Aliases for LY6D Gene

Aliases for LY6D Gene

  • Lymphocyte Antigen 6 Family Member D 2 3 5
  • Lymphocyte Antigen 6 Complex, Locus D 2 3
  • Lymphocyte Antigen 6D 3 4
  • E48 Antigen 3 4
  • Ly-6D 3 4
  • E48 3 4

External Ids for LY6D Gene

Previous GeneCards Identifiers for LY6D Gene

  • GC08M143929
  • GC08M143863
  • GC08M139118
  • GC08M143866

Summaries for LY6D Gene

GeneCards Summary for LY6D Gene

LY6D (Lymphocyte Antigen 6 Family Member D) is a Protein Coding gene. Diseases associated with LY6D include Inferior Myocardial Infarction and Squamous Cell Carcinoma, Head And Neck. Among its related pathways are Metabolism of proteins and B Cell Development Pathways. An important paralog of this gene is LYNX1.

UniProtKB/Swiss-Prot Summary for LY6D Gene

  • May act as a specification marker at earliest stage specification of lymphocytes between B- and T-cell development. Marks the earliest stage of B-cell specification.

Additional gene information for LY6D Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LY6D Gene

Genomics for LY6D Gene

GeneHancer (GH) Regulatory Elements for LY6D Gene

Promoters and enhancers for LY6D Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J142787 Promoter/Enhancer 1.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 515.9 -2.0 -2020 3.1 ZNF217 ZFX ZIC2 RFX1 GATAD2B CTBP1 SIN3A ESRRA MYC ZNF592 LY6D LYNX1 SLURP1 PSCA ENSG00000253715 ENSG00000283686
GH08J142785 Enhancer 0.6 Ensembl dbSUPER 509.9 +0.7 691 0.2 ZFX ZIC2 ESRRA SAP130 GLIS1 ZNF687 LY6D ENSG00000253715 lnc-LYNX1-SLURP2-1
GH08J142786 Promoter/Enhancer 0.6 EPDnew dbSUPER 500.7 +0.0 33 0.1 ZBTB33 ENSG00000253715 LY6D lnc-LYNX1-SLURP2-1
GH08J142731 Promoter/Enhancer 1.3 FANTOM5 Ensembl ENCODE CraniofacialAtlas 10.9 +54.6 54646 1.9 MLLT1 NBN SPI1 NR2F2 HDGF TARDBP MTA2 IKZF1 ZNF512 TRIM22 piR-30791-094 LY6K SLURP1 THEM6 ENSG00000253715 LY6D GPIHBP1 LYNX1 ENSG00000253806
GH08J142814 Enhancer 1.1 FANTOM5 ENCODE 12.4 -29.1 -29106 2.8 ZNF217 CTCF ZIC2 CLOCK ZNF423 RFX1 KLF4 CHD1 RAD21 GATAD2B 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 LY6D on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LY6D

Top Transcription factor binding sites by QIAGEN in the LY6D gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • HNF-4alpha1
  • HNF-4alpha2
  • LCR-F1
  • LUN-1

Genomic Locations for LY6D Gene

Genomic Locations for LY6D Gene
1,711 bases
Minus strand
1,713 bases
Minus strand

Genomic View for LY6D Gene

Genes around LY6D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LY6D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LY6D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LY6D Gene

Proteins for LY6D Gene

  • Protein details for LY6D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Lymphocyte antigen 6D
    Protein Accession:
    Secondary Accessions:
    • B2R5F1
    • D3DWJ0
    • O43783
    • Q6GTV9
    • Q8TBD4
    • Q92933

    Protein attributes for LY6D Gene

    128 amino acids
    Molecular mass:
    13286 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH22806.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LY6D Gene

Post-translational modifications for LY6D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LY6D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LY6D Gene

Domains & Families for LY6D Gene

Gene Families for LY6D Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for LY6D Gene

  • CD59 antigen

Suggested Antigen Peptide Sequences for LY6D Gene

GenScript: Design optimal peptide antigens:
  • E48 antigen (LY6D_HUMAN)
genes like me logo Genes that share domains with LY6D: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LY6D Gene

Function for LY6D Gene

Molecular function for LY6D Gene

UniProtKB/Swiss-Prot Function:
May act as a specification marker at earliest stage specification of lymphocytes between B- and T-cell development. Marks the earliest stage of B-cell specification.
GENATLAS Biochemistry:
lymphocyte antigen complex,member D,homolog with the murine LY-6 family members of small cysteine-rich proteins,expressed in keratinocytes and squamous tumors cells
genes like me logo Genes that share phenotypes with LY6D: view

Animal Model Products

CRISPR Products

miRNA for LY6D Gene

miRTarBase miRNAs that target LY6D

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LY6D Gene

Localization for LY6D Gene

Subcellular locations from UniProtKB/Swiss-Prot for LY6D Gene

Cell membrane; Lipid-anchor, GPI-anchor.

Subcellular locations from

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 LY6D gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for LY6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IBA 21873635
GO:0016020 membrane TAS 7790363
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with LY6D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LY6D Gene

Pathways & Interactions for LY6D Gene

genes like me logo Genes that share pathways with LY6D: view

Pathways by source for LY6D Gene


Gene Ontology (GO) - Biological Process for LY6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,TAS --
GO:0030098 lymphocyte differentiation IEA,IBA 21873635
GO:0035634 response to stilbenoid IEA --
genes like me logo Genes that share ontologies with LY6D: view

No data available for SIGNOR curated interactions for LY6D Gene

Drugs & Compounds for LY6D Gene

No Compound Related Data Available

Transcripts for LY6D Gene

mRNA/cDNA for LY6D Gene

7 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LY6D Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c
SP1: - -
SP2: -

Relevant External Links for LY6D Gene

GeneLoc Exon Structure for

Expression for LY6D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LY6D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LY6D Gene

This gene is overexpressed in Esophagus - Mucosa (x22.4), Skin - Sun Exposed (Lower leg) (x9.0), Skin - Not Sun Exposed (Suprapubic) (x8.3), and Vagina (x4.9).

Protein differential expression in normal tissues from HIPED for LY6D Gene

This gene is overexpressed in Cervix (29.8), Saliva (16.7), Oral epithelium (7.9), and Esophagus (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LY6D Gene

Protein tissue co-expression partners for LY6D Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LY6D

SOURCE GeneReport for Unigene cluster for LY6D Gene:


mRNA Expression by UniProt/SwissProt for LY6D Gene:

Tissue specificity: Expressed exclusively at the outer cell surface of transitional epithelia and the keratinocyte of stratified squamous epithelia.

Evidence on tissue expression from TISSUES for LY6D Gene

  • Nervous system(4.1)
  • Skin(2.7)
genes like me logo Genes that share expression patterns with LY6D: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LY6D Gene

Orthologs for LY6D Gene

This gene was present in the common ancestor of mammals.

Orthologs for LY6D Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LY6D 31 30
  • 99.22 (n)
(Bos Taurus)
Mammalia LY6D 31 30
  • 76.36 (n)
(Canis familiaris)
Mammalia LOC609112 30
  • 75.26 (n)
LY6D 31
  • 63 (a)
(Mus musculus)
Mammalia Ly6d 17 31 30
  • 70.09 (n)
(Rattus norvegicus)
Mammalia Ly6d 30
  • 68.54 (n)
(Monodelphis domestica)
Mammalia LY6D 31
  • 49 (a)
Species where no ortholog for LY6D 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)
  • 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 LY6D Gene

Gene Tree for LY6D (if available)
Gene Tree for LY6D (if available)
Evolutionary constrained regions (ECRs) for LY6D: view image

Paralogs for LY6D Gene

Paralogs for LY6D Gene

genes like me logo Genes that share paralogs with LY6D: view

Variants for LY6D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LY6D Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs2572925 - p.Ala10Thr

Additional dbSNP identifiers (rs#s) for LY6D Gene

Structural Variations from Database of Genomic Variants (DGV) for LY6D Gene

Variant ID Type Subtype PubMed ID
esv2661137 CNV deletion 23128226
nsv1023021 CNV loss 25217958
nsv612714 CNV gain 21841781
nsv824758 CNV gain 20364138
nsv831486 CNV gain 17160897
nsv950004 CNV deletion 24416366

Variation tolerance for LY6D Gene

Residual Variation Intolerance Score: 70.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.73; 57.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LY6D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LY6D Gene

Disorders for LY6D Gene

MalaCards: The human disease database

(2) MalaCards diseases for LY6D Gene - From: DISEASES and Novoseek

Disorder Aliases PubMed IDs
inferior myocardial infarction
  • inferior wall myocardial infarction
squamous cell carcinoma, head and neck
  • hnscc
- elite association - COSMIC cancer census association via MalaCards
Search LY6D in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LY6D

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LY6D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LY6D Gene

Publications for LY6D Gene

  1. The human E48 antigen, highly homologous to the murine Ly-6 antigen ThB, is a GPI-anchored molecule apparently involved in keratinocyte cell-cell adhesion. (PMID: 7790363) Brakenhoff RH … van Dongen GA (The Journal of cell biology 1995) 2 3 4 23 54
  2. Characterization and mapping to human chromosome 8q24.3 of Ly-6-related gene 9804 encoding an apparent homologue of mouse TSA-1. (PMID: 9551972) Shan X … Palfree RG (Journal of immunology (Baltimore, Md. : 1950) 1998) 2 3 4 54
  3. 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 54
  4. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z … Henzel WJ (Protein science : a publication of the Protein Society 2004) 3 4 54
  5. A gain of novel tissue specificity in the human Ly-6 gene E48. (PMID: 9366413) Brakenhoff RH … Snow GB (Journal of immunology (Baltimore, Md. : 1950) 1997) 3 4 54

Products for LY6D Gene

Sources for LY6D Gene