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LY9 lymphocyte antigen 9 [ Homo sapiens (human) ]

Gene ID: 4063, updated on 1-Jun-2020

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
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (160796112..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 peptidylprolyl isomerase A pseudogene 37 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 Functions

What'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_001033667.3NP_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_001261456.2NP_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_001261457.2NP_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
    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, ENST00000263285.11
    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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    160796112..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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