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    Gpc6 glypican 6 [ Mus musculus (house mouse) ]

    Gene ID: 23888, updated on 5-Mar-2024

    Summary

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    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 several processes, including regulation of neurotransmitter receptor localization to postsynaptic specialization membrane; regulation of presynapse assembly; and synaptic membrane adhesion. Is active in synapse. Is expressed in several structures, including alimentary system; branchial arch; central nervous system; 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, Apr 2022]
    Expression
    Broad expression in limb E14.5 (RPKM 4.6), bladder adult (RPKM 4.0) and 20 other tissues See more
    Orthologs
    human all
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis. Kemp JP, et al. Nat Genet, 2017 Oct. PMID 28869591, Free PMC Article
    2. Glypican-6, a new member of the glypican family of cell surface heparan sulfate proteoglycans. Veugelers M, et al. J Biol Chem, 1999 Sep 17. PMID 10480909
    3. Relatively frequent switching of transcription start sites during cerebellar development. Zhang P, et al. BMC Genomics, 2017 Jun 13. PMID 28610618, Free PMC Article
    4. Astrocyte glypicans 4 and 6 promote formation of excitatory synapses via GluA1 AMPA receptors. Allen NJ, et al. Nature, 2012 May 27. PMID 22722203, Free PMC Article
    5. Structure of the protein core of the glypican Dally-like and localization of a region important for hedgehog signaling. Kim MS, et al. Proc Natl Acad Sci U S A, 2011 Aug 9. PMID 21828006, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Glypican-6 and Glypican-4 stimulate embryonic stomach growth by regulating Hedgehog and noncanonical Wnt signaling.
      Title: Glypican-6 and Glypican-4 stimulate embryonic stomach growth by regulating Hedgehog and noncanonical Wnt signaling.
    2. Glypican-6 stimulates intestinal elongation by simultaneously regulating Hedgehog and non-canonical Wnt signaling.
      Title: Glypican-6 stimulates intestinal elongation by simultaneously regulating Hedgehog and non-canonical Wnt signaling.
    3. Adult female Gpc6-/- mice were compared with wild-type control mice of identical C57BL/6 background. Consistent with the phenotype of omodysplasia 1, Gpc6-/-mice had femurs and vertebrae that were shorter than those of wild-type mice. They also had increased femoral bone mineral content and increased cortical thickness.
      Title: Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis.
    4. GPC6 stimulates Hh signaling by binding to Hh and Ptc1 at the cilium and increasing the interaction of the receptor and ligand to promote the growth of developing long bones.
      Title: Glypican-6 promotes the growth of developing long bones by stimulating Hedgehog signaling.
    5. data identify glypicans as a family of novel astrocyte-derived molecules that are necessary and sufficient to promote glutamate receptor clustering and receptivity and to induce the formation of postsynaptically functioning CNS synapses
      Title: Astrocyte glypicans 4 and 6 promote formation of excitatory synapses via GluA1 AMPA receptors.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3)  1 citation
    • Endonuclease-mediated (2) 

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC32221, 6720429C22Rik

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of neurotransmitter receptor localization to postsynaptic specialization membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of neurotransmitter receptor localization to postsynaptic specialization membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of signal transduction IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in collagen-containing extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse EXP
    Inferred from Experiment
    more info
    		 PubMed 
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    glypican-6

    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_001079844.2 → NP_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:23 → 532
      Glypican; Glypican

    2. NM_011821.3 → NP_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:23 → 522
      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_006518929.4 → XP_006518992.1  glypican-6 isoform X1

      UniProtKB/TrEMBL
      Q8BSI4
      Conserved Domains (1) summary
      pfam01153
      Location:23 → 293
      Glypican
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9R087.1 GenPept UniProtKB/Swiss-Prot:Q9R087

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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