Sdc4 syndecan 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sdc4provided by MGI
Official Full Name: syndecan 4provided by MGI
Primary source: MGI:MGI:1349164
See related: Ensembl:ENSMUSG00000017009 AllianceGenome:MGI:1349164
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: S4; Synd4; ryudocan; syndecan-4
Summary: Predicted to enable several functions, including fibronectin binding activity; protein kinase C binding activity; and thrombospondin receptor activity. Involved in regulation of fibroblast migration. Acts upstream of or within inner ear receptor cell stereocilium organization; neural tube closure; and wound healing. Located in cell surface. Is expressed in several structures, including alimentary system; brain; genitourinary system; skeleton; and skin. Orthologous to human SDC4 (syndecan 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in kidney adult (RPKM 79.7), liver adult (RPKM 72.9) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 H3; 2 85.16 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (164266167..164285512, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (164424247..164443188, complement)

Chromosome 2 - NC_000068.8 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sdc4 deletion perturbs intervertebral disc matrix homeostasis and promotes early osteopenia in the aging mouse spine.
Title: Sdc4 deletion perturbs intervertebral disc matrix homeostasis and promotes early osteopenia in the aging mouse spine.
Unravelling the Effects of Syndecan-4 Knockdown on Skeletal Muscle Functions.
Title: Unravelling the Effects of Syndecan-4 Knockdown on Skeletal Muscle Functions.
Cardiomyocyte-specific overexpression of syndecan-4 in mice results in activation of calcineurin-NFAT signalling and exacerbated cardiac hypertrophy.
Title: Cardiomyocyte-specific overexpression of syndecan-4 in mice results in activation of calcineurin-NFAT signalling and exacerbated cardiac hypertrophy.
Cholesterol-induced LRP3 downregulation promotes cartilage degeneration in osteoarthritis by targeting Syndecan-4.
Title: Cholesterol-induced LRP3 downregulation promotes cartilage degeneration in osteoarthritis by targeting Syndecan-4.
A reduction of Syndecan-4 in macrophages promotes atherosclerosis by aggravating the proinflammatory capacity of macrophages.
Title: A reduction of Syndecan-4 in macrophages promotes atherosclerosis by aggravating the proinflammatory capacity of macrophages.
Integrin alpha11beta1 and syndecan-4 dual receptor ablation attenuate cardiac hypertrophy in the pressure overloaded heart.
Title: Integrin α11β1 and syndecan-4 dual receptor ablation attenuate cardiac hypertrophy in the pressure overloaded heart.
Proteomic analysis reveals exercise training induced remodelling of hepatokine secretion and uncovers syndecan-4 as a regulator of hepatic lipid metabolism.
Title: Proteomic analysis reveals exercise training induced remodelling of hepatokine secretion and uncovers syndecan-4 as a regulator of hepatic lipid metabolism.
Roles of Syndecan-4 in cardiac injury and repair.
Title: Roles of Syndecan-4 in cardiac injury and repair.
Syndecan-4 affects myogenesis via Rac1-mediated actin remodeling and exhibits copy-number amplification and increased expression in human rhabdomyosarcoma tumors.
Title: Syndecan-4 affects myogenesis via Rac1-mediated actin remodeling and exhibits copy-number amplification and increased expression in human rhabdomyosarcoma tumors.
Inhibition of syndecan-4 reduces cartilage degradation in murine models of osteoarthritis through the downregulation of HIF-2alpha by miR-96-5p.
Title: Inhibition of syndecan-4 reduces cartilage degradation in murine models of osteoarthritis through the downregulation of HIF-2α by miR-96-5p.

Submit: New GeneRIF Correction See all GeneRIFs (94)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4) 1 citation
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3Uwm8 (e-PCR)
- UniSTS:240181

AW108331 (e-PCR)
- UniSTS:178765

AA959608 (e-PCR)
- UniSTS:159073

NoName (e-PCR)
- UniSTS:234598

Sdc4 (e-PCR), detects polymorphism
- UniSTS:466047

Sdc4 (e-PCR), detects polymorphism
- UniSTS:499190

Gene Ontology Provided by MGI

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

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

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 cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in costamere	IEA Inferred from Electronic Annotation more info
located_in costamere	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: syndecan-4

Names: ryudocan core protein

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.

mRNA and Protein(s)

NM_011521.2 → NP_035651.1 syndecan-4 precursor

See identical proteins and their annotated locations for NP_035651.1

Status: PROVISIONAL

Source sequence(s)

AL590429

Consensus CDS

CCDS17036.1

UniProtKB/Swiss-Prot

O35988

UniProtKB/TrEMBL

Q3U5S6, Q3UKZ1

Related

ENSMUSP00000017153.4, ENSMUST00000017153.4

Conserved Domains (1) summary

pfam01034
Location:139 → 196

Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

164266167..164285512 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036160218.1 → XP_036016111.1 syndecan-4 isoform X1

UniProtKB/Swiss-Prot

O35988

UniProtKB/TrEMBL

Q3U5S6, Q3UKZ1

Conserved Domains (1) summary

pfam01034
Location:139 → 196

Syndecan; Syndecan domain