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    Epyc epiphycan [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314772, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Epycprovided by RGD
    Official Full Name
    epiphycanprovided by RGD
    Primary source
    RGD:1305904
    See related
    EnsemblRapid:ENSRNOG00000004717 AllianceGenome:RGD:1305904
    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
    Dspg3
    Summary
    Predicted to be involved in articular cartilage development and bone development. Predicted to act upstream of or within sensory perception of sound. Predicted to be active in extracellular matrix. Orthologous to human EPYC (epiphycan). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 47.8), Heart (RPKM 43.8) and 3 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Epyc in Genome Data Viewer
    Location:
    7q13
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (34323332..34360845)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (32436620..32474326)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (38897278..38934989)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene lumican Neighboring gene keratocan Neighboring gene coiled-coil glutamate-rich protein 1 Neighboring gene small nucleolar RNA SNORA17

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Epiphycan is specifically expressed in cochlear supporting cells and is necessary for normal hearing. Hanada Y, et al. Biochem Biophys Res Commun, 2017 Oct 21. PMID 28864419
    2. Phenotypic characterization of epiphycan-deficient and epiphycan/biglycan double-deficient mice. Nuka S, et al. Osteoarthritis Cartilage, 2010 Jan. PMID 19932218, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in articular cartilage development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within articular cartilage development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in bone development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within bone development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    epiphycan
    Names
    dermatan sulphate proteoglycan 3

    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_001434571.1 → NP_001421500.1  epiphycan precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A6IG69, B1WBV5, G3V6L6

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086025.1 Reference GRCr8

      Range
      34323332..34360845
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006241286.5 → XP_006241348.1  epiphycan isoform X1

      Conserved Domains (4) summary
      smart00013
      Location:121 → 147
      LRRNT; Leucine rich repeat N-terminal domain
      cd00116
      Location:162 → 239
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:145 → 168
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:169 → 223
      LRR_8; Leucine rich repeat

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108088.1: Suppressed sequence

      Description
      NM_001108088.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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