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

    Gene ID: 232414, updated on 27-Nov-2024

    Summary

    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, Nov 2024]
    Expression
    Broad expression in lung adult (RPKM 4.3), spleen adult (RPKM 3.4) and 15 other tissues See more
    Orthologs
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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

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

    NCBI Reference Sequences (RefSeq)

    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_001205363.1NP_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:137257
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
    2. NM_001205364.1NP_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:110230
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
    3. NM_001205365.1NP_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_172732.3NP_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:111231
      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)