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
  gene page
• Transcription Start Sites
  5 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• 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

• SNPs within 2kb
  521 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  1

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96885	protein coding gene	Chr1:171416172-171434978 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0016767	protein coding gene	Chr1:177409684-177428300 (-)
A/J	MGP_AJ_G0016746	protein coding gene	Chr1:170158238-170177549 (-)
AKR/J	MGP_AKRJ_G0016712	protein coding gene	Chr1:175288464-175311895 (-)
BALB/cJ	MGP_BALBcJ_G0016707	protein coding gene	Chr1:170697482-170715807 (-)
C3H/HeJ	MGP_C3HHeJ_G0016531	protein coding gene	Chr1:175862441-175882742 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0017169	protein coding gene	Chr1:183298817-183319700 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014876	protein coding gene	Chr1:161879043-161897071 (-)
CAST/EiJ	MGP_CASTEiJ_G0016112	protein coding gene	Chr1:175229585-175252558 (-)
CBA/J	MGP_CBAJ_G0016505	protein coding gene	Chr1:189827914-189847609 (-)
DBA/2J	MGP_DBA2J_G0016612	protein coding gene	Chr1:169103239-169122443 (-)
FVB/NJ	MGP_FVBNJ_G0016609	protein coding gene	Chr1:167356798-167375230 (-)
LP/J	MGP_LPJ_G0016683	protein coding gene	Chr1:178493894-178511511 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016636	protein coding gene	Chr1:197122930-197141612 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017205	protein coding gene	Chr1:175157248-175175965 (-)
PWK/PhJ	MGP_PWKPhJ_G0015897	protein coding gene	Chr1:168464354-168482921 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0015681	protein coding gene	Chr1:174082501-174101721 (-)
WSB/EiJ	MGP_WSBEiJ_G0016173	protein coding gene	Chr1:175327461-175346427 (-)

Homology

• 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
  HGNC:6730

  NCBI Gene ID: 4063

  neXtProt AC: NX_Q9HBG7

  UniProt: Q9HBG7

  
  
• Chr Location
  1q23.3; chr1:160796074-160828261 (+)  GRCh38

---

• MGI Vertebrate Homology
  Ly9 stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: LY9
• Gene Tree
  Ly9
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  3 phenotypes from 1 allele in 1 genetic background
  14 phenotype references
  

• All Mutations and Alleles
  8
• Chemically induced (other)
  2
• Endonuclease-mediated
  2
• Gene trapped
  1
• Targeted
  3
• Genomic Mutations
  3 involving Ly9
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  46 strains or lines available

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

• All GO Annotations
  12
• GO References
  6

Expression

• Assay Results
  707
• Tissues
  1
• cDNA Data
  54
• Literature Summary
  1

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  62
• RefSeq
  5
• UniProt
  9
• CCDS
  CCDS35779.1, CCDS69978.1

• Ensembl
  ENSMUSG00000004707 (Evidence)
• NCBI Gene
  17085

Representative Sequences			Length	Strain/Species
genomic	17085	NCBI Gene Model | MGI Sequence Detail	18746	C57BL/6J
transcript	NR_102726	RefSeq | MGI Sequence Detail	2539	ZRU/MplStud
polypeptide	Q01965	UniProt | EBI | MGI Sequence Detail	654	Not Applicable

Protein
Information

• UniProt
  9 Sequences
• Protein Ontology
  PR:000001842 T-lymphocyte surface antigen Ly-9
  (term hierarchy)
• InterPro Domains
  IPR007110 Immunoglobulin-like domain
  IPR036179 Immunoglobulin-like domain superfamily
  IPR013783 Immunoglobulin-like fold
  IPR003599 Immunoglobulin subtype
  IPR013106 Immunoglobulin V-set domain
• GlyGen
  Q01965 8 sites, 1 N-linked glycan (2 sites)

Molecular
Reagents

• All nucleic 71

  Genomic 14

  cDNA 55

  Primer pair 1

  Other 1

  
  

  Microarray probesets 3

Other
Accession IDs

MGD-MRK-12008, MGD-MRK-12051, MGI:2138373

References

• Summaries
  All 84

  Developmental Gene Expression 1

  Gene Ontology 6

  Phenotypes 14
• 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:326541 Cyagen Biosciences Inc., Cyagen Biosciences Website. 2022;

TSS for Ly9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr15054	Chr1:171434946-171434971 (-)	-42 bp
Tssr15053	Chr1:171434889-171434931 (-)	7 bp
Tssr15052	Chr1:171432819-171432836 (-)	2,089 bp
Tssr15051	Chr1:171429581-171429604 (-)	5,324 bp
Tssr15050	Chr1:171429424-171429481 (-)	5,464 bp

Ly9 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Sle1b	Chr1, 75.10 cM		J:94686	Congenic and physical mapping was used to show that Sle1b mapped within an interval containing SLAM family members ordered as Cd244 - Ly9 - Slamf7 - Cd48 - Slamf1 - Cd84 - Slamf6. Haplotype analysis of the aformentioned region were suggestive that the markers contained within the region as contributing to the Sle1b phenotype. The strongest contribution may come from Slamf6.

*cM position of peak correlated region/marker