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LY9 lymphocyte antigen 9 [ Homo sapiens (human) ]

Gene ID: 4063, updated on 5-Mar-2024

Summary

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Official Symbol
LY9provided by HGNC
Official Full Name
lymphocyte antigen 9provided by HGNC
Primary source
HGNC:HGNC:6730
See related
Ensembl:ENSG00000122224 MIM:600684; AllianceGenome:HGNC:6730
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
hly9; mLY9; CD229; SLAMF3
Summary
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]
Expression
Biased expression in lymph node (RPKM 6.9), spleen (RPKM 5.2) and 11 other tissues See more
Orthologs
mouse all
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Genomic context

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See LY9 in Genome Data Viewer
Location:
1q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160796174..160828255)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159933205..159965298)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160765964..160798045)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1952 Neighboring gene SLAM family member 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1955 Neighboring gene uncharacterized LOC105371470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:160751105-160751606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1958 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:160759219-160759411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1961 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:160771561-160771810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:160807002-160807516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1962 Neighboring gene CD244 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1963 Neighboring gene peptidylprolyl isomerase A pseudogene 37 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1964 Neighboring gene intelectin 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The SLAMF3 rs509749 polymorphism correlates with malignant potential in multiple myeloma. Ishibashi M, et al. Exp Hematol, 2020 Oct. PMID 32818503
  2. SLAMF3-Mediated Signaling via ERK Pathway Activation Promotes Aggressive Phenotypic Behaviors in Multiple Myeloma. Ishibashi M, et al. Mol Cancer Res, 2020 Apr. PMID 31974290
  3. Upregulation of SLAMF3 on human T cells is induced by palmitic acid through the STAT5-PI3K/Akt pathway and features the chronic inflammatory profiles of type 2 diabetes. Zhou T, et al. Cell Death Dis, 2019 Jul 22. PMID 31332162, Free PMC Article
  4. Viral CD229 (Ly9) homologs as new manipulators of host immunity. Angulo A, et al. J Leukoc Biol, 2019 May. PMID 30791129
  5. Evaluation of CD229 as a new alternative plasma cell gating marker in the flow cytometric immunophenotyping of monoclonal gammopathies. Tembhare PR, et al. Cytometry B Clin Cytom, 2018 May. PMID 29316178

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLAMF3 promotes Th17 differentiation and is reversed by iguratimod through JAK1/STAT3 pathway in primary Sjogren's syndrome.
    Title: SLAMF3 promotes Th17 differentiation and is reversed by iguratimod through JAK1/STAT3 pathway in primary Sjögren's syndrome.
  2. CD229 interacts with RASAL3 to activate RAS/ERK pathway in multiple myeloma proliferation.
    Title: CD229 interacts with RASAL3 to activate RAS/ERK pathway in multiple myeloma proliferation.
  3. SLAMF3-Mediated Signaling via ERK Pathway Activation Promotes Aggressive Phenotypic Behaviors in Multiple Myeloma.
    Title: SLAMF3-Mediated Signaling via ERK Pathway Activation Promotes Aggressive Phenotypic Behaviors in Multiple Myeloma.
  4. The SLAMF3 rs509749 polymorphism correlates with malignant potential in multiple myeloma.
    Title: The SLAMF3 rs509749 polymorphism correlates with malignant potential in multiple myeloma.
  5. SLAMF3 expression is upregulated on T cells from type 2 diabetes patients and associated with T-cell activation and cytokine production.
    Title: Upregulation of SLAMF3 on human T cells is induced by palmitic acid through the STAT5-PI3K/Akt pathway and features the chronic inflammatory profiles of type 2 diabetes.
  6. Viral Ly9 homologs are new manipulators of host immunity. (Review)
    Title: Viral CD229 (Ly9) homologs as new manipulators of host immunity.
  7. CD229 is a reliable new alternative PC-gating marker in routine laboratory practice.
    Title: Evaluation of CD229 as a new alternative plasma cell gating marker in the flow cytometric immunophenotyping of monoclonal gammopathies.
  8. Authors make a strong correlation between induced SLAMF3 overexpression and the specific loss of MRP-1 expression and its functionalities as a drugs resistance transporter.
    Title: Hepatocyte SLAMF3 reduced specifically the multidrugs resistance protein MRP-1 and increases HCC cells sensitization to anti-cancer drugs.
  9. the results presented here suggest that the tumor suppressor potential of SLAMF3 occurs through activation of Retinoblastoma protein that represses PLK1.
    Title: RB/PLK1-dependent induced pathway by SLAMF3 expression inhibits mitosis and control hepatocarcinoma cell proliferation.
  10. study showed CD229 is overexpressed on the malignant plasma cells of patients across all types of plasma cell dyscrasias including multiple myeloma; CD229 is also expressed on the surface of a fraction of cells carrying the phenotype of chemotherapy-resistant and myeloma-propagating cells within the patients' bone marrow
    Title: CD229 is expressed on the surface of plasma cells carrying an aberrant phenotype and chemotherapy-resistant precursor cells in multiple myeloma.
Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of LY9 PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 downregulates the expression of lymphocyte antigen 9 (LY9) in human B cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in T cell activation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in T-helper 17 cell lineage commitment IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of interleukin-17 production IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
T-lymphocyte surface antigen Ly-9
Names
SLAM family member 3
cell surface molecule Ly-9
signaling lymphocytic activation molecule 3

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001033667.3 → NP_001028839.1  T-lymphocyte surface antigen Ly-9 isoform b precursor

    See identical proteins and their annotated locations for NP_001028839.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. The encoded isoform (b) is significantly shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AI378426, BC064485, DC406206
    Consensus CDS
    CCDS30917.1
    UniProtKB/TrEMBL
    A0A0C4DFU4
    Related
    ENSP00000357018.2, ENST00000368039.2
    Conserved Domains (1) summary
    cd16842
    Location:57 → 151
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family

  2. NM_001261456.2 → NP_001248385.1  T-lymphocyte surface antigen Ly-9 isoform c precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    BC062589, BX090162, DC406206, L42621
    Consensus CDS
    CCDS65695.1
    UniProtKB/Swiss-Prot
    Q9HBG7
    Related
    ENSP00000357016.5, ENST00000368037.9
    Conserved Domains (2) summary
    cd05775
    Location:57 → 151
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    pfam13927
    Location:362 → 431
    Ig_3; Immunoglobulin domain

  3. NM_001261457.2 → NP_001248386.1  T-lymphocyte surface antigen Ly-9 isoform d precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
    Source sequence(s)
    BC027920, BC062589, BC121049, BX090162
    Consensus CDS
    CCDS65696.1
    UniProtKB/TrEMBL
    Q5VYH9
    Related
    ENSP00000376039.4, ENST00000392203.8
    Conserved Domains (2) summary
    cd05775
    Location:57 → 151
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    pfam13927
    Location:156 → 226
    Ig_3; Immunoglobulin domain

  4. NM_002348.4 → NP_002339.2  T-lymphocyte surface antigen Ly-9 isoform a precursor

    See identical proteins and their annotated locations for NP_002339.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AK292048, BC062589
    Consensus CDS
    CCDS30916.1
    UniProtKB/Swiss-Prot
    A8K7N3, Q14775, Q5VYI3, Q6P2J4, Q9H4N5, Q9HBG7, Q9NQ24
    Related
    ENSP00000263285.5, ENST00000263285.11
    Conserved Domains (2) summary
    cd05775
    Location:57 → 151
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    pfam13927
    Location:362 → 431
    Ig_3; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    160796174..160828255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509549.2 → XP_011507851.1  T-lymphocyte surface antigen Ly-9 isoform X1

    Conserved Domains (2) summary
    cd05775
    Location:104 → 198
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    pfam13927
    Location:409 → 478
    Ig_3; Immunoglobulin domain

  2. XM_017001299.2 → XP_016856788.1  T-lymphocyte surface antigen Ly-9 isoform X2

  3. XM_011509556.2 → XP_011507858.1  T-lymphocyte surface antigen Ly-9 isoform X6

    Conserved Domains (2) summary
    cd05775
    Location:104 → 198
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    pfam13927
    Location:203 → 273
    Ig_3; Immunoglobulin domain

  4. XM_011509560.2 → XP_011507862.1  T-lymphocyte surface antigen Ly-9 isoform X8

    Conserved Domains (2) summary
    cd05775
    Location:104 → 198
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    pfam13927
    Location:203 → 273
    Ig_3; Immunoglobulin domain

  5. XM_047420764.1 → XP_047276720.1  T-lymphocyte surface antigen Ly-9 isoform X10

  6. XM_017001301.2 → XP_016856790.1  T-lymphocyte surface antigen Ly-9 isoform X3

  7. XM_047420753.1 → XP_047276709.1  T-lymphocyte surface antigen Ly-9 isoform X4

  8. XM_047420762.1 → XP_047276718.1  T-lymphocyte surface antigen Ly-9 isoform X9

  9. XM_047420765.1 → XP_047276721.1  T-lymphocyte surface antigen Ly-9 isoform X11

  10. XM_047420771.1 → XP_047276727.1  T-lymphocyte surface antigen Ly-9 isoform X13

  11. XM_047420755.1 → XP_047276711.1  T-lymphocyte surface antigen Ly-9 isoform X5

  12. XM_017001303.2 → XP_016856792.1  T-lymphocyte surface antigen Ly-9 isoform X7

  13. XM_017001304.2 → XP_016856793.1  T-lymphocyte surface antigen Ly-9 isoform X12

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    159933205..159965298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336625.1 → XP_054192600.1  T-lymphocyte surface antigen Ly-9 isoform X1

  2. XM_054336626.1 → XP_054192601.1  T-lymphocyte surface antigen Ly-9 isoform X2

  3. XM_054336630.1 → XP_054192605.1  T-lymphocyte surface antigen Ly-9 isoform X6

  4. XM_054336632.1 → XP_054192607.1  T-lymphocyte surface antigen Ly-9 isoform X8

  5. XM_054336634.1 → XP_054192609.1  T-lymphocyte surface antigen Ly-9 isoform X10

  6. XM_054336627.1 → XP_054192602.1  T-lymphocyte surface antigen Ly-9 isoform X3

  7. XM_054336628.1 → XP_054192603.1  T-lymphocyte surface antigen Ly-9 isoform X4

  8. XM_054336633.1 → XP_054192608.1  T-lymphocyte surface antigen Ly-9 isoform X9

  9. XM_054336635.1 → XP_054192610.1  T-lymphocyte surface antigen Ly-9 isoform X11

  10. XM_054336637.1 → XP_054192612.1  T-lymphocyte surface antigen Ly-9 isoform X13

  11. XM_054336629.1 → XP_054192604.1  T-lymphocyte surface antigen Ly-9 isoform X5

  12. XM_054336631.1 → XP_054192606.1  T-lymphocyte surface antigen Ly-9 isoform X7

  13. XM_054336636.1 → XP_054192611.1  T-lymphocyte surface antigen Ly-9 isoform X12

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HBG7.3 GenPept UniProtKB/Swiss-Prot:Q9HBG7

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