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    Sdc4 syndecan 4 [ Mus musculus (house mouse) ]

    Gene ID: 20971, updated on 9-Dec-2024

    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, Dec 2024]
    Expression
    Broad expression in kidney adult (RPKM 79.7), liver adult (RPKM 72.9) and 24 other tissues See more
    Orthologs
    NEW
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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
    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_000068.8Genomic Context describing neighboring genes Neighboring gene microRNA 7678 Neighboring gene STARR-seq mESC enhancer starr_06324 Neighboring gene secretory leukocyte peptidase inhibitor Neighboring gene matrilin 4 Neighboring gene STARR-positive B cell enhancer ABC_E6015 Neighboring gene recombination signal binding protein for immunoglobulin kappa J region-like Neighboring gene STARR-positive B cell enhancer ABC_E4517 Neighboring gene STARR-positive B cell enhancer ABC_E6016 Neighboring gene STARR-seq mESC enhancer starr_06326 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:164266728-164266915 Neighboring gene STARR-seq mESC enhancer starr_06330 Neighboring gene STARR-positive B cell enhancer ABC_E7884 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:164286295-164286478 Neighboring gene SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae) Neighboring gene transformation related protein 53 target 5 Neighboring gene dysbindin domain containing 2 Neighboring gene STARR-positive B cell enhancer ABC_E9539 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

    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

    Preferred Names
    syndecan-4
    Names
    ryudocan core protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      Q3U5S6, Q3UKZ1
      Related
      ENSMUSP00000017153.4, ENSMUST00000017153.4
      Conserved Domains (1) summary
      pfam01034
      Location:139196
      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

    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
      Q3U5S6, Q3UKZ1
      Conserved Domains (1) summary
      pfam01034
      Location:139196
      Syndecan; Syndecan domain