SDC4 syndecan 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SDC4provided by HGNC
Official Full Name: syndecan 4provided by HGNC
Primary source: HGNC:HGNC:10661
See related: Ensembl:ENSG00000124145 MIM:600017; AllianceGenome:HGNC:10661
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SYND4
Summary: 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]
Expression: Broad expression in liver (RPKM 189.5), lung (RPKM 100.6) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.12

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (45325288..45348424, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (47061165..47084301, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (43953928..43977064, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association between syndecan-4 and subclinical atherosclerosis in ankylosing spondylitis.
Title: Association between syndecan-4 and subclinical atherosclerosis in ankylosing spondylitis.
Insufficient Syndecan-4 is associated with chronic lung disease development in preterm infants.
Title: Insufficient Syndecan-4 is associated with chronic lung disease development in preterm infants.
Syndecan-4 is a maestro of gastric cancer cell invasion and communication that underscores poor survival.
Title: Syndecan-4 is a maestro of gastric cancer cell invasion and communication that underscores poor survival.
Syndecan-4 Mediates the Cellular Entry of Adeno-Associated Virus 9.
Title: Syndecan-4 Mediates the Cellular Entry of Adeno-Associated Virus 9.
High expression of syndecan-4 is related to clinicopathological features and poor prognosis of pancreatic adenocarcinoma.
Title: High expression of syndecan-4 is related to clinicopathological features and poor prognosis of pancreatic adenocarcinoma.
Plasma membrane proteoglycans syndecan-2 and syndecan-4 engage with EGFR and RON kinase to sustain carcinoma cell cycle progression.
Title: Plasma membrane proteoglycans syndecan-2 and syndecan-4 engage with EGFR and RON kinase to sustain carcinoma cell cycle progression.
Syndecan-4 is correlated with disease activity and serological characteristic of rheumatoid arthritis.
Title: Syndecan-4 is correlated with disease activity and serological characteristic of rheumatoid arthritis.
Syndecan-1 and -4 influence Wnt signaling and cell migration in human breast cancers.
Title: Syndecan-1 and -4 influence Wnt signaling and cell migration in human breast cancers.
The effects of YKL-40 on angiogenic potential of HUVECs are partly mediated by syndecan-4.
Title: The effects of YKL-40 on angiogenic potential of HUVECs are partly mediated by syndecan-4.
microRNA-140-3p modulates invasiveness, motility, and extracellular matrix adhesion of breast cancer cells by targeting syndecan-4.
Title: microRNA-140-3p modulates invasiveness, motility, and extracellular matrix adhesion of breast cancer cells by targeting syndecan-4.

Submit: New GeneRIF Correction See all GeneRIFs (119)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association analysis identifies three psoriasis susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	The V3 region (amino acids 298-329) of HIV-1 gp120 contains the syndecan-binding site for HIV-1 via 6-O sulfated motifs; a single conserved arginine (Arg-298) in the V3 region of gp120 governs HIV-1 binding to syndecans	PubMed
Nef	nef	HIV-1 Nef enhances the expression of syndecan 4 in human podocyte	PubMed
Tat	tat	Binding of HIV-1 Tat to heparan sulfate proteoglycans is competed out by the heparin-binding factor bFGF	PubMed
	tat	Cell membrane heparin sulfate proteoglycans bind to the basic region of HIV-1 Tat (amino acids 49-57) and act as receptors for extracellular Tat uptake, an effect that may contribute to the angiogenic properties of Tat in promoting Kaposi's sarcoma	PubMed
matrix	gag	HIV-1 matrix protein co-localizes with syndecan-2, syndecan-4, and CD44v3 on activated CD4+ T cells to modulate TNF-alpha and IL2 production	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G54026 (e-PCR)
- UniSTS:109408

RH48325 (e-PCR)
- UniSTS:31610

WI-7527 (e-PCR)
- UniSTS:34441

WI-11633 (e-PCR)
- UniSTS:18320

SDC4_251 (e-PCR)
- UniSTS:277691

G43350 (e-PCR)
- UniSTS:94945

G59912 (e-PCR)
- UniSTS:137194

RH102672 (e-PCR)
- UniSTS:97006

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables fibronectin binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase C binding	IEA Inferred from Electronic Annotation more info
enables thrombospondin receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in inner ear receptor cell stereocilium organization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of T cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of extracellular exosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of focal adhesion assembly	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of stress fiber assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of fibroblast migration	IEA Inferred from Electronic Annotation more info
involved_in ureteric bud development	IEA Inferred from Electronic Annotation more info
involved_in wound healing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in costamere	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
located_in lysosomal lumen	TAS Traceable Author Statement more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: syndecan-4

Names: amphiglycan; ryudocan amphiglycan; ryudocan core protein; syndecan 4 (amphiglycan, ryudocan); syndecan proteoglycan 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.