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    LY9 lymphocyte antigen 9 [ Homo sapiens (human) ]

    Gene ID: 4063, updated on 7-Dec-2018

    Summary

    Official Symbol
    LY9provided by HGNC
    Official Full Name
    lymphocyte antigen 9provided by HGNC
    Primary source
    HGNC:HGNC:6730
    See related
    Ensembl:ENSG00000122224 MIM:600684
    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

    Genomic context

    See LY9 in Genome Data Viewer
    Location:
    1q23.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (160796074..160828256)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160765864..160798045)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SLAM family member 7 Neighboring gene uncharacterized LOC105371470 Neighboring gene CD244 molecule Neighboring gene intelectin 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    T-helper 17 cell lineage commitment IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-17 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    cell surface IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    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)

    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_001033667.2NP_001028839.1  T-lymphocyte surface antigen Ly-9 isoform b

      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/Swiss-Prot
      Q9HBG7
      UniProtKB/TrEMBL
      A0A0C4DFU4
      Related
      ENSP00000357018.2, ENST00000368039.2
      Conserved Domains (1) summary
      cd16842
      Location:57151
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family
    2. NM_001261456.1NP_001248385.1  T-lymphocyte surface antigen Ly-9 isoform c

      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:57151
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:362431
      Ig_3; Immunoglobulin domain
    3. NM_001261457.1NP_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, DC406206
      Consensus CDS
      CCDS65696.1
      UniProtKB/TrEMBL
      Q05CA2, Q0VAI0, Q5VYH9
      Related
      ENSP00000376039.4, ENST00000392203.8
      Conserved Domains (2) summary
      cd05775
      Location:57151
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:156226
      Ig_3; Immunoglobulin domain
    4. NM_002348.4NP_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
      Q9HBG7
      Related
      ENSP00000263285.5, ENST00000263285.10
      Conserved Domains (2) summary
      cd05775
      Location:57151
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:362431
      Ig_3; Immunoglobulin domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      160796074..160828256
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001300.1XP_016856789.1  T-lymphocyte surface antigen Ly-9 isoform X8

    2. XM_017001304.1XP_016856793.1  T-lymphocyte surface antigen Ly-9 isoform X13

    3. XM_017001301.1XP_016856790.1  T-lymphocyte surface antigen Ly-9 isoform X9

    4. XM_011509550.1XP_011507852.1  T-lymphocyte surface antigen Ly-9 isoform X4

      Conserved Domains (2) summary
      cd05775
      Location:104198
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:409478
      Ig_3; Immunoglobulin domain
    5. XM_011509548.1XP_011507850.1  T-lymphocyte surface antigen Ly-9 isoform X2

      Conserved Domains (2) summary
      cd05775
      Location:104198
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:409478
      Ig_3; Immunoglobulin domain
    6. XM_011509549.1XP_011507851.1  T-lymphocyte surface antigen Ly-9 isoform X3

      Conserved Domains (2) summary
      cd05775
      Location:104198
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:409478
      Ig_3; Immunoglobulin domain
    7. XM_011509552.1XP_011507854.1  T-lymphocyte surface antigen Ly-9 isoform X7

      Conserved Domains (2) summary
      cd05775
      Location:104198
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:409478
      Ig_3; Immunoglobulin domain
    8. XM_017001299.1XP_016856788.1  T-lymphocyte surface antigen Ly-9 isoform X6

    9. XM_011509556.1XP_011507858.1  T-lymphocyte surface antigen Ly-9 isoform X11

      Conserved Domains (2) summary
      cd05775
      Location:104198
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:203273
      Ig_3; Immunoglobulin domain
    10. XM_011509560.1XP_011507862.1  T-lymphocyte surface antigen Ly-9 isoform X14

      Conserved Domains (2) summary
      cd05775
      Location:104198
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:203273
      Ig_3; Immunoglobulin domain
    11. XM_017001297.1XP_016856786.1  T-lymphocyte surface antigen Ly-9 isoform X1

    12. XM_017001298.1XP_016856787.1  T-lymphocyte surface antigen Ly-9 isoform X5

    13. XM_017001302.1XP_016856791.1  T-lymphocyte surface antigen Ly-9 isoform X10

    14. XM_017001303.1XP_016856792.1  T-lymphocyte surface antigen Ly-9 isoform X12

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