Ly9 lymphocyte antigen 9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ly9provided by MGI
Official Full Name: lymphocyte antigen 9provided by MGI
Primary source: MGI:MGI:96885
See related: Ensembl:ENSMUSG00000004707 AllianceGenome:MGI:96885
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ly-9; T100; CD229; Lgp100; SLAMF3
Summary: Predicted to be involved in T-helper 17 cell lineage commitment and positive regulation of interleukin-17 production. Predicted to act upstream of or within adaptive immune response; cell adhesion; and innate immune response. Located in cell surface. Orthologous to human LY9 (lymphocyte antigen 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in spleen adult (RPKM 10.3), thymus adult (RPKM 8.8) and 8 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 H3; 1 79.54 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (171416172..171434917, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (171588613..171607410, complement)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SLAMF3 and SLAMF4 are immune checkpoints that constrain macrophage phagocytosis of hematopoietic tumors.
Title: SLAMF3 and SLAMF4 are immune checkpoints that constrain macrophage phagocytosis of hematopoietic tumors.
The Checkpoint Regulator SLAMF3 Preferentially Prevents Expansion of Auto-Reactive B Cells Generated by Graft-vs.-Host Disease.
Title: The Checkpoint Regulator SLAMF3 Preferentially Prevents Expansion of Auto-Reactive B Cells Generated by Graft-vs.-Host Disease.
The authors show that Ly9 influences Invariant natural killer T cell lineage differentiation. Furthermore, treatment of wild-type mice with an agonistic monoclonal antibody directed against Ly9 impaired IL-4 and IFN-gamma production and reduced by half the number of spleen iNKT cells, with a significant decrease in the proportion of NKT2 cells.
Title: Ly9 (SLAMF3) receptor differentially regulates iNKT cell development and activation in mice.
SLAMF3 is an inhibitor of hepatocellular carcinoma cell proliferation and tumor progression.
Title: Identification of SLAMF3 (CD229) as an inhibitor of hepatocellular carcinoma cell proliferation and tumour progression.
Ly9/CD229 cell surface receptor emerges as a uniquely important element for modulating innate T cell function, acting as an inhibitory molecule that regulates invariant natural killer (NK)T cell development and innate-like CD8 T cell expansion.
Title: Cutting edge: Ly9 (CD229), a SLAM family receptor, negatively regulates the development of thymic innate memory-like CD8+ T and invariant NKT cells.
Data show that defective tolerance was observed only in Fcgr2b-deficient mice with autoimmune-type Slam family genes, indicating that epistatic effects of both genes are involved.
Title: Susceptibility loci for the defective foreign protein-induced tolerance in New Zealand Black mice: implication of epistatic effects of Fcgr2b and Slam family genes.
CD229 is a pan-lymphocyte marker and indicate that mAbs against CD229 are able to down-modulate T-cell activation.
Title: Characterization of mouse CD229 (Ly9), a leukocyte cell surface molecule of the CD150 (SLAM) family.
CD229 is a self-ligand, interacting through its N-terminal V-like domain which contains three amino acid residues critical for the homophilic binding interaction.
Title: CD229 (Ly9) lymphocyte cell surface receptor interacts homophilically through its N-terminal domain and relocalizes to the immunological synapse.
mouse novel Ly9 is a new member of the expanding CD150 family of cell surface receptors
Title: Mouse novel Ly9: a new member of the expanding CD150 (SLAM) family of leukocyte cell-surface receptors.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI893573 (e-PCR)
- UniSTS:178507

G42060 (e-PCR)
- UniSTS:105078

M84412 (e-PCR)
- UniSTS:158882

Ly9 (e-PCR), detects polymorphism
- UniSTS:143805

Gene Ontology Provided by MGI

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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adaptive immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within innate immune response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of interleukin-17 production	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info

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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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)

NM_001277968.2 → NP_001264897.1 T-lymphocyte surface antigen Ly-9 isoform 2

Status: VALIDATED

Source sequence(s)

AC083892

Consensus CDS

CCDS69978.1

UniProtKB/TrEMBL

E9PX73, Q8C2D4

Related

ENSMUSP00000004827.8, ENSMUST00000004827.14

Conserved Domains (2) summary

pfam13927
Location:46 → 116

Ig_3; Immunoglobulin domain

cl11960
Location:148 → 246

Ig; Immunoglobulin domain
NM_008534.4 → NP_032560.2 T-lymphocyte surface antigen Ly-9 isoform 1 precursor

See identical proteins and their annotated locations for NP_032560.2

Status: VALIDATED

Source sequence(s)

AC083892

Consensus CDS

CCDS35779.1

UniProtKB/Swiss-Prot

Q01965, Q9ES29, Q9ES35, Q9ES36

UniProtKB/TrEMBL

Q4VBG4

Related

ENSMUSP00000069319.8, ENSMUST00000068878.14

Conserved Domains (4) 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

smart00410
Location:52 → 129

IG_like; Immunoglobulin like

pfam13927
Location:156 → 226

Ig_3; Immunoglobulin domain

cl11960
Location:258 → 356

Ig; Immunoglobulin domain