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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. Diseases associated with SDC4 include Thyroid Cancer and Juvenile Astrocytoma. Among its related pathways are Chondroitin sulfate/dermatan sulfate metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include cytoskeletal protein binding and fibronectin binding. An important paralog of this gene is SDC3.

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

GeneHancer (GH) Regulatory Elements for SDC4 Gene

Promoters and enhancers for SDC4 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
GH20J045334 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 658.5 +6.3 6344 14.4 CLOCK MLX ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC SSRP1 GLIS1 SDC4 NCOA5 PCIF1 ZNF335 CD40 ENSG00000271984 ZSWIM1 SNX21 ENSG00000233352 LOC105372630
GH20J044397 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 9.8 +939.2 939169 22.8 HDGF PKNOX1 FOXA2 ARNT MLX ZFP64 ARID4B SIN3A YBX1 DMAP1 HNF4A MIR3646 SRSF6 FITM2 LINC01430 LINC01620 OSER1 SDC4 OSER1-DT
GH20J045811 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 9.9 -464.2 -464219 2.5 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF48 GLIS2 ELK1 ZNF207 FOS UBE2C WFDC3 NCOA5 TP53RK PCIF1 ENSG00000271984 ZNF335 CD40 SPATA25 DNTTIP1
GH20J044702 Enhancer 1.2 Ensembl ENCODE dbSUPER 9.9 +643.6 643609 4.8 PKNOX1 YBX1 RARA ZNF366 FOS RUNX3 RXRA ZBTB11 ELF1 NR2F2 KCNK15 KCNK15-AS1 SDC4 ENSG00000132832 HSPD1P21 WISP2
GH20J045992 Enhancer 1.2 FANTOM5 ENCODE 9.9 -645.2 -645152 1.6 PKNOX1 CLOCK NEUROD1 SIN3A ZBTB7B IRF4 ELK1 FOS DEK TSHZ1 CD40 ZNF335 PCIF1 ENSG00000271984 NCOA5 PIGT SLC35C2 SDC4 WFDC3 PLTP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SDC4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SDC4 gene promoter:
  • AP-1
  • c-Jun
  • ATF-2
  • MyoD
  • NF-kappaB

Genomic Locations for SDC4 Gene

Genomic Locations for SDC4 Gene
chr20:45,325,285-45,348,424
(GRCh38/hg38)
Size:
23,140 bases
Orientation:
Minus strand
chr20:43,953,928-43,977,064
(GRCh37/hg19)
Size:
23,137 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=2126, isoforms=2101, isoforms=297, posLast=6363, posLast=6161, and posLast=3939
  • 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

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

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

UniProtKB/Swiss-Prot Function:
Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).
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

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:0042802 identical protein binding IPI 18093920
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:
  • Sdc4 Sdc4<tm1Goe>
  • Sdc4 Sdc4<tm1Tmu>
  • Sdc4 Sdc4<tm2b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SDC4

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

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

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
  • Heparan sulfuric acid
  • Heparan sulphate
  • Heparan sulphuric acid
  • alpha-Idosane
  • Heparan N-sulfate
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:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SDC4

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, 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)
  • Blood(2)
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
chimpanzee
(Pan troglodytes)
Mammalia SDC4 34 33
  • 98.65 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SDC4 34 33
  • 85.52 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SDC4 34 33
  • 84.52 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sdc4 16 34 33
  • 81.52 (n)
rat
(Rattus norvegicus)
Mammalia Sdc4 33
  • 81.22 (n)
oppossum
(Monodelphis domestica)
Mammalia SDC4 34
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDC4 34
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves SDC4 34 33
  • 63.26 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SDC4 34
  • 54 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii sdc4 34 33
  • 57.09 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8832 33
fruit fly
(Drosophila melanogaster)
Insecta Sdc 34
  • 12 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sdn-1 34
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SDC4: view image

Paralogs for SDC4 Gene

Paralogs for SDC4 Gene

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

  • SDC4_HUMAN
  • B4E1S6_HUMAN

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 Variation AA Info Type
rs1000247104 -- 45,330,063(-) A/T intron_variant
rs1000429595 -- 45,346,310(-) G/C intron_variant
rs1000532198 -- 45,328,181(-) C/T intron_variant
rs1000799643 -- 45,347,521(-) C/T intron_variant
rs1000856150 -- 45,340,780(-) G/A 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)

Additional Variant Information for SDC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDC4

SNP Genotyping and Copy Number Assay Products

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

Disorders for SDC4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SDC4 Gene - From: LncRNADisease and DISEASES

Disorder Aliases PubMed IDs
thyroid cancer
  • malignant neoplasm of thyroid gland
juvenile astrocytoma
  • pediatric astrocytoma
- elite association - COSMIC cancer census association via MalaCards
Search SDC4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SDC4

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 SDC4: view

No data available for 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 44 58
  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 58
  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 58
  4. Syndecan-syntenin-ALIX regulates the biogenesis of exosomes. (PMID: 22660413) Baietti MF … David G (Nature cell biology 2012) 3 4 58
  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 44 58

Products for SDC4 Gene

  • Boster Bio Antibodies for SDC4
  • Boster Bio ELISA Kits for SDC4

Sources for SDC4 Gene

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