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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
  • E48 Antigen 3 4
  • Ly-6D 3 4
  • E48 3 4
  • Lymphocyte Antigen 6D 3

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 Squamous Cell Carcinoma, Head And Neck. Among its related pathways are B Cell Development Pathways and Post-translational modification- synthesis of GPI-anchored proteins.

UniProtKB/Swiss-Prot 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.

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LY6D Gene

Genomics for LY6D Gene

Regulatory Elements for LY6D Gene

Enhancers for LY6D 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
GH08G142787 1.4 FANTOM5 ENCODE dbSUPER 15.9 -1.9 -1905 2.9 HDGF PKNOX1 NFIB SIN3A ZBTB7B ZNF207 FOS ZNF592 MBD2 RAD51 LYNX1 LY6D SLURP1 PSCA ENSG00000283686
GH08G142814 1.6 FANTOM5 Ensembl ENCODE 12.4 -29.1 -29107 2.8 HDGF PKNOX1 SIN3A YBX1 ZBTB7B ZNF121 GLIS2 ELK1 ZNF207 ZNF143 LYNX1 JRK LY6D ZNF696 TIGD5 ZNF623 LOC101928087 GPIHBP1 LY6E GLI4
GH08G142731 1.3 FANTOM5 Ensembl ENCODE 10.9 +54.4 54446 1.5 CTCF HDGF GTF2F1 PKNOX1 ESRRA SIN3A YBX1 GATA3 CTBP1 RELB LY6K SLURP1 THEM6 ENSG00000253715 LY6D GPIHBP1 LYNX1 PIR37820 ENSG00000253806
GH08G142990 1.3 FANTOM5 ENCODE 10.7 -206.4 -206408 4.4 HDGF ATF1 PKNOX1 ARNT TCF12 ZNF766 ELK1 KLF13 ZNF662 ZNF491 ZNF623 C8orf31 LOC100133669 CYP11B2 LY6D ENSG00000253715 TSNARE1 LYPD2 CDC42P3 LOC105375794
GH08G143029 1 ENCODE dbSUPER 11.6 -242.9 -242867 0.2 CTCF PKNOX1 SAP130 SIN3A RAD21 FOXK2 ZNF207 SMC3 ZNF143 DEK LOC100133669 ENSG00000253715 LY6D LY6H SLURP1 GC08P143031 PIR51584
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LY6D on UCSC Golden Path with GeneCards custom track

Genomic Location for LY6D Gene

Chromosome:
8
Start:
142,784,880 bp from pter
End:
142,786,592 bp from pter
Size:
1,713 bases
Orientation:
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:
    Q14210-LY6D_HUMAN
    Recommended name:
    Lymphocyte antigen 6D
    Protein Accession:
    Q14210
    Secondary Accessions:
    • B2R5F1
    • D3DWJ0
    • O43783
    • Q6GTV9
    • Q8TBD4
    • Q92933

    Protein attributes for LY6D Gene

    Size:
    128 amino acids
    Molecular mass:
    13286 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • 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

Protein Domains for LY6D Gene

Suggested Antigen Peptide Sequences for LY6D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

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

Function for LY6D Gene

Molecular function for LY6D Gene

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
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.
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

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LY6D

No data available for Enzyme Numbers (IUBMB) , 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

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 LY6D gene
Compartment Confidence
plasma membrane 5
extracellular 5

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 IEA,IBA --
GO:0016020 membrane TAS 7790363
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with LY6D: view

Pathways & Interactions for LY6D Gene

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

Pathways by source for LY6D Gene

Interacting Proteins for LY6D Gene

Gene Ontology (GO) - Biological Process for LY6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006501 C-terminal protein lipidation TAS --
GO:0007155 cell adhesion TAS,IEA --
GO:0030098 lymphocyte differentiation IEA --
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

Unigene Clusters for LY6D Gene

Lymphocyte antigen 6 complex, locus D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LY6D

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

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c
SP1: - -
SP2: -
SP3:

Relevant External Links for LY6D Gene

GeneLoc Exon Structure for
LY6D
ECgene alternative splicing isoforms for
LY6D

Expression for LY6D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for LY6D Gene



Protein tissue co-expression partners for LY6D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LY6D Gene:

LY6D

SOURCE GeneReport for Unigene cluster for LY6D Gene:

Hs.415762

mRNA Expression by UniProt/SwissProt for LY6D Gene:

Q14210-LY6D_HUMAN
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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia LY6D 34 35
  • 99.22 (n)
cow
(Bos Taurus)
Mammalia LY6D 34 35
  • 76.36 (n)
dog
(Canis familiaris)
Mammalia LOC609112 34
  • 75.26 (n)
LY6D 35
  • 63 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ly6d 34 16 35
  • 70.09 (n)
rat
(Rattus norvegicus)
Mammalia Ly6d 34
  • 68.54 (n)
oppossum
(Monodelphis domestica)
Mammalia LY6D 35
  • 49 (a)
OneToOne
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

ENSEMBL:
Gene Tree for LY6D (if available)
TreeFam:
Gene Tree for LY6D (if available)

Paralogs for LY6D Gene

No data available for Paralogs for LY6D Gene

Variants for LY6D Gene

Sequence variations from dbSNP and Humsavar for LY6D Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs1000890224 -- 142,784,508(+) TGGCT(C/T)CAAAG downstream-variant-500B
rs1000946080 -- 142,787,700(+) CTGCT(C/T)AGCCC upstream-variant-2KB
rs1001495164 -- 142,785,701(+) GAGGG(A/G)GTCCG intron-variant
rs1003763494 -- 142,786,721(+) CCCCC(A/G)CCAGG upstream-variant-2KB
rs1003836444 -- 142,786,583(+) TGGGC(A/G)GGGGT utr-variant-5-prime

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)

Relevant External Links for LY6D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LY6D

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

Disorders for LY6D Gene

MalaCards: The human disease database

(1) MalaCards diseases for LY6D Gene - From: DISEASES, Novoseek, and GeneCards

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

Relevant External Links for LY6D

Genetic Association Database (GAD)
LY6D
Human Genome Epidemiology (HuGE) Navigator
LY6D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LY6D
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 R.H. … van Dongen G.A.M.S. (J. Cell Biol. 1995) 2 3 4 22 64
  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 R.G.E. (J. Immunol. 1998) 2 3 4 64
  3. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z. … Henzel W.J. (Protein Sci. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. A gain of novel tissue specificity in the human Ly-6 gene E48. (PMID: 9366413) Brakenhoff R.H. … Snow G.B. (J. Immunol. 1997) 3 4 64

Products for LY6D Gene

Sources for LY6D Gene

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