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

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

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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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

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Alleles

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

General gene information

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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

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Preferred Names
ly6/PLAUR domain-containing protein 1
Names
ly-6/neurotoxin-like protein 2

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_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.

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