Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LYNX1 Gene

Aliases for LYNX1 Gene

  • Ly6/Neurotoxin 1 2 3 5
  • Testicular Tissue Protein Li 112 3 4
  • Endogenous Prototoxin LYNX1 3 4
  • Secreted LY6/PLAUR Domain-Containing Protein 2 3
  • Secreted Ly-6/UPAR Domain-Containing Protein 2 3
  • Secreted Ly-6/UPAR-Related Protein 2 3
  • Secreted Ly6/UPAR Related Protein 2 3
  • Ly-6 Neurotoxin-Like Protein 1 3
  • Ly-6/Neurotoxin-Like Protein 1 3
  • SLURP-2 3
  • SLURP2 3

External Ids for LYNX1 Gene

Previous GeneCards Identifiers for LYNX1 Gene

  • GC08M142160
  • GC08M144089
  • GC08M143650
  • GC08M143908
  • GC00U920623
  • GC08M143844
  • GC08M139097

Summaries for LYNX1 Gene

Entrez Gene Summary for LYNX1 Gene

  • This gene encodes a member of the Ly-6/neurotoxin gene family, a group of lymphocyte antigens that attach to the cell surface by a glycosylphosphatidylinositol anchor and have a unique structure showing conserved 8-10 cysteine residues with a characteristic spacing pattern. Functional analysis indicates that this protein is not a ligand or neurotransmitter but has the capacity to enhance nicotinic acetylcholine receptor function in the presence of acetylcholine. This gene may also play a role in the pathogenesis of psoriasis vulgaris. Alternatively spliced variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for LYNX1 Gene

LYNX1 (Ly6/Neurotoxin 1) is a Protein Coding gene. Diseases associated with LYNX1 include Psoriasis.

UniProtKB/Swiss-Prot for LYNX1 Gene

  • Acts in different tissues through interaction to nicotinic acetylcholine receptors (nAChRs) (PubMed:21252236). The proposed role as modulator of nAChR activity seems to be dependent on the nAChR subtype and stoichiometry, and to involve an effect on nAChR trafficking and its cell surface expression, and on single channel properties of the nAChR inserted in the plasma membrane. Modulates functional properties of nicotinic acetylcholine receptors (nAChRs) to prevent excessive excitation, and hence neurodegeneration. Enhances desensitization by increasing both the rate and extent of desensitization of alpha-4:beta-2-containing nAChRs and slowing recovery from desensitization. Promotes large amplitude ACh-evoked currents through alpha-4:beta-2 nAChRs. Is involved in regulation of the nAChR pentameric assembly in the endoplasmic reticulum. Shifts stoichiometry from high sensitivity alpha-4(2):beta-2(3) to low sensitivity alpha-4(3):beta-2(2) nAChR (By similarity). In vitro modulates alpha-3:beta-4-containing nAChRs. Reduces cell surface expression of (alpha-3:beta-4)(2):beta-4 and (alpha-3:beta-4)(2):alpha-5 nAChRs suggesting an interaction with nAChR alpha-3(-):(+)beta-4 subunit interfaces and an allosteric mode. Corresponding single channel effects characterized by decreased unitary conductance, altered burst proportions and enhanced desensitization/inactivation seem to depend on nAChR alpha:alpha subunit interfaces and are greater in (alpha-3:beta-2)(2):alpha-3 when compared to (alpha-3:beta-2)(2):alpha-5 nAChRs (PubMed:28100642). Prevents plasticity in the primary visual cortex late in life (By similarity).

Additional gene information for LYNX1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYNX1 Gene

Genomics for LYNX1 Gene

Regulatory Elements for LYNX1 Gene

Enhancers for LYNX1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08H142787 1.4 FANTOM5 ENCODE dbSUPER 61.6 -10.6 -10649 2 HDGF PKNOX1 ESRRA NFIB SIN3A ZIC2 ZBTB7B ZKSCAN1 MTA3 CTBP1 LYNX1 LY6D EEF1D ZNF623 ENSG00000255050 SLURP1 PSCA ENSG00000283686
GH08H142814 1.6 FANTOM5 Ensembl ENCODE 46.3 -37.9 -37851 2 HDGF PKNOX1 SIN3A YBX1 ZBTB7B ZNF121 GLIS2 ELK1 ZNF207 ZNF143 LYNX1 ZNF623 JRK EEF1D AK3P2 LY6D ZNF696 TIGD5 ENSG00000255050 GPIHBP1
GH08H142776 0.9 ENCODE 52.9 +0.3 328 2 KLF17 DEAF1 SIN3A DMAP1 RAD21 RARA YY1 EGR1 ZNF143 THAP11 LYNX1 THEM6 TSTA3 SLURP2
GH08H142762 0.9 ENCODE 35.2 +14.3 14301 1 ELF3 PKNOX1 FOXA2 MLX ZSCAN9 RAD21 RARA ATF7 CREM THAP11 LYNX1 THEM6 GC08M142768 PIR62770 ENSG00000253196
GH08H142782 1.1 Ensembl ENCODE dbSUPER 28.4 -4.8 -4754 0 ZBTB10 CTCF ZNF654 MAZ RB1 REST RAD21 KLF16 ZNF143 SMC3 LYNX1 LY6D ENSG00000253715 ENSG00000284505
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LYNX1 on UCSC Golden Path with GeneCards custom track

Promoters for LYNX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000231995 348 1401 ELF3 KLF17 DEAF1 SIN3A DMAP1 RAD21 RARA YY1 EGR1 ZNF143

Genomic Location for LYNX1 Gene

Chromosome:
8
Start:
142,764,334 bp from pter
End:
142,777,848 bp from pter
Size:
13,515 bases
Orientation:
Minus strand

Genomic View for LYNX1 Gene

Genes around LYNX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYNX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYNX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYNX1 Gene

Proteins for LYNX1 Gene

  • Protein details for LYNX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P0DP58-LYNX1_HUMAN
    Recommended name:
    Ly-6/neurotoxin-like protein 1
    Protein Accession:
    P0DP58
    Secondary Accessions:
    • A0A140VJN6
    • D3DWI7
    • G3XAC2
    • Q86SR0
    • Q9BZG9

    Protein attributes for LYNX1 Gene

    Size:
    116 amino acids
    Molecular mass:
    12641 Da
    Quaternary structure:
    • Interacts with nAChRs containing alpha-4:beta-2 (CHRNA4:CHRNB2) and alpha-7 (CHRNA7) subunits. Interacts with CHRNA4 probably in the endoplasmic reticulum prior to nAChR pentameric assembly (By similarity).
    Miscellaneous:
    • Isoform 1 is considered to be an endogenous "prototoxin", that shares a N-terminal three-finger structure with snake alpha-neurotoxins.

    Three dimensional structures from OCA and Proteopedia for LYNX1 Gene

    Alternative splice isoforms for LYNX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LYNX1 Gene

Post-translational modifications for LYNX1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LYNX1 Gene

Domains & Families for LYNX1 Gene

Gene Families for LYNX1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Predicted secreted proteins
  • Transporters

Protein Domains for LYNX1 Gene

Suggested Antigen Peptide Sequences for LYNX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LYNX1: view

No data available for UniProtKB/Swiss-Prot for LYNX1 Gene

Function for LYNX1 Gene

Molecular function for LYNX1 Gene

UniProtKB/Swiss-Prot Function:
Acts in different tissues through interaction to nicotinic acetylcholine receptors (nAChRs) (PubMed:21252236). The proposed role as modulator of nAChR activity seems to be dependent on the nAChR subtype and stoichiometry, and to involve an effect on nAChR trafficking and its cell surface expression, and on single channel properties of the nAChR inserted in the plasma membrane. Modulates functional properties of nicotinic acetylcholine receptors (nAChRs) to prevent excessive excitation, and hence neurodegeneration. Enhances desensitization by increasing both the rate and extent of desensitization of alpha-4:beta-2-containing nAChRs and slowing recovery from desensitization. Promotes large amplitude ACh-evoked currents through alpha-4:beta-2 nAChRs. Is involved in regulation of the nAChR pentameric assembly in the endoplasmic reticulum. Shifts stoichiometry from high sensitivity alpha-4(2):beta-2(3) to low sensitivity alpha-4(3):beta-2(2) nAChR (By similarity). In vitro modulates alpha-3:beta-4-containing nAChRs. Reduces cell surface expression of (alpha-3:beta-4)(2):beta-4 and (alpha-3:beta-4)(2):alpha-5 nAChRs suggesting an interaction with nAChR alpha-3(-):(+)beta-4 subunit interfaces and an allosteric mode. Corresponding single channel effects characterized by decreased unitary conductance, altered burst proportions and enhanced desensitization/inactivation seem to depend on nAChR alpha:alpha subunit interfaces and are greater in (alpha-3:beta-2)(2):alpha-3 when compared to (alpha-3:beta-2)(2):alpha-5 nAChRs (PubMed:28100642). Prevents plasticity in the primary visual cortex late in life (By similarity).

Gene Ontology (GO) - Molecular Function for LYNX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030548 acetylcholine receptor regulator activity IDA 21252236
GO:0033130 acetylcholine receptor binding IDA 16575903
genes like me logo Genes that share ontologies with LYNX1: view
genes like me logo Genes that share phenotypes with LYNX1: view

Animal Models for LYNX1 Gene

MGI Knock Outs for LYNX1:

Animal Model Products

CRISPR Products

miRNA for LYNX1 Gene

miRTarBase miRNAs that target LYNX1

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LYNX1 Gene

Localization for LYNX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYNX1 Gene

Cell membrane; Lipid-anchor, GPI-anchor. Cell projection, dendrite. Endoplasmic reticulum. Note=Detected in Purkinje cells soma and proximal dendrites. {ECO:0000250 UniProtKB:P0DP60}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LYNX1 gene
Compartment Confidence
plasma membrane 3
extracellular 3
endoplasmic reticulum 3

Gene Ontology (GO) - Cellular Components for LYNX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 16575903
GO:0005783 endoplasmic reticulum IEA --
GO:0005886 plasma membrane IEA --
GO:0030425 dendrite IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with LYNX1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LYNX1 Gene

Pathways & Interactions for LYNX1 Gene

SuperPathways for LYNX1 Gene

No Data Available

Interacting Proteins for LYNX1 Gene

Gene Ontology (GO) - Biological Process for LYNX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0095500 acetylcholine receptor signaling pathway IDA 27485575
GO:0099601 regulation of neurotransmitter receptor activity IDA 21252236
genes like me logo Genes that share ontologies with LYNX1: view

No data available for Pathways by source and SIGNOR curated interactions for LYNX1 Gene

Drugs & Compounds for LYNX1 Gene

No Compound Related Data Available

Transcripts for LYNX1 Gene

Unigene Clusters for LYNX1 Gene

Ly6/neurotoxin 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYNX1 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9
SP1: - - - - - - - -
SP2: - - - -
SP3: -
SP4:
SP5:
SP6: - -
SP7: -

Relevant External Links for LYNX1 Gene

GeneLoc Exon Structure for
LYNX1
ECgene alternative splicing isoforms for
LYNX1

Expression for LYNX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LYNX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LYNX1 Gene

This gene is overexpressed in Brain - Cortex (x4.7).

Protein differential expression in normal tissues from HIPED for LYNX1 Gene

This gene is overexpressed in Urine (24.2), Frontal cortex (16.8), Cerebrospinal fluid (16.1), and Milk (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LYNX1 Gene



NURSA nuclear receptor signaling pathways regulating expression of LYNX1 Gene:

LYNX1

SOURCE GeneReport for Unigene cluster for LYNX1 Gene:

Hs.158665

Evidence on tissue expression from TISSUES for LYNX1 Gene

  • Nervous system(4.4)
  • Skin(2.4)
genes like me logo Genes that share expression patterns with LYNX1: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LYNX1 Gene

Orthologs for LYNX1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LYNX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LYNX1 34 33
  • 98.56 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LYNX1 33
  • 86.78 (n)
mouse
(Mus musculus)
Mammalia Lynx1 16 33
  • 80.75 (n)
2300005B03Rik 34
  • 56 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lynx1 33
  • 79.31 (n)
dog
(Canis familiaris)
Mammalia LYNX1 34
  • 52 (a)
OneToOne
Species where no ortholog for LYNX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LYNX1 Gene

ENSEMBL:
Gene Tree for LYNX1 (if available)
TreeFam:
Gene Tree for LYNX1 (if available)

Paralogs for LYNX1 Gene

No data available for Paralogs for LYNX1 Gene

Variants for LYNX1 Gene

Sequence variations from dbSNP and Humsavar for LYNX1 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs1000084537 -- 142,768,330(+) GGGGA(-/C)CCCCG intron-variant
rs1000154996 -- 142,769,410(+) GGAGG(G/T)GGGCA intron-variant
rs1000164389 -- 142,777,654(+) GGACC(A/G)CCGGC intron-variant, upstream-variant-2KB
rs1000270374 -- 142,772,916(+) GGTGT(A/G)AGAAG intron-variant, utr-variant-3-prime
rs1000307501 -- 142,779,498(+) TGTCA(C/T)CTAAA upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for LYNX1 Gene

Variant ID Type Subtype PubMed ID
esv2661137 CNV deletion 23128226
esv2737931 CNV deletion 23290073
esv2737932 CNV deletion 23290073
esv2737933 CNV deletion 23290073
esv33000 CNV gain 17666407
nsv1023021 CNV loss 25217958
nsv396254 CNV deletion 16902084
nsv612713 CNV loss 21841781
nsv824758 CNV gain 20364138
nsv824759 CNV gain 20364138
nsv831485 CNV loss 17160897
nsv831486 CNV gain 17160897
nsv950004 CNV deletion 24416366

Variation tolerance for LYNX1 Gene

Residual Variation Intolerance Score: 67.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.79; 33.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LYNX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYNX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYNX1 Gene

Disorders for LYNX1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LYNX1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
psoriasis
- elite association - COSMIC cancer census association via MalaCards
Search LYNX1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LYNX1

Genetic Association Database (GAD)
LYNX1
Human Genome Epidemiology (HuGE) Navigator
LYNX1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LYNX1
genes like me logo Genes that share disorders with LYNX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LYNX1 Gene

Publications for LYNX1 Gene

  1. SLURP-2, a novel member of the human Ly-6 superfamily that is up-regulated in psoriasis vulgaris. (PMID: 12573258) Tsuji H … Inoko H (Genomics 2003) 2 3 22 60
  2. Transcriptional regulation of SLURP2, a psoriasis-associated gene, is under control of IL-22 in the skin: A special reference to the nested gene LYNX1. (PMID: 26033490) Moriwaki Y … Misawa H (International immunopharmacology 2015) 3 4 60
  3. NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1. (PMID: 21252236) Lyukmanova EN … Kirpichnikov MP (The Journal of biological chemistry 2011) 3 4 60
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  5. SLURP-2: A novel cholinergic signaling peptide in human mucocutaneous epithelium. (PMID: 16575903) Arredondo J … Grando SA (Journal of cellular physiology 2006) 3 22 60

Products for LYNX1 Gene

Sources for LYNX1 Gene

Content
Loading form....