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Aliases for LY9 Gene

Aliases for LY9 Gene

  • Lymphocyte Antigen 9 2 3 4 5
  • Signaling Lymphocytic Activation Molecule 3 3 4
  • Cell Surface Molecule Ly-9 3 4
  • SLAM Family Member 3 3 4
  • SLAMF3 3 4
  • CD229 Antigen 4
  • CD229 3
  • Hly9 3
  • MLY9 3

External Ids for LY9 Gene

Previous GeneCards Identifiers for LY9 Gene

  • GC01P158558
  • GC01P156498
  • GC01P157543
  • GC01P157982
  • GC01P157579
  • GC01P159032
  • GC01P132122

Summaries for LY9 Gene

Entrez Gene Summary for LY9 Gene

  • LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008]

GeneCards Summary for LY9 Gene

LY9 (Lymphocyte Antigen 9) is a Protein Coding gene. Diseases associated with LY9 include systemic lupus erythematosus. Among its related pathways are Hematopoietic Stem Cell Differentiation Pathways and Lineage-specific Markers. GO annotations related to this gene include receptor activity. An important paralog of this gene is SLAMF6.

UniProtKB/Swiss-Prot for LY9 Gene

  • Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. May participate in adhesion reactions between T lymphocytes and accessory cells by homophilic interaction. Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). May be involved in the maintenance of peripheral cell tolerance by serving as a negative regulator of the immune response. May disable autoantibody responses and inhibit IFN-gamma secretion by CD4(+) T-cells. May negatively regulate the size of thymic innate CD8(+) T-cells and the development of invariant natural killer T (iNKT) cells (By similarity).

Gene Wiki entry for LY9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LY9 Gene

Genomics for LY9 Gene

Regulatory Elements for LY9 Gene

Promoters for LY9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LY9 on UCSC Golden Path with GeneCards custom track

Genomic Location for LY9 Gene

Chromosome:
1
Start:
160,796,074 bp from pter
End:
160,828,261 bp from pter
Size:
32,188 bases
Orientation:
Plus strand

Genomic View for LY9 Gene

Genes around LY9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LY9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LY9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LY9 Gene

Proteins for LY9 Gene

  • Protein details for LY9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBG7-LY9_HUMAN
    Recommended name:
    T-lymphocyte surface antigen Ly-9
    Protein Accession:
    Q9HBG7
    Secondary Accessions:
    • A8K7N3
    • Q14775
    • Q5VYI3
    • Q6P2J4
    • Q9H4N5
    • Q9NQ24

    Protein attributes for LY9 Gene

    Size:
    655 amino acids
    Molecular mass:
    72139 Da
    Quaternary structure:
    • Interacts with SH2D1A, SH2D1B and INPP5D. Interacts (via phosphorylated cytoplasmic domain) with PTPN11; the interaction is blocked by SH2D1A.
    SequenceCaution:
    • Sequence=CAH72360.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAH73509.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for LY9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LY9 Gene

Proteomics data for LY9 Gene at MOPED

Post-translational modifications for LY9 Gene

  • Glycosylation at Asn 68, Asn 95, Asn 120, Asn 169, Asn 173, Asn 285, Asn 413, and Asn 424
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for LY9 Gene

Domains & Families for LY9 Gene

Protein Domains for LY9 Gene

Graphical View of Domain Structure for InterPro Entry

Q9HBG7

UniProtKB/Swiss-Prot:

LY9_HUMAN :
  • The ITSMs (immunoreceptor tyrosine-based switch motifs) with the consensus sequence T-X-Y-X-X-[VI] present in SLAM family receptors have overlapping specificity for activating and inhibitory SH2 domain-containing binding partners. Especially they mediate the interaction with the SH2 domain of SH2D1A and SH2D1B. A three-pronged mechanism is proposed involving threonine (position -2), phosphorylated tyrosine (position 0) and valine/isoleucine (position +3).
Domain:
  • The ITSMs (immunoreceptor tyrosine-based switch motifs) with the consensus sequence T-X-Y-X-X-[VI] present in SLAM family receptors have overlapping specificity for activating and inhibitory SH2 domain-containing binding partners. Especially they mediate the interaction with the SH2 domain of SH2D1A and SH2D1B. A three-pronged mechanism is proposed involving threonine (position -2), phosphorylated tyrosine (position 0) and valine/isoleucine (position +3).
  • Contains 2 Ig-like C2-type (immunoglobulin-like) domains.
  • Contains 2 Ig-like V-type (immunoglobulin-like) domains.
genes like me logo Genes that share domains with LY9: view

Function for LY9 Gene

Molecular function for LY9 Gene

GENATLAS Biochemistry:
lymphocyte surface antigen,murine Ly-9,immunoglobulin superfamily,putatively involved in adhesion reaction between T lymphocyte and accessory cells
UniProtKB/Swiss-Prot Function:
Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. May participate in adhesion reactions between T lymphocytes and accessory cells by homophilic interaction. Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). May be involved in the maintenance of peripheral cell tolerance by serving as a negative regulator of the immune response. May disable autoantibody responses and inhibit IFN-gamma secretion by CD4(+) T-cells. May negatively regulate the size of thymic innate CD8(+) T-cells and the development of invariant natural killer T (iNKT) cells (By similarity).

Gene Ontology (GO) - Molecular Function for LY9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with LY9: view
genes like me logo Genes that share phenotypes with LY9: view

Animal Models for LY9 Gene

MGI Knock Outs for LY9:

Animal Model Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LY9 Gene

Localization for LY9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LY9 Gene

Membrane; Single-pass type I membrane protein. Cell membrane.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LY9 Gene COMPARTMENTS Subcellular localization image for LY9 gene
Compartment Confidence
plasma membrane 5

No data available for Gene Ontology (GO) - Cellular Components for LY9 Gene

Pathways & Interactions for LY9 Gene

genes like me logo Genes that share pathways with LY9: view

Pathways by source for LY9 Gene

Interacting Proteins for LY9 Gene

Selected Interacting proteins: Q9HBG7-LY9_HUMAN for LY9 Gene via I2D

Gene Ontology (GO) - Biological Process for LY9 Gene

None

No data available for SIGNOR curated interactions for LY9 Gene

Drugs & Compounds for LY9 Gene

(1) Drugs for LY9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with LY9: view

Transcripts for LY9 Gene

Unigene Clusters for LY9 Gene

Lymphocyte antigen 9:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LY9 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b · 14c ^ 15a ·
SP1: - - - - - -
SP2: - - - - - - -
SP3: - -
SP4: -
SP5: -
SP6: - -
SP7: - - - -
SP8: - -
SP9: - - - - -
SP10: - - -
SP11: - - - - -

ExUns: 15b ^ 16
SP1:
SP2:
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for LY9 Gene

GeneLoc Exon Structure for
LY9
ECgene alternative splicing isoforms for
LY9

Expression for LY9 Gene

mRNA expression in normal human tissues for LY9 Gene

mRNA differential expression in normal tissues according to GTEx for LY9 Gene

This gene is overexpressed in Whole Blood (x17.1) and Spleen (x8.6).

Protein differential expression in normal tissues from HIPED for LY9 Gene

This gene is overexpressed in CD4 Tcells (27.6), Peripheral blood mononuclear cells (23.6), and CD8 Tcells (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for LY9 Gene



SOURCE GeneReport for Unigene cluster for LY9 Gene Hs.403857

mRNA Expression by UniProt/SwissProt for LY9 Gene

Q9HBG7-LY9_HUMAN
Tissue specificity: Increased surface expression on T-cells of systemic lupus erythematosus (SLE) patients.
genes like me logo Genes that share expression patterns with LY9: view

Protein tissue co-expression partners for LY9 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for LY9 Gene

Orthologs for LY9 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LY9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LY9 35
  • 98.52 (n)
  • 97.25 (a)
LY9 36
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LY9 36
  • 61 (a)
OneToOne
LY9 35
  • 76.45 (n)
  • 61.83 (a)
dog
(Canis familiaris)
Mammalia LY9 35
  • 76.3 (n)
  • 60.48 (a)
LY9 36
  • 59 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ly9 36
  • 56 (a)
OneToOne
Ly9 16
Ly9 35
  • 71.22 (n)
  • 55.83 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia LY9 36
  • 33 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ly9 35
  • 70.98 (n)
  • 54.6 (a)
Species with no ortholog for LY9:
  • 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)
  • 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 LY9 Gene

ENSEMBL:
Gene Tree for LY9 (if available)
TreeFam:
Gene Tree for LY9 (if available)

Paralogs for LY9 Gene

Paralogs for LY9 Gene

genes like me logo Genes that share paralogs with LY9: view

Variants for LY9 Gene

Sequence variations from dbSNP and Humsavar for LY9 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs509749 - 160,823,770(+) ACACC(A/G)TGTAT reference, missense
rs65463 -- 160,803,291(-) aaaaa(A/T)ttttt intron-variant
rs489156 -- 160,820,879(-) caccg(C/T)gtcca intron-variant
rs505728 -- 160,824,795(+) taaca(C/T)ggtga intron-variant
rs516509 -- 160,820,210(+) TAAAC(C/T)TCAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LY9 Gene

Variant ID Type Subtype PubMed ID
nsv831714 CNV Gain 17160897
esv2671152 CNV Deletion 23128226
nsv825087 CNV Loss 20364138
esv2662152 CNV Deletion 23128226
dgv84n67 CNV Loss 20364138

Variation tolerance for LY9 Gene

Residual Variation Intolerance Score: 89.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.55; 44.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LY9 Gene

HapMap Linkage Disequilibrium report
LY9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LY9 Gene

Disorders for LY9 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LY9 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
systemic lupus erythematosus
  • lupus nephritis
- elite association - COSMIC cancer census association via MalaCards
Search LY9 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LY9

Genetic Association Database (GAD)
LY9
Human Genome Epidemiology (HuGE) Navigator
LY9
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LY9
genes like me logo Genes that share disorders with LY9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LY9 Gene

Publications for LY9 Gene

  1. Isolation and characterization of cDNA clones for Humly9: the human homologue of mouse Ly9. (PMID: 8537117) Sandrin M.S. … McKenzie I.F. (Immunogenetics 1996) 2 3 4 67
  2. Mouse novel Ly9: a new member of the expanding CD150 (SLAM) family of leukocyte cell-surface receptors. (PMID: 12242590) Tovar V. … Engel P. (Immunogenetics 2002) 3 23
  3. Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells. (PMID: 11689425) Morra M. … Terhorst C. (EMBO J. 2001) 3 23
  4. Physical and genetic linkage of the genes encoding Ly-9 and CD48 on mouse and human chromosomes 1. (PMID: 7797269) Kingsmore S.F. … Seldin M.F. (Immunogenetics 1995) 2 3
  5. Identification of SLAMF3 (CD229) as an Inhibitor of Hepatocellular Carcinoma Cell Proliferation and Tumour Progression. (PMID: 24376606) Marcq I. … Bouhlal H. (PLoS ONE 2013) 3

Products for LY9 Gene

Sources for LY9 Gene

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