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

Gene ID: 232414, updated on 21-Apr-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, Apr 2022]
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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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. 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
  2. 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
  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. 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
  5. DNGR-1 is dispensable for CD8+ T-cell priming during respiratory syncytial virus infection. Durant LR, et al. Eur J Immunol, 2014 Aug. PMID 24777856

See all (60) 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)
  • Targeted (12)  1 citation
  • Endonuclease-mediated (5) 

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 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
  
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 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

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