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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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