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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

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 adhesion molecules (CAMs) and ECM-receptor interaction. GO annotations related to this gene include cytoskeletal protein binding and fibronectin binding. An important paralog of this gene is SDC1.

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 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around SDC4 on UCSC Golden Path with GeneCards custom track

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

Proteomics data for SDC4 Gene at MOPED

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 Ser 39, Ser 61, Ser 63, Ser 97, Thr 101, and Ser 126
  • 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

Protein Domains 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).
genes like me logo Genes that share phenotypes with SDC4: view

Animal Models for SDC4 Gene

MGI Knock Outs for SDC4:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for SDC4 Gene COMPARTMENTS Subcellular localization image for SDC4 gene
Compartment Confidence
extracellular 5
golgi apparatus 5
plasma membrane 5
lysosome 4
vacuole 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:0005886 plasma membrane TAS --
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:0005975 carbohydrate metabolic process TAS --
GO:0007603 phototransduction, visible light TAS --
GO:0010762 regulation of fibroblast migration IEA --
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:

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 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, MOPED, and MaxQB for SDC4 Gene



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.
genes like me logo Genes that share expression patterns with SDC4: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners 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
cow
(Bos Taurus)
Mammalia SDC4 35
  • 84.52 (n)
  • 85.71 (a)
SDC4 36
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SDC4 35
  • 85.52 (n)
  • 84.85 (a)
SDC4 36
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sdc4 35
  • 81.52 (n)
  • 82.38 (a)
Sdc4 16
Sdc4 36
  • 79 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SDC4 35
  • 98.65 (n)
  • 97.98 (a)
SDC4 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sdc4 35
  • 81.22 (n)
  • 80.71 (a)
oppossum
(Monodelphis domestica)
Mammalia SDC4 36
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDC4 36
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves SDC4 35
  • 63.26 (n)
  • 60.22 (a)
SDC4 36
  • 52 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SDC4 36
  • 54 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii sdc4 35
  • 57.09 (n)
  • 48.5 (a)
sdc4 36
  • 38 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8832 35
fruit fly
(Drosophila melanogaster)
Insecta Sdc 36
  • 12 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sdn-1 36
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 36
  • 25 (a)
OneToMany
Species with no ortholog for SDC4:
  • 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
VAR_021851 -
rs3529 -- 45,345,218(+) CCCTC(A/G)GTGTG intron-variant
rs4599 -- 45,325,767(-) ACTGT(A/G)TGTAG utr-variant-3-prime
rs7138 -- 45,325,418(-) GGGTC(C/G)TCTTC utr-variant-3-prime
rs8060 -- 45,325,763(-) TATGT(A/G/T)GTTCA utr-variant-3-prime

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

HapMap Linkage Disequilibrium report
SDC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) 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. 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 67
  2. 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 23
  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. Reversible oxidation of phosphatase and tensin homolog (PTEN) alters its interactions with signaling and regulatory proteins. (PMID: 26561776) Verrastro I. … Pitt A.R. (Free Radic. Biol. Med. 2016) 3
  5. Cell communication using intrinsically disordered proteins: what can syndecans say? (PMID: 24956062) Leonova E.I. … Galzitskaya O.V. (J. Biomol. Struct. Dyn. 2015) 3

Products for SDC4 Gene

Sources for SDC4 Gene

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