC3 Gene

Proteins for SDC3 Gene

  • Protein details for SDC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75056-SDC3_HUMAN
    Recommended name:
    Syndecan-3
    Protein Accession:
    O75056
    Secondary Accessions:
    • Q5T1Z6
    • Q5T1Z7
    • Q96CT3
    • Q96PR8

    Protein attributes for SDC3 Gene

    Size:
    442 amino acids
    Molecular mass:
    45497 Da
    Quaternary structure:
    • Interacts with TIAM1.
    SequenceCaution:
    • Sequence=BAA32313.2; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

neXtProt entry for SDC3 Gene

Post-translational modifications for SDC3 Gene

  • O-glycosylated within the Thr/Ser-rich region which could interact with lectin domains on other molecules.
  • Glycosylation at posLast=8080, isoforms=82, posLast=8484, posLast=9191, posLast=253253, isoforms=265, posLast=314314, isoforms=344, and posLast=367367
  • Modification sites at PhosphoSitePlus

Other Protein References for SDC3 Gene

No data available for DME Specific Peptides for SDC3 Gene

Domains & Families for SDC3 Gene

Gene Families for SDC3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for SDC3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O75056

UniProtKB/Swiss-Prot:

SDC3_HUMAN :
  • Belongs to the syndecan proteoglycan family.
Family:
  • Belongs to the syndecan proteoglycan family.
genes like me logo Genes that share domains with SDC3: view

Function for SDC3 Gene

Molecular function for SDC3 Gene

UniProtKB/Swiss-Prot Function:
Cell surface proteoglycan that may bear heparan sulfate (By similarity). May have 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.

Phenotypes From GWAS Catalog for SDC3 Gene

Gene Ontology (GO) - Molecular Function for SDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18093920
GO:0042802 identical protein binding IPI 18093920
genes like me logo Genes that share ontologies with SDC3: view
genes like me logo Genes that share phenotypes with SDC3: view

Animal Models for SDC3 Gene

MGI Knock Outs for SDC3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SDC3 Gene

Localization for SDC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDC3 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SDC3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
lysosome 5
golgi apparatus 4
mitochondrion 2
nucleus 2
cytoskeleton 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005796 Golgi lumen TAS --
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IBA --
GO:0016020 membrane ISS --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SDC3: view

Pathways & Interactions for SDC3 Gene

genes like me logo Genes that share pathways with SDC3: view

Gene Ontology (GO) - Biological Process for SDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
GO:0016477 cell migration IBA --
GO:0030203 glycosaminoglycan metabolic process TAS --
genes like me logo Genes that share ontologies with SDC3: view

No data available for SIGNOR curated interactions for SDC3 Gene

Drugs & Compounds for SDC3 Gene

No Compound Related Data Available

Transcripts for SDC3 Gene

Unigene Clusters for SDC3 Gene

Syndecan 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SDC3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9a · 9b · 9c
SP1: - - - - -
SP2: - - -
SP3:
SP4: -
SP5: -
SP6:

Relevant External Links for SDC3 Gene

GeneLoc Exon Structure for
SDC3
ECgene alternative splicing isoforms for
SDC3

Expression for SDC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SDC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SDC3 Gene

This gene is overexpressed in Adrenal (29.9), Fetal Brain (11.1), Prostate (8.4), Colon (7.1), and Urinary Bladder (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SDC3 Gene



NURSA nuclear receptor signaling pathways regulating expression of SDC3 Gene:

SDC3

SOURCE GeneReport for Unigene cluster for SDC3 Gene:

Hs.158287

mRNA Expression by UniProt/SwissProt for SDC3 Gene:

O75056-SDC3_HUMAN
Tissue specificity: Expressed in the nervous system, the adrenal gland, and the spleen.

Evidence on tissue expression from TISSUES for SDC3 Gene

  • Nervous system(4.9)
  • Muscle(4.4)
  • Skin(3.2)
  • Eye(2.4)
genes like me logo Genes that share expression patterns with SDC3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SDC3 Gene

Orthologs for SDC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SDC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SDC3 33 34
  • 99.33 (n)
cow
(Bos Taurus)
Mammalia SDC3 33 34
  • 90.8 (n)
dog
(Canis familiaris)
Mammalia SDC3 33 34
  • 88.19 (n)
rat
(Rattus norvegicus)
Mammalia Sdc3 33
  • 84.01 (n)
mouse
(Mus musculus)
Mammalia Sdc3 33 16 34
  • 83.33 (n)
oppossum
(Monodelphis domestica)
Mammalia SDC3 34
  • 64 (a)
OneToOne
chicken
(Gallus gallus)
Aves SDC3 33 34
  • 65.43 (n)
lizard
(Anolis carolinensis)
Reptilia SDC3 34
  • 50 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sdc3 33
  • 53.51 (n)
African clawed frog
(Xenopus laevis)
Amphibia sdc3-A 33
zebrafish
(Danio rerio)
Actinopterygii sdc3 34
  • 36 (a)
OneToOne
Dr.28157 33
fruit fly
(Drosophila melanogaster)
Insecta Sdc 34
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sdn-1 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 34
  • 32 (a)
OneToMany
Species where no ortholog for SDC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SDC3 Gene

ENSEMBL:
Gene Tree for SDC3 (if available)
TreeFam:
Gene Tree for SDC3 (if available)

Paralogs for SDC3 Gene

Paralogs for SDC3 Gene

(1) SIMAP similar genes for SDC3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SDC3: view

Variants for SDC3 Gene

Sequence variations from dbSNP and Humsavar for SDC3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs2282440 association, Obesity, association with 30,874,473(-) G/A coding_sequence_variant, missense_variant
rs2491132 association, Obesity, association with 30,876,800(-) C/A/G/T coding_sequence_variant, missense_variant
rs1000100437 -- 30,880,579(-) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000194733 -- 30,905,288(-) T/A/G genic_upstream_transcript_variant, intron_variant
rs1000259642 -- 30,899,607(-) T/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SDC3 Gene

Variant ID Type Subtype PubMed ID
dgv27e212 CNV loss 25503493
esv2244846 CNV deletion 18987734
esv2746253 CNV deletion 23290073
esv2746264 CNV deletion 23290073
esv2746275 CNV deletion 23290073
esv3386830 CNV insertion 20981092
nsv1130952 CNV deletion 24896259
nsv1133833 CNV deletion 24896259
nsv160199 CNV deletion 16902084
nsv160596 CNV deletion 16902084
nsv461006 CNV loss 19166990
nsv470707 CNV gain 18288195
nsv519204 CNV gain 19592680
nsv545948 CNV loss 21841781
nsv545949 CNV loss 21841781
nsv950377 CNV deletion 24416366

Variation tolerance for SDC3 Gene

Residual Variation Intolerance Score: 82% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.65; 94.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SDC3 Gene

Human Gene Mutation Database (HGMD)
SDC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDC3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDC3 Gene

Disorders for SDC3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SDC3 Gene - From: HGMD, OMIM, GTR, and DISEASES

Disorder Aliases PubMed IDs
body mass index quantitative trait locus 11
  • bmiq11
charcot-marie-tooth disease, dominant intermediate c
  • cmtdic
enamel caries
  • dental caries limited to enamel
- elite association - COSMIC cancer census association via MalaCards
Search SDC3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SDC3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SDC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SDC3 Gene

Publications for SDC3 Gene

  1. Role of syndecan-3 polymorphisms in obesity and female hyperandrogenism. (PMID: 19820907) Schüring AN … Götte M (Journal of molecular medicine (Berlin, Germany) 2009) 3 22 44 58
  2. Cloning and characterization of human syndecan-3. (PMID: 11527150) Berndt C … Reina M (Journal of cellular biochemistry 2001) 2 3 4 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. Positive association of obesity with single nucleotide polymorphisms of syndecan 3 in the Korean population. (PMID: 17018662) Ha E … Kim JW (The Journal of clinical endocrinology and metabolism 2006) 3 44 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for SDC3 Gene

Sources for SDC3 Gene

Content
Loading form....