About   Help   FAQ
Ly9 Gene Detail
Summary
  • Symbol
    Ly9
  • Name
    lymphocyte antigen 9
  • Synonyms
    CD229, Lgp100, SLAMF3, T100
  • Feature Type
    protein coding gene
  • IDs
    MGI:96885
    NCBI Gene: 17085
  • Alliance
    genome feature page
  • Transcription Start Sites
    5 TSS
  • Candidate for QTL
    1 QTL
Location &
Maps
more
  • Sequence Map
    Chr1:171416172-171434917 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 1, 79.54 cM
  • Mapping Data
    45 experiments
Strain
Comparison
more
  • SNPs within 2kb
    521 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_96885
 protein coding gene Chr1:171416172-171434978 (-)
129S1/SvImJ ENSMUSG00200045181
 protein coding gene Chr1:169343547-169362296 (-)
A/J ENSMUSG00195047615
 protein coding gene Chr1:168664047-168682828 (-)
AKR/J ENSMUSG00220029164
 protein coding gene Chr1:168387702-168406463 (-)
BALB/cJ ENSMUSG00180041766
 protein coding gene Chr1:168983854-169002601 (-)
C3H/HeJ ENSMUSG00175038727
 protein coding gene Chr1:168994871-169013624 (-)
C57BL/6NJ ENSMUSG00215043739
 protein coding gene Chr1:168373312-168392101 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0014876
 protein coding gene Chr1:161879043-161897071 (-)
CAST/EiJ ENSTCUG00005045179
 protein coding gene Chr1:166938741-166957042 (-)
CBA/J ENSMUSG00210037175
 protein coding gene Chr1:168862071-168880835 (-)
DBA/2J ENSMUSG00185027942
 protein coding gene Chr1:173164172-173182933 (-)
FVB/NJ ENSMUSG00205034285
 protein coding gene Chr1:167822910-167841669 (-)
JF1/MsJ ENSUMUG00000008434
 protein coding gene Chr1:172089006-172107779 (-)
LP/J ENSMUSG00230024288
 protein coding gene Chr1:172760615-172779366 (-)
NOD/ShiLtJ ENSMUSG00190035091
 protein coding gene Chr1:168670483-168689242 (-)
NZO/HlLtJ ENSMUSG00225004473
 protein coding gene Chr1:176347522-176366289 (-)
PWK/PhJ ENSLUMG00010031765
 protein coding gene Chr1:167630700-167649469 (-)
SPRET/EiJ ENSMSPG00010044383
 protein coding gene Chr1:170990766-171008142 (-)
WSB/EiJ ENSIUOG00005038222
 protein coding gene Chr1:168010119-168028866 (-)



Homology
more
  • Human Ortholog
    LY9, lymphocyte antigen 9
  • Vertebrate Orthologs
    2
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    LY9, lymphocyte antigen 9
  • Synonyms
    CD229, hly9, mLY9, SLAMF3
  • Links
    NCBI Gene ID: 4063
    UniProt: Q9HBG7

  • Chr Location
    1q23.3; chr1:160796074-160828483 (+)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    3 phenotypes from 1 allele in 1 genetic background
    16 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
This locus controls an antigen on thymocytes, lymphocytes and bone marrow cells. The a allele determines Ly9.1 antigen in A/J, 129/Re, BALB/c and C3H/He; the b allele determines antigen Ly9.2 in the C57 family of strains, HTI/Go, MA/My, F/St and C58/Lw. Null mutants are viable, healthy and fertile.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    15
  • GO References
    6
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    598
  • Tissues
    1
  • cDNA Data
    54
  • Literature Summary
    1
Sequences &
Gene Models
less
Representative SequencesLengthStrain/SpeciesFlank
genomic 17085 NCBI Gene Model | MGI Sequence Detail 18746 C57BL/6J ±  kb
transcript NR_102726 RefSeq | MGI Sequence Detail 2539 ZRU/MplStud  
polypeptide Q01965 UniProt | EBI | MGI Sequence Detail 654 Not Applicable  
For the selected sequence
Protein
Information
less
Molecular
Reagents
less
  • All nucleic 71
    Genomic 14
    cDNA 55
    Primer pair 1
    Other 1

    Microarray probesets 3
Other
Accession IDs
less
MGD-MRK-12008, MGD-MRK-12051, MGI:2138373
References
more
  • Summaries
    All 95
    Developmental Gene Expression 1
    Gene Ontology 6
    Phenotypes 16
  • Earliest
    J:6136 Durda PJ, et al., T100: a new murine cell surface glycoprotein detected by anti-Lyt-2.1 serum. J Immunol. 1979 Apr;122(4):1407-12
  • Latest
    J:377135 Zhu K, et al., CD2 and its ligands are involved in development and activation of MAIT cells. J Exp Med. 2025 Dec 1;222(12):e20250431
Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources
Funding Information
Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
Send questions and comments to User Support. 		last database update
09/01/2026
MGI 6.24 		The Jackson Laboratory