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Ly9 lymphocyte antigen 9 [ Rattus norvegicus (Norway rat) ]

Gene ID: 289227, updated on 13-Apr-2024

Summary

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Official Symbol
Ly9provided by RGD
Official Full Name
lymphocyte antigen 9provided by RGD
Primary source
RGD:1308341
See related
Ensembl:ENSRNOG00000025069 AllianceGenome:RGD:1308341
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to be involved in T-helper 17 cell lineage commitment and positive regulation of interleukin-17 production. Predicted to be located in cell surface and plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human LY9 (lymphocyte antigen 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Spleen (RPKM 124.2), Thymus (RPKM 103.7) and 3 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Ly9 in Genome Data Viewer
Location:
13q24
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (86610762..86633314, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (84079345..84100783, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (90002779..90022346, complement)

Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene CD244 molecule like 1 Neighboring gene large ribosomal subunit protein eL31-like Neighboring gene CD244 molecule Neighboring gene uncharacterized LOC102549964 Neighboring gene SLAM family member 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Isolation and characterization of cDNA clones for mouse Ly-9. Sandrin MS, et al. J Immunol, 1992 Sep 1. PMID 1506686
  2. Increased expression of SLAM receptors SLAMF3 and SLAMF6 in systemic lupus erythematosus T lymphocytes promotes Th17 differentiation. Chatterjee M, et al. J Immunol, 2012 Feb 1. PMID 22184727, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

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
  
involved_in positive regulation of interleukin-17 production ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cell surface ISO
Inferred from Sequence Orthology
more info
  
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
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

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)

  1. NM_001191673.2 → NP_001178602.1  T-lymphocyte surface antigen Ly-9 precursor

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    A0A8I5ZS62, A0A8I6GJS8
    Related
    ENSRNOP00000092458.1, ENSRNOT00000103580.1
    Conserved Domains (3) summary
    cd05775
    Location:57 → 152
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    smart00410
    Location:52 → 130
    IG_like; Immunoglobulin like
    pfam13927
    Location:157 → 227
    Ig_3; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086031.1 Reference GRCr8

    Range
    86610762..86633314 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063272129.1 → XP_063128199.1  T-lymphocyte surface antigen Ly-9 isoform X1

    UniProtKB/TrEMBL
    A0A8I6A5H0
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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