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Aliases for SDC4 Gene

Aliases for SDC4 Gene

  • Syndecan 4 2 3 5
  • Syndecan 4 (Amphiglycan, Ryudocan) 2 3
  • Syndecan Proteoglycan 4 2 3
  • Ryudocan Core Protein 3 4
  • Amphiglycan 3 4
  • SYND4 3 4
  • Ryudocan Amphiglycan 3
  • Syndecan-4 3

External Ids for SDC4 Gene

Previous GeneCards Identifiers for SDC4 Gene

  • GC20M043682
  • GC20M044592
  • GC20M044639
  • GC20M043387
  • GC20M043953
  • GC20M040695

Summaries for SDC4 Gene

Entrez Gene Summary for SDC4 Gene

  • 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]

GeneCards Summary for SDC4 Gene

SDC4 (Syndecan 4) is a Protein Coding gene. Among its related pathways are Cell surface interactions at the vascular wall and Glycosaminoglycan metabolism. GO annotations related to this gene include cytoskeletal protein binding and fibronectin binding. An important paralog of this gene is SDC2.

UniProtKB/Swiss-Prot for SDC4 Gene

  • Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).

Gene Wiki entry for SDC4 Gene

Additional gene information for SDC4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDC4 Gene

Genomics for SDC4 Gene

Regulatory Elements for SDC4 Gene

Enhancers for SDC4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20H045334 2 FANTOM5 Ensembl ENCODE dbSUPER 8.5 +6.3 6344 14.4 MLX ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC ZC3H11A SSRP1 GLIS1 NCOA5 PCIF1 ZNF335 ZSWIM1 SPATA25 SNX21 CD40 ENSG00000233352 LOC105372630 RPL5P2
GH20H044397 1.6 Ensembl ENCODE dbSUPER 9.8 +939.2 939170 22.8 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B YBX1 DMAP1 YY1 SRSF6 FITM2 LINC01620 LINC01430 SDC4 HNF4A OSER1-AS1 MIR3646
GH20H044702 1.3 Ensembl ENCODE dbSUPER 9.9 +643.6 643610 4.8 PKNOX1 YBX1 RARA ZNF366 FOS RUNX3 ZBTB11 USF2 ELF1 NR2F2 KCNK15-AS1 KCNK15 SDC4 LINC01260 HSPD1P21 WISP2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SDC4 on UCSC Golden Path with GeneCards custom track

Promoters for SDC4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000137659 624 2001 ZFP64 ARID4B SIN3A ZNF2 YY1 GLIS2 FOS SP3 SP5 MXD4

Genomic Locations for SDC4 Gene

Genomic Locations for SDC4 Gene
23,140 bases
Minus strand

Genomic View for SDC4 Gene

Genes around SDC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDC4 Gene

Proteins for SDC4 Gene

  • Protein details for SDC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • O00773
    • Q16833
    • Q53FN9
    • Q6FGN3

    Protein attributes for SDC4 Gene

    198 amino acids
    Molecular mass:
    21642 Da
    Quaternary structure:
    • Homodimer. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its cytoplasmic domain) with NUDT16L1 (By similarity). Interacts with CDCP1 and SDCBP.

    Three dimensional structures from OCA and Proteopedia for SDC4 Gene

    Alternative splice isoforms for SDC4 Gene


neXtProt entry for SDC4 Gene

Post-translational modifications for SDC4 Gene

  • Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3.
  • Glycosylation at Ser39, Ser61, Ser63, isoforms=297, isoforms=2101, and isoforms=2126
  • Modification sites at PhosphoSitePlus

Other Protein References for SDC4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Protein Products

No data available for DME Specific Peptides for SDC4 Gene

Domains & Families for SDC4 Gene

Gene Families for SDC4 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted membrane proteins
  • Transporters

Suggested Antigen Peptide Sequences for SDC4 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the syndecan proteoglycan family.
  • Belongs to the syndecan proteoglycan family.
genes like me logo Genes that share domains with SDC4: view

Function for SDC4 Gene

Molecular function for SDC4 Gene

GENATLAS Biochemistry:
syndecan 4,heparan sulfate proteoglycan 3 (22kDa),endothelial cell surface associated,cooperating with integrins in a Rho dependent manner in the assembly of focal adhesion and actin stress fibers
UniProtKB/Swiss-Prot Function:
Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).

Phenotypes From GWAS Catalog for SDC4 Gene

Gene Ontology (GO) - Molecular Function for SDC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001968 fibronectin binding IEA --
GO:0005080 protein kinase C binding IEA --
GO:0005515 protein binding IPI 12571249
GO:0070053 thrombospondin receptor activity IMP 17879962
genes like me logo Genes that share ontologies with SDC4: view
genes like me logo Genes that share phenotypes with SDC4: view

Animal Models for SDC4 Gene

MGI Knock Outs for SDC4:

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SDC4 Gene

Localization for SDC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDC4 Gene

Isoform 1: Membrane; Single-pass type I membrane protein. Secreted. Note=Shedding of the ectodomain produces a soluble form. {ECO:0000269 PubMed:9169435}.
Isoform 2: Secreted.

Subcellular locations from

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 SDC4 gene
Compartment Confidence
plasma membrane 5
extracellular 5
golgi apparatus 5
lysosome 4
cytoskeleton 2
endoplasmic reticulum 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005796 Golgi lumen TAS --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane NAS 1500433
GO:0005925 focal adhesion IEA --
genes like me logo Genes that share ontologies with SDC4: view

Pathways & Interactions for SDC4 Gene

genes like me logo Genes that share pathways with SDC4: view

SIGNOR curated interactions for SDC4 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SDC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0001657 ureteric bud development IEA --
GO:0001843 neural tube closure IEA --
GO:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
genes like me logo Genes that share ontologies with SDC4: view

Drugs & Compounds for SDC4 Gene

(1) Additional Compounds for SDC4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
heparan sulfate
  • alpha-Idosane
  • Heparan N-sulfate
  • Heparan N-sulphate
  • Heparan sulfate
  • Heparan sulphate
genes like me logo Genes that share compounds with SDC4: view

Transcripts for SDC4 Gene

mRNA/cDNA for SDC4 Gene

(2) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(300) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SDC4 Gene

Syndecan 4:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SDC4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP2: -

Relevant External Links for SDC4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SDC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SDC4 Gene

mRNA differential expression in normal tissues according to GTEx for SDC4 Gene

This gene is overexpressed in Liver (x4.2).

Protein differential expression in normal tissues from HIPED for SDC4 Gene

This gene is overexpressed in Nasal epithelium (38.1) and Amniocyte (9.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SDC4 Gene

NURSA nuclear receptor signaling pathways regulating expression of SDC4 Gene:


SOURCE GeneReport for Unigene cluster for SDC4 Gene:


mRNA Expression by UniProt/SwissProt for SDC4 Gene:

Tissue specificity: Expressed in epithelial and fibroblastic cells.

Evidence on tissue expression from TISSUES for SDC4 Gene

  • Lung(4.6)
  • Nervous system(4.6)
  • Liver(4.5)
  • Stomach(4.4)
  • Heart(2.9)
  • Kidney(2.8)
  • Muscle(2.8)
  • Skin(2.5)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with SDC4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SDC4 Gene

Orthologs for SDC4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SDC4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SDC4 33 34
  • 98.65 (n)
(Canis familiaris)
Mammalia SDC4 33 34
  • 85.52 (n)
(Bos Taurus)
Mammalia SDC4 33 34
  • 84.52 (n)
(Mus musculus)
Mammalia Sdc4 33 16 34
  • 81.52 (n)
(Rattus norvegicus)
Mammalia Sdc4 33
  • 81.22 (n)
(Monodelphis domestica)
Mammalia SDC4 34
  • 66 (a)
(Ornithorhynchus anatinus)
Mammalia SDC4 34
  • 56 (a)
(Gallus gallus)
Aves SDC4 33 34
  • 63.26 (n)
(Anolis carolinensis)
Reptilia SDC4 34
  • 54 (a)
(Danio rerio)
Actinopterygii sdc4 33 34
  • 57.09 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8832 33
fruit fly
(Drosophila melanogaster)
Insecta Sdc 34
  • 12 (a)
(Caenorhabditis elegans)
Secernentea sdn-1 34
  • 18 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 34
  • 25 (a)
Species where no ortholog for SDC4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SDC4 Gene

Gene Tree for SDC4 (if available)
Gene Tree for SDC4 (if available)

Paralogs for SDC4 Gene

Paralogs for SDC4 Gene

(7) SIMAP similar genes for SDC4 Gene using alignment to 2 proteins: Pseudogenes for SDC4 Gene

genes like me logo Genes that share paralogs with SDC4: view

Variants for SDC4 Gene

Sequence variations from dbSNP and Humsavar for SDC4 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1000247104 -- 45,330,063(+) ATGCC(A/T)AACTT intron-variant
rs1000429595 -- 45,346,310(+) CAGGA(C/G)GTCTG intron-variant
rs1000532198 -- 45,328,181(+) AAGTG(C/T)ACACA intron-variant
rs1000799643 -- 45,347,521(+) GCCTT(C/T)TCTCC intron-variant
rs1000856150 -- 45,340,780(+) AGAGG(A/G)GATGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SDC4 Gene

Variant ID Type Subtype PubMed ID
nsv1056102 CNV loss 25217958

Variation tolerance for SDC4 Gene

Residual Variation Intolerance Score: 43.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.24; 88.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SDC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDC4 Gene

Disorders for SDC4 Gene

Relevant External Links for SDC4

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SDC4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SDC4 Gene

Publications for SDC4 Gene

  1. The altered expression of syndecan 4 in the uninvolved skin of venous leg ulcer patients may predispose to venous leg ulcer. (PMID: 18638267) Nagy N … Széll M (Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society 2008) 3 22 45 60
  2. Human ryudocan core protein: molecular cloning and characterization of the cDNA, and chromosomal localization of the gene. (PMID: 7916598) Kojima T … Saito H (Biochemical and biophysical research communications 1993) 2 3 4 60
  3. Molecular cloning of amphiglycan, a novel integral membrane heparan sulfate proteoglycan expressed by epithelial and fibroblastic cells. (PMID: 1500433) David G … van den Berghe H (The Journal of cell biology 1992) 2 3 4 60
  4. Syndecan-syntenin-ALIX regulates the biogenesis of exosomes. (PMID: 22660413) Baietti MF … David G (Nature cell biology 2012) 3 4 60
  5. Common polymorphisms in ITGA2, PON1 and THBS2 are associated with coronary atherosclerosis in a candidate gene association study of the Chinese Han population. (PMID: 20485444) Wang Y … Huang W (Journal of human genetics 2010) 3 45 60

Products for SDC4 Gene

Sources for SDC4 Gene

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