U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Clec9a C-type lectin domain containing 9A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 502901, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Clec9aprovided by RGD
    Official Full Name
    C-type lectin domain containing 9Aprovided by RGD
    Primary source
    RGD:1562513
    See related
    EnsemblRapid:ENSRNOG00000051690 AllianceGenome:RGD:1562513
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1562513
    Summary
    Predicted to enable carbohydrate binding activity. Predicted to be involved in positive regulation of cytokine production and receptor-mediated endocytosis. Predicted to be located in membrane. Predicted to be active in cell surface. Orthologous to human CLEC9A (C-type lectin domain containing 9A). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 92.2), Lung (RPKM 84.2) and 7 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Clec9a in Genome Data Viewer
    Location:
    4q42
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (164546323..164561380)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (162859742..162875742)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (163173593..163189532)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene C-type lectin domain family 12, member B Neighboring gene C-type lectin domain family 1, member B Neighboring gene C-type lectin domain family 1, member A Neighboring gene uncharacterized LOC120102409 Neighboring gene C-type lectin domain containing 7A

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Tumor therapy in mice via antigen targeting to a novel, DC-restricted C-type lectin. Sancho D, et al. J Clin Invest, 2008 Jun. PMID 18497879, Free PMC Article
    2. CLEC9A is a novel activation C-type lectin-like receptor expressed on BDCA3+ dendritic cells and a subset of monocytes. Huysamen C, et al. J Biol Chem, 2008 Jun 13. PMID 18408006, Free PMC Article
    3. The complete inventory of receptors encoded by the rat natural killer cell gene complex. Flornes LM, et al. Immunogenetics, 2010 Aug. PMID 20544345, Free PMC Article
    4. 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

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cytokine production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in receptor-mediated endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in receptor-mediated endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in receptor-mediated endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    C-type lectin domain family 9 member A
    Names
    C-type lectin domain family 9, member A

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001109354.1 → NP_001102824.1  C-type lectin domain family 9 member A

      See identical proteins and their annotated locations for NP_001102824.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473964
      UniProtKB/Swiss-Prot
      D4AD02, D9Z4I7
      UniProtKB/TrEMBL
      A6IM47
      Related
      ENSRNOP00000071858.1, ENSRNOT00000088108.3
      Conserved Domains (1) summary
      cd03593
      Location:113 → 234
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    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
      164546323..164561380
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D4AD02.1 GenPept UniProtKB/Swiss-Prot:D4AD02

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools