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    Clec4n C-type lectin domain family 4, member n [ Mus musculus (house mouse) ]

    Gene ID: 56620, updated on 14-Nov-2021

    Summary

    Official Symbol
    Clec4nprovided by MGI
    Official Full Name
    C-type lectin domain family 4, member nprovided by MGI
    Primary source
    MGI:MGI:1861231
    See related
    Ensembl:ENSMUSG00000023349
    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
    Nkcl; Clec6a; Clecsf10
    Expression
    Biased expression in liver E18 (RPKM 6.6), spleen adult (RPKM 5.8) and 13 other tissues See more
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    Genomic context

    See Clec4n in Genome Data Viewer
    Location:
    6 F2; 6 58.3 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (123206802..123223983)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (123229843..123247024)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (123179861..123197042)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene C-type lectin domain family 4, member b2 Neighboring gene predicted gene, 22946 Neighboring gene peptidylprolyl isomerase A pseudogene 6_1344.1 Neighboring gene C-type lectin domain family 4, member d Neighboring gene C-type lectin domain family 4, member e

    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)
    • Targeted (3)  1 citation
    • Endonuclease-mediated (1) 

    General gene information

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables carbohydrate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables carbohydrate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables carbohydrate binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables mannose binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables pattern recognition receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables pattern recognition receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in antifungal innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in antifungal innate immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in biological process involved in interspecies interaction between organisms IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in defense response to fungus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in detection of yeast IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within immune system process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in innate immune response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of I-kappaB kinase/NF-kappaB signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of T-helper 17 type immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cytokine production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of intracellular signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of positive regulation of peptidyl-tyrosine phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to yeast IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in stimulatory C-type lectin receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    C-type lectin domain family 6 member A
    Names
    C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 10
    C-type lectin superfamily member 10
    DC-associated C-type lectin 2
    dectin-2
    dendritic cell-associated C-type lectin 2
    natural killer complex lectin

    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_001190320.1NP_001177249.1  C-type lectin domain family 6 member A isoform 2

      See identical proteins and their annotated locations for NP_001177249.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC164111
      Consensus CDS
      CCDS51896.1
      UniProtKB/TrEMBL
      Q3U3M9
      Related
      ENSMUSP00000113733.2, ENSMUST00000117130.8
      Conserved Domains (1) summary
      cd03590
      Location:49174
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    2. NM_001190321.1NP_001177250.1  C-type lectin domain family 6 member A isoform 3

      See identical proteins and their annotated locations for NP_001177250.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AC164111
      Consensus CDS
      CCDS51895.1
      UniProtKB/Swiss-Prot
      Q9JKF4
      Related
      ENSMUSP00000108173.3, ENSMUST00000112554.9
      Conserved Domains (1) summary
      cd03590
      Location:45170
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    3. NM_020001.2NP_064385.1  C-type lectin domain family 6 member A isoform 1

      See identical proteins and their annotated locations for NP_064385.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC164111, AK131697
      Consensus CDS
      CCDS20512.1
      UniProtKB/Swiss-Prot
      Q9JKF4
      UniProtKB/TrEMBL
      Q3V2N1
      Related
      ENSMUSP00000024118.5, ENSMUST00000024118.11
      Conserved Domains (1) summary
      cd03590
      Location:79204
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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
      123206802..123223983
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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