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    Clec9a C-type lectin domain family 9, member a [ Mus musculus (house mouse) ]

    Gene ID: 232414, updated on 10-Dec-2024

    Summary

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    Official Symbol
    Clec9aprovided by MGI
    Official Full Name
    C-type lectin domain family 9, member aprovided by MGI
    Primary source
    MGI:MGI:2444608
    See related
    Ensembl:ENSMUSG00000046080 AllianceGenome:MGI:2444608
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    DNGR-1; 9830005G06Rik
    Summary
    Predicted to enable carbohydrate binding activity. Involved in receptor-mediated endocytosis. Located in cell surface. Orthologous to human CLEC9A (C-type lectin domain containing 9A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lung adult (RPKM 4.3), spleen adult (RPKM 3.4) and 15 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Clec9a in Genome Data Viewer
    Location:
    6 F3; 6 63.3 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (129385825..129401727)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (129408862..129424764)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_17478 Neighboring gene C-type lectin domain family 12, member a Neighboring gene STARR-seq mESC enhancer starr_17479 Neighboring gene STARR-positive B cell enhancer ABC_E6498 Neighboring gene C-type lectin domain family 12, member B Neighboring gene STARR-positive B cell enhancer ABC_E4872 Neighboring gene C-type lectin domain family 1, member b Neighboring gene STARR-positive B cell enhancer mm9_chr6:129384284-129384585 Neighboring gene C-type lectin domain family 1, member a Neighboring gene STARR-seq mESC enhancer starr_17480 Neighboring gene predicted gene, 45969 Neighboring gene C-type lectin domain family 7, member a

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. A pH- and ionic strength-dependent conformational change in the neck region regulates DNGR-1 function in dendritic cells. Hanč P, et al. EMBO J, 2016 Nov 15. PMID 27753620, Free PMC Article
    2. Efficient and versatile manipulation of the peripheral CD4+ T-cell compartment by antigen targeting to DNGR-1/CLEC9A. Joffre OP, et al. Eur J Immunol, 2010 May. PMID 20333625, Free PMC Article
    3. Optimal Generation of Tissue-Resident but Not Circulating Memory T Cells during Viral Infection Requires Crosspriming by DNGR-1(+) Dendritic Cells. Iborra S, et al. Immunity, 2016 Oct 18. PMID 27692611, Free PMC Article
    4. Self-adjuvanting nanoemulsion targeting dendritic cell receptor Clec9A enables antigen-specific immunotherapy. Zeng B, et al. J Clin Invest, 2018 May 1. PMID 29485973, Free PMC Article
    5. Structure of the Complex of F-Actin and DNGR-1, a C-Type Lectin Receptor Involved in Dendritic Cell Cross-Presentation of Dead Cell-Associated Antigens. Hanč P, et al. Immunity, 2015 May 19. PMID 25979418, Free PMC Article

    See all (66) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Secreted gelsolin inhibits DNGR-1-dependent cross-presentation and cancer immunity.
      Title: Secreted gelsolin inhibits DNGR-1-dependent cross-presentation and cancer immunity.
    2. Adjuvant-free peptide vaccine targeting Clec9a on dendritic cells can induce robust antitumor immune response through Syk/IL-21 axis.
      Title: Adjuvant-free peptide vaccine targeting Clec9a on dendritic cells can induce robust antitumor immune response through Syk/IL-21 axis.
    3. The receptor DNGR-1 signals for phagosomal rupture to promote cross-presentation of dead-cell-associated antigens.
      Title: The receptor DNGR-1 signals for phagosomal rupture to promote cross-presentation of dead-cell-associated antigens.
    4. RNF41 regulates the damage recognition receptor Clec9A and antigen cross-presentation in mouse dendritic cells.
      Title: RNF41 regulates the damage recognition receptor Clec9A and antigen cross-presentation in mouse dendritic cells.
    5. Targeting Antigens to Different Receptors on Conventional Type 1 Dendritic Cells Impacts the Immune Response.
      Title: Targeting Antigens to Different Receptors on Conventional Type 1 Dendritic Cells Impacts the Immune Response.
    6. Cross-presentation of dead-cell-associated antigens by DNGR-1(+) dendritic cells contributes to chronic allograft rejection in mice.
      Title: Cross-presentation of dead-cell-associated antigens by DNGR-1(+) dendritic cells contributes to chronic allograft rejection in mice.
    7. Myosin II-deficient necrotic cells are impaired in their ability to stimulate DNGR-1 or to serve as substrates for Conventional type 1 dendritic cells cross-presentation to CD8(+) T cells.
      Title: Myosin II Synergizes with F-Actin to Promote DNGR-1-Dependent Cross-Presentation of Dead Cell-Associated Antigens.
    8. Self-adjuvanting nanoemulsion targeting dendritic cell receptor Clec9A enables antigen-specific immunotherapy.
      Title: Self-adjuvanting nanoemulsion targeting dendritic cell receptor Clec9A enables antigen-specific immunotherapy.
    9. DNGR-1 deficiency leads to exacerbated caerulein-induced necrotizing pancreatitis and increased pathology during systemic Candida albicans infection without affecting fungal burden.
      Title: DNGR-1 in dendritic cells limits tissue damage by dampening neutrophil recruitment.
    10. Clec9A and Clec12A exhibit different intrinsic capacities to elicit MHC I and MHC II presentation following direct antigen targeting
      Title: Antibody-mediated targeting of antigen to C-type lectin-like receptors Clec9A and Clec12A elicits different vaccination outcomes.
    Submit: New GeneRIF Correction See all GeneRIFs (29)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (5) 
    • Targeted (12)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    C-type lectin domain family 9 member A
    Names
    dendritic cell natural killer lectin group receptor 1

    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_001205363.1 → NP_001192292.1  C-type lectin domain family 9 member A isoform 1

      See identical proteins and their annotated locations for NP_001192292.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC138620, AK036399
      Consensus CDS
      CCDS57454.1
      UniProtKB/Swiss-Prot
      Q8BRU4
      Related
      ENSMUSP00000056625.9, ENSMUST00000058352.15
      Conserved Domains (1) summary
      cd03593
      Location:137 → 257
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. NM_001205364.1 → NP_001192293.1  C-type lectin domain family 9 member A isoform 3

      See identical proteins and their annotated locations for NP_001192293.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC138620, EU339279
      Consensus CDS
      CCDS57455.1
      UniProtKB/Swiss-Prot
      Q8BRU4
      Related
      ENSMUSP00000128622.3, ENSMUST00000164513.8
      Conserved Domains (1) summary
      cd03593
      Location:110 → 230
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    3. NM_001205365.1 → NP_001192294.1  C-type lectin domain family 9 member A isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three consecutive exons in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC138620, EU339281
      UniProtKB/Swiss-Prot
      Q8BRU4
      Related
      ENSMUSP00000144990.2, ENSMUST00000204860.3

    4. NM_172732.3 → NP_766320.2  C-type lectin domain family 9 member A isoform 2

      See identical proteins and their annotated locations for NP_766320.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC138620, AK041288
      Consensus CDS
      CCDS39658.1
      UniProtKB/Swiss-Prot
      B0ZBM3, B0ZBM5, B0ZBM6, B0ZBM7, Q5M8M6, Q8BRU4, Q8CBB4
      Related
      ENSMUSP00000085394.6, ENSMUST00000088075.8
      Conserved Domains (1) summary
      cd03593
      Location:111 → 231
      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_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      129385825..129401727
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BRU4.1 GenPept UniProtKB/Swiss-Prot:Q8BRU4

    Gene LinkOut

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

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