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    LY9 lymphocyte antigen 9 [ Homo sapiens (human) ]

    Gene ID: 4063, updated on 16-Jun-2026
    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
    all
    Try the new Gene page
    Try the new Transcripts and proteins table
    See LY9 in Genome Data Viewer
    Location:
    1q23.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160796174..160828255)
    RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159933205..159965298)
    RS_2024_09 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

    Go to nucleotide: Graphics FASTA GenBank

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Related articles in PubMed

    1. SLAMF3 promotes Th17 differentiation and is reversed by iguratimod through JAK1/STAT3 pathway in primary Sjögren's syndrome. Hu P, et al. Int Immunopharmacol, 2024 Jan 5. PMID 38061117
    2. The SLAMF3 rs509749 polymorphism correlates with malignant potential in multiple myeloma. Ishibashi M, et al. Exp Hematol, 2020 Oct. PMID 32818503
    3. 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
    4. 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
    5. Viral CD229 (Ly9) homologs as new manipulators of host immunity. Angulo A, et al. J Leukoc Biol, 2019 May. PMID 30791129

    See all (41) 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)

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

    Review eQTL and phenotype association data in this region using PheGenI

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    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

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    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 immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of interleukin-17 production IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    Preferred Names
    T-lymphocyte surface antigen Ly-9
    Names
    SLAM family member 3
    cell surface molecule Ly-9
    signaling lymphocytic activation molecule 3

    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/TrEMBL
      A0ACI8RAJ8
      Related
      ENSP00000357016.5, ENST00000368037.10
      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
      A0ACI8PR60, 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
      UniProtKB/TrEMBL
      A0ACI8PR60
      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_2025_08

    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

      UniProtKB/TrEMBL
      A0ACI8PR60
      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

      UniProtKB/TrEMBL
      A0ACI8RAJ8
      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

      UniProtKB/TrEMBL
      A0ACI8RAJ8

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

      UniProtKB/TrEMBL
      A0ACI8PR60

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

      UniProtKB/TrEMBL
      A0ACI8PR60, A0ACI8R2L6
      Related
      ENSP00000543909.1, ENST00000873850.1

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

      UniProtKB/TrEMBL
      A0ACI8PR60

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

      UniProtKB/TrEMBL
      A0ACI8R4D6, A0ACI8RAJ8
      Related
      ENSP00000543907.1, ENST00000873848.1

    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

      UniProtKB/TrEMBL
      A0ACI8RAJ8

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

      UniProtKB/TrEMBL
      A0ACI8RAJ8

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

      UniProtKB/TrEMBL
      A0ACI8RYK1

    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

      UniProtKB/TrEMBL
      A0ACI8PR60

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

      UniProtKB/TrEMBL
      A0ACI8RAJ8

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

      UniProtKB/TrEMBL
      A0ACI8RAJ8

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

      UniProtKB/TrEMBL
      A0ACI8PR60

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

      UniProtKB/TrEMBL
      A0ACI8PR60, A0ACI8R2L6

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

      UniProtKB/TrEMBL
      A0ACI8PR60

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

      UniProtKB/TrEMBL
      A0ACI8R4D6, A0ACI8RAJ8

    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

      UniProtKB/TrEMBL
      A0ACI8RAJ8

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

      UniProtKB/TrEMBL
      A0ACI8RAJ8

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

      UniProtKB/TrEMBL
      A0ACI8RYK1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HBG7.3 GenPept UniProtKB/Swiss-Prot:Q9HBG7

    Gene LinkOut

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