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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 Metabolism of fat-soluble vitamins and Adhesion. 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

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
GH20G045334 2 FANTOM5 Ensembl ENCODE dbSUPER 8.5 +6.3 6344 14.4 MLX ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC SSRP1 GLIS1 RCOR2 NCOA5 PCIF1 ZNF335 ZSWIM1 CD40 SPATA25 DBNDD2 SYS1-DBNDD2 SYS1 PIGT
GH20G045428 0.2 dbSUPER 12.1 -80.0 -80046 0.5 DBNDD2 TP53TG5 SDC4 SYS1-DBNDD2 SYS1 DNTTIP1 LOC105372631 GC20P045440
GH20G045353 1.4 Ensembl ENCODE dbSUPER 0.4 -6.5 -6525 2.0 FOXA2 KLF17 RAD21 GATA2 SCRT2 FOS ZNF654 CEBPB REST ZNF488 DBNDD2 TP53TG5 PIGT SYS1 MATN4 RBPJL SDC4
GH20G045357 1.3 ENCODE dbSUPER 0.4 -10.8 -10809 4.4 PKNOX1 FOXA2 ATF1 MLX ARID4B SIN3A DMAP1 FEZF1 YY1 GATA2 DBNDD2 TP53TG5 NCOA5 SYS1 PIGT SDC4
GH20G045361 0.7 ENCODE 0.4 -13.5 -13472 0.2 ELF3 SOX13 FOXA2 SAP130 ZNF644 RARA KAT2B HOMEZ MIXL1 THAP11 SYS1 SDC4
- 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 PKNOX1 ZFP64 ARID4B SIN3A ZNF2 YY1 FOS SP3 SP5 MXD4

Genomic Location for SDC4 Gene

Chromosome:
20
Start:
45,325,285 bp from pter
End:
45,348,424 bp from pter
Size:
23,140 bases
Orientation:
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:
    P31431-SDC4_HUMAN
    Recommended name:
    Syndecan-4
    Protein Accession:
    P31431
    Secondary Accessions:
    • O00773
    • Q16833
    • Q53FN9
    • Q6FGN3

    Protein attributes for SDC4 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

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 isoforms=239, Ser61, isoforms=263, Ser97, Thr101, and Ser126
  • Modification sites at PhosphoSitePlus

Other Protein References for SDC4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SDC4 (syndecan-4)

No data available for DME Specific Peptides for SDC4 Gene

Domains & Families for SDC4 Gene

Gene Families for SDC4 Gene

Suggested Antigen Peptide Sequences for SDC4 Gene

Graphical View of Domain Structure for InterPro Entry

P31431

UniProtKB/Swiss-Prot:

SDC4_HUMAN :
  • Belongs to the syndecan proteoglycan family.
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).

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

Clone Products

Flow Cytometry 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

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

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

Activates:
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
9050-30-0
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

Clone Products

Flow Cytometry Products

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP1:
SP2: -

Relevant External Links for SDC4 Gene

GeneLoc Exon Structure for
SDC4
ECgene alternative splicing isoforms for
SDC4

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:

SDC4

SOURCE GeneReport for Unigene cluster for SDC4 Gene:

Hs.632267

mRNA Expression by UniProt/SwissProt for SDC4 Gene:

P31431-SDC4_HUMAN
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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia SDC4 34 35
  • 98.65 (n)
dog
(Canis familiaris)
Mammalia SDC4 34 35
  • 85.52 (n)
cow
(Bos Taurus)
Mammalia SDC4 34 35
  • 84.52 (n)
mouse
(Mus musculus)
Mammalia Sdc4 34 16 35
  • 81.52 (n)
rat
(Rattus norvegicus)
Mammalia Sdc4 34
  • 81.22 (n)
oppossum
(Monodelphis domestica)
Mammalia SDC4 35
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDC4 35
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves SDC4 34 35
  • 63.26 (n)
lizard
(Anolis carolinensis)
Reptilia SDC4 35
  • 54 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii sdc4 34 35
  • 57.09 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8832 34
fruit fly
(Drosophila melanogaster)
Insecta Sdc 35
  • 12 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sdn-1 35
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 35
  • 25 (a)
OneToMany
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

ENSEMBL:
Gene Tree for SDC4 (if available)
TreeFam:
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.org 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
SDC4

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)
SDC4
Human Genome Epidemiology (HuGE) Navigator
SDC4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SDC4

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. … SzAcll M. (Wound Repair Regen 2008) 3 22 46 64
  2. Human ryudocan core protein: molecular cloning and characterization of the cDNA, and chromosomal localization of the gene. (PMID: 7916598) Kojima T. … Saito H. (Biochem. Biophys. Res. Commun. 1993) 2 3 4 64
  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. (J. Cell Biol. 1992) 2 3 4 64
  4. Syndecan-syntenin-ALIX regulates the biogenesis of exosomes. (PMID: 22660413) Baietti M.F. … David G. (Nat. Cell Biol. 2012) 3 4 64
  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. (J. Hum. Genet. 2010) 3 46 64

Products for SDC4 Gene

Sources for SDC4 Gene

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