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Gpc6 glypican 6 [ Mus musculus (house mouse) ]

Gene ID: 23888, updated on 13-Dec-2022

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 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
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Genomic context

See Gpc6 in Genome Data Viewer
Location:
14; 14 E4
Exon count:
11
Annotation release Status Assembly Chr Location
109 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 predicted gene, 18836 Neighboring gene predicted gene, 52093 Neighboring gene predicted gene, 41246 Neighboring gene predicted gene, 52112 Neighboring gene predicted gene, 52111 Neighboring gene predicted gene, 52110 Neighboring gene microRNA 6239 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)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (2) 

General gene information

Markers

Homology

Clone Names

  • MGC32221, 6720429C22Rik

Gene Ontology Provided by MGI

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
PubMed 
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 
is_active_in synapse EXP
Inferred from Experiment
more info
PubMed 
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in synapse IDA
Inferred from Direct Assay
more info
PubMed 

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_001079844.2NP_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
    A0A6P5QZX3, Q3TP69, Q3V1C9
    Related
    ENSMUSP00000077893.5, ENSMUST00000078849.12
    Conserved Domains (1) summary
    pfam01153
    Location:23522
    Glypican

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Conserved Domains (1) summary
    pfam01153
    Location:23293
    Glypican