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    Clec5a C-type lectin domain containing 5A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 679787, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Clec5aprovided by RGD
    Official Full Name
    C-type lectin domain containing 5Aprovided by RGD
    Primary source
    RGD:1584755
    See related
    EnsemblRapid:ENSRNOG00000026306 AllianceGenome:RGD:1584755
    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 enable virus receptor activity. Predicted to be involved in several processes, including innate immune response; osteoblast development; and positive regulation of cytokine production. Predicted to act upstream of or within myeloid cell differentiation and negative regulation of myeloid cell apoptotic process. Predicted to be located in cell surface; cytosol; and plasma membrane. Orthologous to human CLEC5A (C-type lectin domain containing 5A). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 23.0), Heart (RPKM 9.1) and 7 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Clec5a in Genome Data Viewer
    Location:
    4q23
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (70373855..70383560, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (69407125..69416872, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (68810330..68819921, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 9 subfamily A member 7, pseudogene 1 Neighboring gene olfactory receptor family 9 subfamily A member 4 Neighboring gene taste receptor, type 2, member 138 Neighboring gene maltase-glucoamylase

    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. CLEC5A Promotes Neuronal Pyroptosis in Rat Spinal Cord Injury Models by Interacting with TREM1 and Elevating NLRC4 Expression. Tan Y, et al. eNeuro, 2024 Oct. PMID 39187376, Free PMC Article
    2. Expression and functional role of MDL-1 (CLEC5A) in mouse myeloid lineage cells. Aoki N, et al. J Leukoc Biol, 2009 Mar. PMID 19074552
    3. CLEC5A is critical for dengue-virus-induced lethal disease. Chen ST, et al. Nature, 2008 May 29. PMID 18496526
    4. Signal adaptor DAP10 associates with MDL-1 and triggers osteoclastogenesis in cooperation with DAP12. Inui M, et al. Proc Natl Acad Sci U S A, 2009 Mar 24. PMID 19251634, Free PMC Article
    5. Myelodysplastic syndromes are induced by histone methylation–altering ASXL1 mutations. Inoue D, et al. J Clin Invest, 2013 Nov. PMID 24216483, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CLEC5A Promotes Neuronal Pyroptosis in Rat Spinal Cord Injury Models by Interacting with TREM1 and Elevating NLRC4 Expression.
      Title: CLEC5A Promotes Neuronal Pyroptosis in Rat Spinal Cord Injury Models by Interacting with TREM1 and Elevating NLRC4 Expression.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables virus receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables virus receptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within myeloid cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of myeloid cell apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in osteoblast development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in symbiont entry into host cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma 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
    C-type lectin domain family 5 member A
    Names
    C-type lectin domain family 5, member A

    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_001109377.2 → NP_001102847.1  C-type lectin domain family 5 member A isoform 1

      See identical proteins and their annotated locations for NP_001102847.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A6IEY3, D3ZPN6
      Related
      ENSRNOP00000034438.4, ENSRNOT00000033265.6
      Conserved Domains (1) summary
      cd03593
      Location:73 → 186
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. NM_001430320.1 → NP_001417249.1  C-type lectin domain family 5 member A isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A0G2JTX6, A6IEY2

    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
      70373855..70383560 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006236369.5 → XP_006236431.1  C-type lectin domain family 5 member A isoform X1

      Related
      ENSRNOP00000086836.1, ENSRNOT00000111357.2
      Conserved Domains (1) summary
      cd03593
      Location:48 → 161
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. XM_039108332.2 → XP_038964260.1  C-type lectin domain family 5 member A isoform X2

      Conserved Domains (1) summary
      cl02432
      Location:73 → 117
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    Nucleotide Protein Strain
    Heading Accession and Version

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