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Sdc4 syndecan 4 [ Mus musculus (house mouse) ]

Gene ID: 20971, updated on 13-Dec-2022

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, Apr 2022]
Expression
Broad expression in kidney adult (RPKM 79.7), liver adult (RPKM 72.9) and 24 other tissues See more
Orthologs
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Genomic context

See Sdc4 in Genome Data Viewer
Location:
2 H3; 2 85.16 cM
Exon count:
6
Annotation release Status Assembly Chr Location
109 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_000068.8Genomic Context describing neighboring genes Neighboring gene microRNA 7678 Neighboring gene secretory leukocyte peptidase inhibitor Neighboring gene matrilin 4 Neighboring gene recombination signal binding protein for immunoglobulin kappa J region-like Neighboring gene SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae) Neighboring gene transformation related protein 53 target 5 Neighboring gene dysbindin (dystrobrevin binding protein 1) domain containing 2 Neighboring gene phosphatidylinositol glycan anchor biosynthesis, class T

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables fibronectin binding ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
 
enables thrombospondin receptor activity ISO
Inferred from Sequence Orthology
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
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
located_in extracellular region 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
 
located_in membrane raft ISO
Inferred from Sequence Orthology
more info
 

General protein information

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)

  1. NM_011521.2NP_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
    A0A8C6HR20, Q3U5S6
    Related
    ENSMUSP00000017153.4, ENSMUST00000017153.4
    Conserved Domains (1) summary
    pfam01034
    Location:139196
    Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    164266167..164285512 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    O35988
    UniProtKB/TrEMBL
    A0A8C6HR20, Q3U5S6
    Conserved Domains (1) summary
    pfam01034
    Location:139196
    Syndecan; Syndecan domain