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    Ly49s4 Ly49 stimulatory receptor 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 494195, updated on 13-Apr-2024

    Summary

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    Symbol
    Ly49s4provided by RGD
    Full Name
    Ly49 stimulatory receptor 4provided by RGD
    Primary source
    RGD:1549723
    See related
    AllianceGenome:RGD:1549723
    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 integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Annotation information
    Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
    Expression
    Biased expression in Spleen (RPKM 7.0), Lung (RPKM 2.3) and 3 other tissues See more
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    Genomic context

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    Location:
    4q42
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (165807295..165830157, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (164122071..164144931, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (164470396..164493252, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene killer cell lectin-like receptor subfamily A, member 22 Neighboring gene Ly49 stimulatory receptor 6 Neighboring gene Ly49 inhibitory receptor 4 Neighboring gene killer cell lectin-like receptor, subfamily A, member 4, pseudogene 2

    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. Strain-dependent expression of four structurally related rat Ly49 receptors; correlation with NK gene complex haplotype and NK alloreactivity. Kveberg L, et al. Immunogenetics, 2006 Nov. PMID 17028855
    2. The genes and gene organization of the Ly49 region of the rat natural killer cell gene complex. Nylenna O, et al. Eur J Immunol, 2005 Jan. PMID 15593300

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Ly49 stimulatory receptor 4

    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_001009487.1 → NP_001009487.1  Ly49 stimulatory receptor 4

      See identical proteins and their annotated locations for NP_001009487.1

      Status: PROVISIONAL

      Description
      Transcript Variant: This variant (1, coding) represents the functional allele that is not present in some strains, including the strain of the reference genome.
      Source sequence(s)
      AY649831
      UniProtKB/TrEMBL
      A0A0G2K3K6, Q5MPX1
      Conserved Domains (2) summary
      cd03593
      Location:142 → 257
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
      pfam08391
      Location:38 → 155
      Ly49; Ly49-like protein, N-terminal region

    RNA

    1. NR_172009.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1, non-coding) contains a premature stop codon, and represents the non-functional allele present in some strains, including the strain of the reference genome. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, coding, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      JAXUCZ010000004

    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_086022.1 Reference GRCr8

      Range
      165807295..165830157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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