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    LYNX1 Ly6/neurotoxin 1 [ Homo sapiens (human) ]

    Gene ID: 66004, updated on 9-Dec-2024

    Summary

    Official Symbol
    LYNX1provided by HGNC
    Official Full Name
    Ly6/neurotoxin 1provided by HGNC
    Primary source
    HGNC:HGNC:29604
    See related
    Ensembl:ENSG00000180155 MIM:606110; AllianceGenome:HGNC:29604
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a GPI-anchored, cell membrane bound member of the Ly6/uPAR (LU) superfamily of proteins containing the unique three-finger LU domain. This protein interacts with nicotinic acetylcholine receptors (nAChRs), and is thought to function as a modulator of nAChR activity to prevent excessive excitation. Alternatively spliced transcript variants have been found for this gene. Read-through transcription between this gene and the neighboring downstream gene (SLURP2) generates naturally-occurring transcripts (LYNX1-SLURP2) that encode a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Sep 2017]
    Expression
    Broad expression in brain (RPKM 28.8), heart (RPKM 21.3) and 18 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See LYNX1 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (142771197..142777872, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (143914639..143921325, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (143852615..143859288, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene LY6/PLAUR domain containing 2 Neighboring gene uncharacterized LOC124902033 Neighboring gene LYNX1-SLURP2 readthrough Neighboring gene secreted LY6/PLAUR domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19608 Neighboring gene lymphocyte antigen 6 family member D Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:143896321-143897520 Neighboring gene glycosylphosphatidylinositol anchored molecule like

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough LYNX1-SLURP2

    Readthrough gene: LYNX1-SLURP2, Included gene: SLURP2

    Clone Names

    • MGC40364

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acetylcholine receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables acetylcholine receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables acetylcholine receptor inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables acetylcholine receptor regulator activity IDA
    Inferred from Direct Assay
    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
     
    involved_in regulation of neurotransmitter receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of neurotransmitter receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    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

    Preferred Names
    ly-6/neurotoxin-like protein 1
    Names
    Ly-6 neurotoxin-like protein 1
    endogenous prototoxin LYNX1
    testicular tissue protein Li 112

    NCBI Reference Sequences (RefSeq)

    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_001356370.1NP_001343299.1  ly-6/neurotoxin-like protein 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' terminal exon compared to variant 1. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC083841, AF321824, BF994257, BU683767
      Consensus CDS
      CCDS6389.1
      UniProtKB/Swiss-Prot
      A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9
      Conserved Domains (1) summary
      cd00117
      Location:2193
      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 ...
    2. NM_177457.5NP_803252.1  ly-6/neurotoxin-like protein 1 precursor

      See identical proteins and their annotated locations for NP_803252.1

      Status: REVIEWED

      Description
      Transcript Variant:This variant (3) contains an alternate 5' terminal exon compared to variant 1. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC083841, AF321824, BU683767
      Consensus CDS
      CCDS6389.1
      UniProtKB/Swiss-Prot
      A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9
      Related
      ENSP00000478390.1, ENST00000621401.4
      Conserved Domains (1) summary
      cd00117
      Location:2193
      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. NM_177476.4NP_803429.1  ly-6/neurotoxin-like protein 1 precursor

      See identical proteins and their annotated locations for NP_803429.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC083841, BG701653, BM172253, BU683767
      Consensus CDS
      CCDS6389.1
      UniProtKB/Swiss-Prot
      A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9
      Related
      ENSP00000478402.1, ENST00000620006.4
      Conserved Domains (1) summary
      cd00117
      Location:2193
      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 ...
    4. NM_177477.4NP_803430.1  ly-6/neurotoxin-like protein 1 precursor

      See identical proteins and their annotated locations for NP_803430.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC083841, BU683767, HY110957
      Consensus CDS
      CCDS6389.1
      UniProtKB/Swiss-Prot
      A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9
      Related
      ENSP00000498325.1, ENST00000652477.1
      Conserved Domains (1) summary
      cd00117
      Location:2193
      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 ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      142771197..142777872 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      143914639..143921325 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)