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    Gpc6 glypican 6 [ Mus musculus (house mouse) ]

    Gene ID: 23888, updated on 9-Dec-2024

    Summary

    Official Symbol
    Gpc6provided by MGI
    Official Full Name
    glypican 6provided by MGI
    Primary source
    MGI:MGI:1346322
    See related
    Ensembl:ENSMUSG00000058571 AllianceGenome:MGI:1346322
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    Predicted to be involved in cell migration and regulation of neurotransmitter receptor localization to postsynaptic specialization membrane. Is active in synapse. Is expressed in several structures, including alimentary system; brain; branchial arch; embryo mesenchyme; and sensory organ. Human ortholog(s) of this gene implicated in omodysplasia 1. Orthologous to human GPC6 (glypican 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in limb E14.5 (RPKM 4.6), bladder adult (RPKM 4.0) and 20 other tissues See more
    Orthologs
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    Genomic context

    See Gpc6 in Genome Data Viewer
    Location:
    14 E4; 14 60.34 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (117162332..118216941)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (116924920..117979529)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_37619 Neighboring gene STARR-seq mESC enhancer starr_37620 Neighboring gene STARR-seq mESC enhancer starr_37621 Neighboring gene predicted gene, 18836 Neighboring gene predicted gene, 52093 Neighboring gene predicted gene, 41246 Neighboring gene predicted gene, 52112 Neighboring gene STARR-seq mESC enhancer starr_37623 Neighboring gene STARR-seq mESC enhancer starr_37624 Neighboring gene STARR-seq mESC enhancer starr_37625 Neighboring gene STARR-positive B cell enhancer mm9_chr14:118024574-118024874 Neighboring gene STARR-seq mESC enhancer starr_37629 Neighboring gene predicted gene, 52111 Neighboring gene STARR-seq mESC enhancer starr_37631 Neighboring gene STARR-seq mESC enhancer starr_37632 Neighboring gene predicted gene, 52110 Neighboring gene microRNA 6239 Neighboring gene STARR-positive B cell enhancer ABC_E7351 Neighboring gene nuclear encoded tRNA pheylalanine 5 (anticodon GAA) Neighboring gene predicted gene, 31633 Neighboring gene dopachrome tautomerase

    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)
    • Endonuclease-mediated (3) 
    • Targeted (3)  1 citation

    Interactions

    General gene information

    Clone Names

    • MGC32221, 6720429C22Rik

    Gene Ontology Provided by MGI

    Component Evidence Code Pubs
    located_in Golgi lumen  
    is_active_in cell surface  
    located_in collagen-containing extracellular matrix  
    located_in extracellular region  
    is_active_in glutamatergic synapse  
    located_in plasma membrane PubMed 
    located_in side of membrane  
    is_active_in synapse PubMed 
    is_active_in synapse  
    is_active_in synapse PubMed 

    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_001079844.2NP_001073313.1  glypican-6 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001073313.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC132136, AK135442, AK149312, AK164668
      Consensus CDS
      CCDS37008.1
      UniProtKB/TrEMBL
      Q3TP69, Q8R3X6
      Related
      ENSMUSP00000120362.2, ENSMUST00000125435.2
      Conserved Domains (1) summary
      pfam01153
      Location:23532
      Glypican; Glypican
    2. NM_011821.3NP_035951.1  glypican-6 isoform 2 precursor

      See identical proteins and their annotated locations for NP_035951.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AC132136, AK132531, AK135442, AK164668
      Consensus CDS
      CCDS27330.1
      UniProtKB/Swiss-Prot
      Q9R087
      UniProtKB/TrEMBL
      Q3TP69, Q3V1C9
      Related
      ENSMUSP00000077893.5, ENSMUST00000078849.12
      Conserved Domains (1) summary
      pfam01153
      Location:23522
      Glypican

    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_000080.7 Reference GRCm39 C57BL/6J

      Range
      117162332..118216941
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006518929.4XP_006518992.1  glypican-6 isoform X1

      UniProtKB/TrEMBL
      Q8BSI4
      Conserved Domains (1) summary
      pfam01153
      Location:23293
      Glypican
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