Aliases for LY6E Gene

Aliases for LY6E Gene

  • Lymphocyte Antigen 6 Family Member E 2 3 5
  • RIG-E 2 3 4
  • SCA-2 2 3 4
  • TSA-1 2 3 4
  • Lymphocyte Antigen 6 Complex, Locus E 2 3
  • Retinoic Acid-Induced Gene E Protein 3 4
  • Retinoic Acid Induced Gene E 2 3
  • Thymic Shared Antigen 1 3 4
  • Lymphocyte Antigen 6E 3 4
  • Stem Cell Antigen 2 3 4
  • Ly-6E 3 4
  • RIGE 3 4
  • SCA2 3 4
  • LY6E 5
  • 9804 4
  • TSA1 4

External Ids for LY6E Gene

Previous GeneCards Identifiers for LY6E Gene

  • GC08P142338
  • GC08P144322
  • GC08P143874
  • GC08P144205
  • GC08P144171
  • GC08P139353
  • GC08P144099

Summaries for LY6E Gene

GeneCards Summary for LY6E Gene

LY6E (Lymphocyte Antigen 6 Family Member E) is a Protein Coding gene. Diseases associated with LY6E include T-Cell Lymphoma, Subcutaneous Panniculitis-Like and Acute Promyelocytic Leukemia. Among its related pathways are Metabolism of proteins and Ectoderm Differentiation. An important paralog of this gene is GPIHBP1.

UniProtKB/Swiss-Prot Summary for LY6E Gene

  • GPI-anchored cell surface protein that regulates T-lymphocytes proliferation, differentiation, and activation. Regulates the T-cell receptor (TCR) signaling by interacting with component CD3Z/CD247 at the plasma membrane, leading to CD3Z/CD247 phosphorylation modulation.
  • (Microbial infection) Promotes entry, likely through an enhanced virus-cell fusion process, of various viruses including HIV-1, West Nile virus, dengue virus and Zika virus (PubMed:28130445). In contrast, the paramyxovirus PIV5, which enters at the plasma membrane, does not require LY6E (PubMed:28130445, PubMed:29610346). Mechanistically, adopts a microtubule-like organization upon viral infection and enhances viral uncoating after endosomal escape (PubMed:28130445, PubMed:30190477).

Gene Wiki entry for LY6E Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LY6E Gene

Genomics for LY6E Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LY6E Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J143014 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 606.9 +0.4 359 5.3 CREB1 PRDM10 ZNF629 IKZF1 POLR2A BACH1 TARDBP ZHX2 FOXA1 LARP7 LY6E-DT LY6E RF00017-7363 LY6L
GH08J143012 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 8.2 -4.3 -4336 2 HNRNPL GATAD2A RBFOX2 RXRB REST SP1 CEBPA SOX13 ZBTB26 ZKSCAN8 LY6E-DT LY6E LY6K THEM6 piR-32810-132 RF00017-7363 CYP11B2
GH08J143275 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 2.3 +260.9 260888 6.9 BRCA1 SP1 HNRNPL CREB1 GATAD2A CTCF ZBTB33 ZNF629 TFE3 SIX5 MINCR GLI4 GPAA1 ZNF623 PARP10 ENSG00000255050 EEF1D ZNF707 ZFP41 ZC3H3
GH08J142087 Enhancer 0.6 dbSUPER 4.6 -925.9 -925884 7.5 KDM1A CTCF ZNF444 MAFK ZNF205 PTBP1 ZFHX2 BCOR ZNF768 ZMYM3 LY6E ENSG00000261710 lnc-ADGRB1-7 HSALNG0069142 TSNARE1 ENSG00000226490
GH08J142814 Enhancer 1.1 FANTOM5 ENCODE 2.4 -202.3 -202284 2.8 HNRNPL CREB1 CTCF ZBTB33 YBX1 ZNF692 TARDBP FOXA1 RFX1 ZNF776 LYNX1 JRK LY6D ZNF696 TIGD5 ZNF623 GPIHBP1 LY6E GLI4 ENSG00000283686
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LY6E on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LY6E

Top Transcription factor binding sites by QIAGEN in the LY6E gene promoter:
  • c-Rel
  • C/EBPalpha
  • En-1
  • IRF-1
  • LCR-F1
  • Lmo2
  • LUN-1
  • NF-kappaB
  • NF-kappaB1
  • TBP

Genomic Locations for LY6E Gene

Genomic Locations for LY6E Gene
chr8:143,017,982-143,023,832
(GRCh38/hg38)
Size:
5,851 bases
Orientation:
Plus strand
chr8:144,099,399-144,105,249
(GRCh37/hg19)
Size:
5,851 bases
Orientation:
Plus strand

Genomic View for LY6E Gene

Genes around LY6E on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LY6E Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LY6E Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LY6E Gene

Proteins for LY6E Gene

  • Protein details for LY6E Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16553-LY6E_HUMAN
    Recommended name:
    Lymphocyte antigen 6E
    Protein Accession:
    Q16553
    Secondary Accessions:
    • B2R4X5
    • D3DWJ2
    • Q0VDE5

    Protein attributes for LY6E Gene

    Size:
    131 amino acids
    Molecular mass:
    13507 Da
    Quaternary structure:
    • Interacts with CHRNA4.

neXtProt entry for LY6E Gene

Post-translational modifications for LY6E Gene

  • Glycosylation at Asn99
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LY6E Gene

Domains & Families for LY6E Gene

Gene Families for LY6E Gene

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

Protein Domains for LY6E Gene

InterPro:
Blocks:
  • CD59 antigen
ProtoNet:

Suggested Antigen Peptide Sequences for LY6E Gene

GenScript: Design optimal peptide antigens:
  • Lymphocyte antigen 6 complex, locus E, isoform CRA_a (D3DWJ1_HUMAN)
  • Thymic shared antigen 1 (LY6E_HUMAN)
genes like me logo Genes that share domains with LY6E: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LY6E Gene

Function for LY6E Gene

Molecular function for LY6E Gene

UniProtKB/Swiss-Prot Function:
GPI-anchored cell surface protein that regulates T-lymphocytes proliferation, differentiation, and activation. Regulates the T-cell receptor (TCR) signaling by interacting with component CD3Z/CD247 at the plasma membrane, leading to CD3Z/CD247 phosphorylation modulation.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Promotes entry, likely through an enhanced virus-cell fusion process, of various viruses including HIV-1, West Nile virus, dengue virus and Zika virus (PubMed:28130445). In contrast, the paramyxovirus PIV5, which enters at the plasma membrane, does not require LY6E (PubMed:28130445, PubMed:29610346). Mechanistically, adopts a microtubule-like organization upon viral infection and enhances viral uncoating after endosomal escape (PubMed:28130445, PubMed:30190477).
UniProtKB/Swiss-Prot Induction:
By retinoic acid; in promyelocytic leukemia NB4 and in myeloblast HL-60 cell lines. Activated by IFN-alpha in monocytic cell line U-937 and in peripheral blood monocyte cells.
GENATLAS Biochemistry:
lymphocyte antigen 6 complex,member E,homolog with the murine LY-6 family members of small cysteine-rich proteins,involved in signal transduction

Phenotypes From GWAS Catalog for LY6E Gene

Gene Ontology (GO) - Molecular Function for LY6E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030550 acetylcholine receptor inhibitor activity IBA 21873635
genes like me logo Genes that share ontologies with LY6E: view
genes like me logo Genes that share phenotypes with LY6E: view

Animal Models for LY6E Gene

MGI Knock Outs for LY6E:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LY6E

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LY6E Gene

Localization for LY6E Gene

Subcellular locations from UniProtKB/Swiss-Prot for LY6E Gene

Cell membrane. Lipid-anchor, GPI-anchor.

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 LY6E gene
Compartment Confidence
extracellular 5
plasma membrane 4
mitochondrion 2
nucleus 2
cytosol 2
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LY6E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IBA 21873635
GO:0031225 anchored component of membrane IBA 21873635
genes like me logo Genes that share ontologies with LY6E: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LY6E Gene

Pathways & Interactions for LY6E Gene

genes like me logo Genes that share pathways with LY6E: view

Pathways by source for LY6E Gene

Gene Ontology (GO) - Biological Process for LY6E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007166 cell surface receptor signaling pathway TAS 8650192
GO:2000272 negative regulation of signaling receptor activity IEA --
genes like me logo Genes that share ontologies with LY6E: view

No data available for SIGNOR curated interactions for LY6E Gene

Drugs & Compounds for LY6E Gene

(1) Additional Compounds for LY6E Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LY6E: view

Transcripts for LY6E Gene

mRNA/cDNA for LY6E Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LY6E

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LY6E Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e · 7f · 7g · 7h · 7i · 7j · 7k · 7l · 7m ^ 8
SP1: - - -
SP2: - -
SP3: - - -
SP4: - -
SP5: - - - - - - - -
SP6: - - - -
SP7: - - - -
SP8: - - - -
SP9: - - - - -
SP10: - - - -
SP11: - - - - -
SP12: - - - - -
SP13: - - -
SP14: - - - - - - - - - - - - - - - -
SP15: - -
SP16: - - -

Relevant External Links for LY6E Gene

GeneLoc Exon Structure for
LY6E

Expression for LY6E Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LY6E Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LY6E Gene

This gene is overexpressed in Testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LY6E Gene



Protein tissue co-expression partners for LY6E Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LY6E

SOURCE GeneReport for Unigene cluster for LY6E Gene:

Hs.521903

mRNA Expression by UniProt/SwissProt for LY6E Gene:

Q16553-LY6E_HUMAN
Tissue specificity: Widely expressed, predominantly in liver, kidney, ovary, spleen and peripheral blood Leukocytes.

Evidence on tissue expression from TISSUES for LY6E Gene

  • Nervous system(4.9)
  • Blood(4.5)
  • Skin(4.4)
  • Pancreas(4.1)
  • Lung(3.6)
  • Liver(3.5)
  • Kidney(3.3)
  • Intestine(3)
  • Spleen(3)
  • Muscle(2.8)
  • Bone marrow(2.7)
  • Heart(2.6)
  • Lymph node(2.6)
  • Stomach(2.2)
  • Adrenal gland(2.2)
genes like me logo Genes that share expression patterns with LY6E: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for LY6E Gene

Orthologs for LY6E Gene

This gene was present in the common ancestor of chordates.

Orthologs for LY6E Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LY6E 30 31
  • 98.98 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LY6E 30 31
  • 77.57 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LY6E 30 31
  • 73.33 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ly6e 30
  • 68.48 (n)
Mouse
(Mus musculus)
Mammalia Ly6e 30 17 31
  • 68.18 (n)
OneToOne
Chicken
(Gallus gallus)
Aves LY6E 30 31
  • 56.8 (n)
OneToMany
-- 31
  • 40 (a)
OneToMany
-- 31
  • 40 (a)
OneToMany
-- 31
  • 33 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 44 (a)
OneToMany
-- 31
  • 31 (a)
OneToMany
Species where no ortholog for LY6E was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • 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 Vase (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 LY6E Gene

ENSEMBL:
Gene Tree for LY6E (if available)
TreeFam:
Gene Tree for LY6E (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LY6E: view image

Paralogs for LY6E Gene

Paralogs for LY6E Gene

(1) SIMAP similar genes for LY6E Gene using alignment to 7 proteins:

  • LY6E_HUMAN
  • D3DWJ1_HUMAN
  • E5RGI6_HUMAN
  • E5RI33_HUMAN
  • E5RI58_HUMAN
  • E5RIQ1_HUMAN
  • E7EWF8_HUMAN
genes like me logo Genes that share paralogs with LY6E: view

Variants for LY6E Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LY6E Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
711022 Likely Benign: not provided 143,021,703(+) G/A MISSENSE_VARIANT
782281 Benign: not provided 143,021,699(+) G/A SYNONYMOUS_VARIANT
782282 Benign: not provided 143,021,724(+) G/A MISSENSE_VARIANT
788736 Benign: not provided 143,021,708(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for LY6E Gene

Structural Variations from Database of Genomic Variants (DGV) for LY6E Gene

Variant ID Type Subtype PubMed ID
nsv465991 CNV loss 19166990
nsv612717 CNV loss 21841781

Variation tolerance for LY6E Gene

Residual Variation Intolerance Score: 71.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.76; 66.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LY6E Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LY6E

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LY6E Gene

Disorders for LY6E Gene

MalaCards: The human disease database

(5) MalaCards diseases for LY6E Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
t-cell lymphoma, subcutaneous panniculitis-like
  • sptcl
acute promyelocytic leukemia
  • apl
west nile virus
  • west nile virus, susceptibility to
subvalvular aortic stenosis
  • fixed subaortic stenosis
amyotrophic lateral sclerosis 1
  • als1
- elite association - COSMIC cancer census association via MalaCards
Search LY6E in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LY6E

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LY6E: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LY6E Gene

Publications for LY6E Gene

  1. RIG-E, a human homolog of the murine Ly-6 family, is induced by retinoic acid during the differentiation of acute promyelocytic leukemia cell. (PMID: 8650192) Mao M … Chen Z (Proceedings of the National Academy of Sciences of the United States of America 1996) 2 3 4 23
  2. Identification through bioinformatics of cDNAs encoding human thymic shared Ag-1/stem cell Ag-2. A new member of the human Ly-6 family. (PMID: 8757598) Capone MC … Zlotnik A (Journal of immunology (Baltimore, Md. : 1950) 1996) 2 3 4
  3. LY6E mediates an evolutionarily conserved enhancement of virus infection by targeting a late entry step. (PMID: 30190477) Mar KB … Schoggins JW (Nature communications 2018) 3 4
  4. Interferon-inducible LY6E Protein Promotes HIV-1 Infection. (PMID: 28130445) Yu J … Liu SL (The Journal of biological chemistry 2017) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for LY6E Gene

  • Signalway Proteins for LY6E

Sources for LY6E Gene