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    Clec2d C-type lectin domain family 2, member D [ Rattus norvegicus (Norway rat) ]

    Gene ID: 113937, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Clec2dprovided by RGD
    Official Full Name
    C-type lectin domain family 2, member Dprovided by RGD
    Primary source
    RGD:620070
    See related
    EnsemblRapid:ENSRNOG00000048726 AllianceGenome:RGD:620070
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ocil; Clec2d5
    Summary
    Predicted to enable natural killer cell lectin-like receptor binding activity. Predicted to act upstream of or within negative regulation of osteoclast differentiation and protection from natural killer cell mediated cytotoxicity. Predicted to be located in cell surface and endoplasmic reticulum. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC2D (C-type lectin domain family 2 member D). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 37.5), Thymus (RPKM 25.8) and 7 other tissues See more
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    Genomic context

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    See Clec2d in Genome Data Viewer
    Location:
    4q42
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (163902124..163925587)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (162216052..162239530)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (162278252..162302881)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene C-type lectin domain family 2 member D2 like 1 Neighboring gene C-type lectin domain family 2 member D2 like 2 Neighboring gene protein phosphatase 2, regulatory subunit B', alpha like 1 Neighboring gene uncharacterized LOC102549299 Neighboring gene C-type lectin domain family 2 member D-like 1 Neighboring gene C-type lectin domain family 2, member G like 1 Neighboring gene chromobox 3 like 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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

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    Related articles in PubMed

    1. Characterization of alternatively spliced transcript variants of CLEC2D gene. Germain C, et al. J Biol Chem, 2010 Nov 12. PMID 20843815, Free PMC Article
    2. Cloning and analysis of rat osteoclast inhibitory lectin gene promoter. Quan JX, et al. J Cell Biochem, 2009 Mar 1. PMID 19127542
    3. A novel osteoblast-derived C-type lectin that inhibits osteoclast formation. Zhou H, et al. J Biol Chem, 2001 May 4. PMID 11278931
    4. Osteoclast inhibitory lectin, a family of new osteoclast inhibitors. Zhou H, et al. J Biol Chem, 2002 Dec 13. PMID 12374791
    5. Genetically linked C-type lectin-related ligands for the NKRP1 family of natural killer cell receptors. Iizuka K, et al. Nat Immunol, 2003 Aug. PMID 12858173

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. transcriptionaL level gene expression regulation of rat OCIL gene
      Title: Cloning and analysis of rat osteoclast inhibitory lectin gene promoter.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables natural killer cell lectin-like receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables natural killer cell lectin-like receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of osteoclast differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protection from natural killer cell mediated cytotoxicity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in external side of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    C-type lectin domain family 2 member D5
    Names
    osteoclast inhibitory 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_130402.3 → NP_569086.1  C-type lectin domain family 2 member D5

      See identical proteins and their annotated locations for NP_569086.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/Swiss-Prot
      Q925N7
      UniProtKB/TrEMBL
      A6IM26
      Related
      ENSRNOP00000071394.2, ENSRNOT00000090431.3
      Conserved Domains (1) summary
      PHA02642
      Location:71 → 230
      PHA02642; C-type lectin-like protein; Provisional

    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
      163902124..163925587
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039106901.2 → XP_038962829.1  C-type lectin domain family 2 member D5 isoform X2

      Related
      ENSRNOP00000050011.4, ENSRNOT00000043078.5
      Conserved Domains (1) summary
      PHA02642
      Location:71 → 230
      PHA02642; C-type lectin-like protein; Provisional

    2. XM_039106900.2 → XP_038962828.1  C-type lectin domain family 2 member D5 isoform X1

      UniProtKB/Swiss-Prot
      Q925N7
      UniProtKB/TrEMBL
      A6IM26
      Conserved Domains (1) summary
      PHA02642
      Location:71 → 230
      PHA02642; C-type lectin-like protein; Provisional

    3. XM_039106902.2 → XP_038962830.1  C-type lectin domain family 2 member D5 isoform X3

      Conserved Domains (1) summary
      PHA02642
      Location:15 → 174
      PHA02642; C-type lectin-like protein; Provisional

    4. XM_039106899.2 → XP_038962827.1  C-type lectin domain family 2 member D5 isoform X1

      UniProtKB/Swiss-Prot
      Q925N7
      UniProtKB/TrEMBL
      A6IM26
      Conserved Domains (1) summary
      PHA02642
      Location:71 → 230
      PHA02642; C-type lectin-like protein; Provisional
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q925N7.1 GenPept UniProtKB/Swiss-Prot:Q925N7

    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