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    lypd6 LY6/PLAUR domain containing 6 [ Danio rerio (zebrafish) ]

    Gene ID: 447932, updated on 4-Jan-2025

    Summary

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    Official Symbol
    lypd6provided by ZNC
    Official Full Name
    LY6/PLAUR domain containing 6provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040912-117
    See related
    Ensembl:ENSDARG00000004307 AllianceGenome:ZFIN:ZDB-GENE-040912-117
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:101899
    Summary
    Predicted to enable acetylcholine receptor inhibitor activity. Acts upstream of or within Spemann organizer formation and positive regulation of canonical Wnt signaling pathway. Located in plasma membrane. Is expressed in several structures, including DEL; hypoblast; margin; nervous system; and optic vesicle. Orthologous to human LYPD6 (LY6/PLAUR domain containing 6). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
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    Genomic context

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    See lypd6 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (23068148..23118350, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (23260677..23307481, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene Rho family GTPase 3b Neighboring gene metabolism of cobalamin associated Db Neighboring gene uncharacterized LOC137496471 Neighboring gene LY6/PLAUR domain containing 6B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Identification of a Ly-6 superfamily gene expressed in lateral line neuromasts in zebrafish. Ji D, et al. Dev Genes Evol, 2015 Jan. PMID 25586305
    2. Identification and expression of a novel member of Ly-6 superfamily in zebrafish Denio rerio. Ji D, et al. Dev Genes Evol, 2012 Apr. PMID 22415300
    3. Lypd6 enhances Wnt/β-catenin signaling by promoting Lrp6 phosphorylation in raft plasma membrane domains. Özhan G, et al. Dev Cell, 2013 Aug 26. PMID 23987510
    4. Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet syndrome treatment. Baraban SC, et al. Nat Commun, 2013. PMID 24002024, Free PMC Article
    5. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lypd6 appears to control Lrp6 activation specifically in membrane rafts, which is essential for downstream signaling.
      Title: Lypd6 enhances Wnt/β-catenin signaling by promoting Lrp6 phosphorylation in raft plasma membrane domains.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables acetylcholine receptor inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables acetylcholine receptor regulator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within Spemann organizer formation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within Spemann organizer formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of canonical Wnt signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of Wnt signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ly6/PLAUR domain-containing protein 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_001004670.1 → NP_001004670.1  ly6/PLAUR domain-containing protein 6 precursor

      See identical proteins and their annotated locations for NP_001004670.1

      Status: PROVISIONAL

      Source sequence(s)
      BC081426
      UniProtKB/Swiss-Prot
      Q66IA6
      UniProtKB/TrEMBL
      A0A8M9Q4J3
      Related
      ENSDARP00000013064.6, ENSDART00000020884.7
      Conserved Domains (1) summary
      pfam16975
      Location:41 → 145
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007120.7 Reference GRCz11 Primary Assembly

      Range
      23068148..23118350 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021478643.2 → XP_021334318.1  ly6/PLAUR domain-containing protein 6 isoform X1

      UniProtKB/Swiss-Prot
      Q66IA6
      UniProtKB/TrEMBL
      A0A8M9Q4J3
      Conserved Domains (1) summary
      pfam16975
      Location:41 → 145
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q66IA6.1 GenPept UniProtKB/Swiss-Prot:Q66IA6

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials