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

Gene ID: 66004, updated on 19-Sep-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
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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 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 IEA
Inferred from Electronic Annotation
more info
 
enables acetylcholine receptor regulator activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables acetylcholine receptor regulator activity IDA
Inferred from Direct Assay
more info
PubMed 
enables ion channel inhibitor activity IEA
Inferred from Electronic Annotation
more info
 
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 
involved_in synaptic transmission, cholinergic IEA
Inferred from Electronic Annotation
more info
 
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)