U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Lypd1 Ly6/Plaur domain containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 72585, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Lypd1provided by MGI
    Official Full Name
    Ly6/Plaur domain containing 1provided by MGI
    Primary source
    MGI:MGI:1919835
    See related
    Ensembl:ENSMUSG00000026344 AllianceGenome:MGI:1919835
    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
    Also known as
    Lynx2; Lypdc1; 2700050C12Rik; C530008O16Rik
    Summary
    Enables acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Acts upstream of or within several processes, including behavioral fear response; negative regulation of protein localization to plasma membrane; and synaptic signaling. Located in membrane. Is expressed in several structures, including alimentary system; branchial arch; limb; nervous system; and sensory organ. Orthologous to human LYPD1 (LY6/PLAUR domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in CNS E18 (RPKM 5.8), cortex adult (RPKM 5.8) and 24 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Lypd1 in Genome Data Viewer
    Location:
    1 E3; 1 54.7 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (125795359..125841134, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (125867622..125913175, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_02109 Neighboring gene STARR-seq mESC enhancer starr_02110 Neighboring gene STARR-seq mESC enhancer starr_02112 Neighboring gene STARR-seq mESC enhancer starr_02113 Neighboring gene crumbs homolog 1 pseudogene Neighboring gene G protein-coupled receptor 39 Neighboring gene predicted gene, 41943 Neighboring gene NCK-associated protein 5 Neighboring gene STARR-seq mESC enhancer starr_02114 Neighboring gene predicted gene, 35562 Neighboring gene STARR-seq mESC enhancer starr_02115 Neighboring gene STARR-seq mESC enhancer starr_02116 Neighboring gene RIKEN cDNA 4930599A14 gene

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PHTS, a novel putative tumor suppressor, is involved in the transformation reversion of HeLaHF cells independently of the p53 pathway. Yu DH, et al. Exp Cell Res, 2006 Apr 1. PMID 16413018
    2. Lypd1-DTR/+: A New Mouse Model for Specifically Damaging the Type Ic Spiral Ganglion Neurons of the Cochlea. Zhang D, et al. Neurosci Bull, 2023 Sep. PMID 37222854, Free PMC Article
    3. Neural system-enriched gene expression: relationship to biological pathways and neurological diseases. Zhang J, et al. Physiol Genomics, 2004 Jul 8. PMID 15126645
    4. Identification of GPI-anchored protein LYPD1 as an essential factor for odontoblast differentiation in tooth development. Fu Y, et al. J Biol Chem, 2023 May. PMID 36963497, Free PMC Article
    5. Runx1 controls auditory sensory neuron diversity in mice. Shrestha BR, et al. Dev Cell, 2023 Feb 27. PMID 36800995, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of GPI-anchored protein LYPD1 as an essential factor for odontoblast differentiation in tooth development.
      Title: Identification of GPI-anchored protein LYPD1 as an essential factor for odontoblast differentiation in tooth development.
    2. Lynx2 and Ly6g6e have roles in intracellular trafficking and allosteric potentiation of alpha4beta2 nAChRs, respectively
      Title: Mechanisms of inhibition and potentiation of α4β2 nicotinic acetylcholine receptors by members of the Ly6 protein family.
    3. altered glutamatergic signaling in the prefrontal cortex of Lynx2 mutant mice contributes to increased anxiety-related behaviors
      Title: A role for LYNX2 in anxiety-related behavior.
    4. cloning and characterization of lynx2; lynx2 is expressed in a large number of neuronal structures but only in discrete postmitotic neurons
      Title: Identification of lynx2, a novel member of the ly-6/neurotoxin superfamily, expressed in neuronal subpopulations during mouse development.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables acetylcholine receptor binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables acetylcholine receptor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables acetylcholine receptor inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables acetylcholine receptor inhibitor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables acetylcholine receptor inhibitor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in acetylcholine receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within acetylcholine receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within behavioral fear response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of protein localization to plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of protein localization to plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within response to nicotine IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within synaptic transmission, cholinergic IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in 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
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    ly6/PLAUR domain-containing protein 1
    Names
    ly-6/neurotoxin-like protein 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001311089.1 → NP_001298018.1  ly6/PLAUR domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001298018.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate first exon compared to variant 1, which results in translation initiation at a downstream AUG. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AC153655, AK082941, BQ175060
      Consensus CDS
      CCDS78672.1
      UniProtKB/TrEMBL
      E0CXP0, F8WHH7
      Related
      ENSMUSP00000027582.5, ENSMUST00000027582.10

    2. NM_001311090.1 → NP_001298019.1  ly6/PLAUR domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001298019.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate first exon compared to variant 1, which results in translation initiation at a downstream AUG. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AC153655, AK012406, BQ175060, BY073265
      Consensus CDS
      CCDS78672.1
      UniProtKB/TrEMBL
      E0CXP0, F8WHH7
      Related
      ENSMUSP00000125158.2, ENSMUST00000162899.8

    3. NM_145100.4 → NP_659568.2  ly6/PLAUR domain-containing protein 1 isoform a precursor

      See identical proteins and their annotated locations for NP_659568.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC153655, AK045592, BQ175060
      Consensus CDS
      CCDS15243.1
      UniProtKB/Swiss-Prot
      Q3V2X5, Q3V447, Q8BLC3, Q9JJ96
      Related
      ENSMUSP00000125149.2, ENSMUST00000159417.2

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      125795359..125841134 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006529885.5 → XP_006529948.3  ly6/PLAUR domain-containing protein 1 isoform X2

    2. XM_011248088.3 → XP_011246390.2  ly6/PLAUR domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      cl10471
      Location:149 → 236
      LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

    3. XM_017312443.2 → XP_017167932.1  ly6/PLAUR domain-containing protein 1 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BLC3.1 GenPept UniProtKB/Swiss-Prot:Q8BLC3

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous