Sdc4 syndecan 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sdc4provided by RGD
Official Full Name: syndecan 4provided by RGD
Primary source: RGD:3650
See related: Ensembl:ENSRNOG00000014297 AllianceGenome:RGD:3650
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RYUDOCA; RATRYUDOCA
Summary: Enables fibronectin binding activity; identical protein binding activity; and protein kinase C binding activity. Involved in positive regulation of cellular component biogenesis; positive regulation of protein kinase activity; and ureteric bud development. Located in several cellular components, including costamere; focal adhesion; and membrane raft. Used to study bacterial infectious disease. Orthologous to human SDC4 (syndecan 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 1109.5), Liver (RPKM 640.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q42

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (173574239..173592923, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (153154888..153173576, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (160872503..160891190, complement)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exploring Syndecan-4 and MLP and Their Interaction in Primary Cardiomyocytes and H9c2 Cells.
Title: Exploring Syndecan-4 and MLP and Their Interaction in Primary Cardiomyocytes and H9c2 Cells.
Syndecan-4/PAR-3 signaling regulates focal adhesion dynamics in mesenchymal cells.
Title: Syndecan-4/PAR-3 signaling regulates focal adhesion dynamics in mesenchymal cells.
syntenin-1 negatively regulates syndecan-4 function via oligomerization and/or syndecan-4 interaction, impacting cytoskeletal organization and cell migration.
Title: New structural insight of C-terminal region of Syntenin-1, enhancing the molecular dimerization and inhibitory function related on Syndecan-4 signaling.
syndecan-4 is involved in establishment of the lamellar structure of the annulus fibrosus of the intervertebral disc
Title: The transmembrane heparan sulphate proteoglycan syndecan-4 is involved in establishment of the lamellar structure of the annulus fibrosus of the intervertebral disc.
This study provided evidence for the differential regulation by MAPK and NF-kappaB pathways in the over-expression of syndecan-4 promoted by TNF-alpha in NP cells
Title: TNF-α and TGF-β1 regulate Syndecan-4 expression in nucleus pulposus cells: role of the mitogen-activated protein kinase and NF-κB pathways.
Locally generated Sdc4 may play a role in regulating TRPC6 channels, and may contribute to glomerular pathology.
Title: Syndecan-4 ectodomain evokes mobilization of podocyte TRPC6 channels and their associated pathways: An essential role for integrin signaling.
Syndecan-2 and -4 form heterdimer and this interaction regulates syndecan-mediated cellular functions.
Title: Trans-regulation of Syndecan Functions by Hetero-oligomerization.
SDC4 participates in amelogenesis, and FGF10 may modulate dental epithelial cell behaviors through the regulation of SDC4 expression.
Title: Expression and roles of syndecan-4 in dental epithelial cell differentiation.
in healthy discs, SDC4, through its heparan sulfate side chains, contributes to maintenance of the hypoxic tissue niche by controlling baseline expression of Sox9.
Title: HIF-1-PHD2 axis controls expression of syndecan 4 in nucleus pulposus cells.
data suggest that the transmembrane domain plays a major role in regulating syndecan-4 functions, and show that a domain hierarchy exists in the regulation of syndecan-4
Title: Hierarchy between the transmembrane and cytoplasmic domains in the regulation of syndecan-4 functions.

Submit: New GeneRIF Correction See all GeneRIFs (29)

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

RH127752 (e-PCR)
- UniSTS:211062

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

D3Arb12 (e-PCR)
- UniSTS:227530

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables fibronectin binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables thrombospondin receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within inner ear receptor cell stereocilium organization	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exosomal secretion	ISO Inferred from Sequence Orthology 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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of stress fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of aortic smooth muscle cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of fibroblast migration	ISO Inferred from Sequence Orthology more info
involved_in ureteric bud development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within wound healing	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	IDA Inferred from Direct Assay 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: Ryudocan/syndecan 4; SYND4; 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_012649.4 → NP_036781.1 syndecan-4 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

P34901

UniProtKB/TrEMBL

A6JX82

Related

ENSRNOP00000019386.2, ENSRNOT00000019386.4

Conserved Domains (1) summary

pfam01034
Location:143 → 200

Syndecan; Syndecan domain