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Clec2d C-type lectin domain family 2, member d [ Mus musculus (house mouse) ]

Gene ID: 93694, updated on 27-Feb-2024

Summary

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Official Symbol
Clec2dprovided by MGI
Official Full Name
C-type lectin domain family 2, member dprovided by MGI
Primary source
MGI:MGI:2135589
See related
Ensembl:ENSMUSG00000030157 AllianceGenome:MGI:2135589
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
Clrb; Ocil; Clr-b
Summary
Enables natural killer cell lectin-like receptor binding activity. Acts upstream of or within negative regulation of osteoclast differentiation and protection from natural killer cell mediated cytotoxicity. Located in external side of plasma membrane. Is expressed in several structures, including gut; liver; skeleton; spleen; and urinary system. Orthologous to human CLEC2D (C-type lectin domain family 2 member D). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung adult (RPKM 34.9), large intestine adult (RPKM 31.4) and 17 other tissues See more
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Genomic context

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Location:
6 F3; 6 63.16 cM
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (129157578..129163498)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (129180615..129186535)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene killer cell lectin-like receptor subfamily B member 1, pseudogene 1 Neighboring gene predicted gene, 53342 Neighboring gene STARR-seq mESC enhancer starr_17476 Neighboring gene STARR-seq mESC enhancer starr_17477 Neighboring gene predicted gene, 26160 Neighboring gene STARR-positive B cell enhancer ABC_E4870 Neighboring gene predicted gene, 38906 Neighboring gene STARR-positive B cell enhancer ABC_E6494 Neighboring gene STARR-positive B cell enhancer ABC_E9102 Neighboring gene RIKEN cDNA 2310001H17 gene Neighboring gene STARR-positive B cell enhancer ABC_E690 Neighboring gene STARR-positive B cell enhancer ABC_E6495 Neighboring gene STARR-positive B cell enhancer ABC_E4871 Neighboring gene STARR-positive B cell enhancer ABC_E8140 Neighboring gene STARR-positive B cell enhancer ABC_E9019

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. The Inhibitory NKR-P1B:Clr-b Recognition Axis Facilitates Detection of Oncogenic Transformation and Cancer Immunosurveillance. Tanaka M, et al. Cancer Res, 2018 Jul 1. PMID 29691253
  2. Interferon-Dependent Induction of Clr-b during Mouse Cytomegalovirus Infection Protects Bystander Cells from Natural Killer Cells via NKR-P1B-Mediated Inhibition. Kirkham CL, et al. J Innate Immun, 2017. PMID 28288457, Free PMC Article
  3. Poxvirus infection-associated downregulation of C-type lectin-related-b prevents NK cell inhibition by NK receptor protein-1B. Williams KJ, et al. J Immunol, 2012 May 15. PMID 22491247
  4. Parathyroid hormone-related protein regulates osteoclast inhibitory lectin expression via multiple signaling pathways in osteoblast-like cells. Zheng F, et al. Endocrine, 2009 Feb. PMID 18987998
  5. Osteoclast inhibitory lectin, an immune cell product that is required for normal bone physiology in vivo. Kartsogiannis V, et al. J Biol Chem, 2008 Nov 7. PMID 18782774, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. C-type lectin receptor 2d forms homodimers and heterodimers with TLR2 to negatively regulate IRF5-mediated antifungal immunity.
    Title: C-type lectin receptor 2d forms homodimers and heterodimers with TLR2 to negatively regulate IRF5-mediated antifungal immunity.
  2. Mouse cytomegalovirus m153 protein stabilizes expression of the inhibitory NKR-P1B ligand Clr-b.
    Title: Mouse Cytomegalovirus m153 Protein Stabilizes Expression of the Inhibitory NKR-P1B Ligand Clr-b.
  3. these findings demonstrate that Clr-b is an IFN-stimulated gene on healthy bystander cells, in addition to a missing-self marker on MCMV-infected cells, and thereby enhances the dynamic range of innate self-nonself discrimination by NK cells
    Title: Interferon-Dependent Induction of Clr-b during Mouse Cytomegalovirus Infection Protects Bystander Cells from Natural Killer Cells via NKR-P1B-Mediated Inhibition.
  4. Data suggest that killer cell lectin-like receptors NKR-P1B:Clr-b (Klrb1:Clec2d) interactions may provide a model for human hematopoietic cell transplants.
    Title: Genetic investigation of MHC-independent missing-self recognition by mouse NK cells using an in vivo bone marrow transplantation model.
  5. Reductions of Clr-b may be involved in sensitizing poxvirus-infected cells to natural killer (NK) cells.
    Title: Poxvirus infection-associated downregulation of C-type lectin-related-b prevents NK cell inhibition by NK receptor protein-1B.
  6. LLT1 and CD161 have roles in modulating immune responses to pathogens; and interferon-gamma contributes to modulate immune responses
    Title: Induction of lectin-like transcript 1 (LLT1) protein cell surface expression by pathogens and interferon-γ contributes to modulate immune responses.
  7. PTHrp(1-34) regulates OCIL expression in vitro through cAMP/PKA, Ca(2+)/CaMK II, and MAPK signaling pathways.
    Title: Parathyroid hormone-related protein regulates osteoclast inhibitory lectin expression via multiple signaling pathways in osteoblast-like cells.
  8. OCIL is a physiological negative regulator of bone.
    Title: Osteoclast inhibitory lectin, an immune cell product that is required for normal bone physiology in vivo.
  9. cloning and characterization of a cognate ligand, Ocil, for the inhibitory NK receptors (NKR)-P1B and NKR-P1D. Ocil/Clr-b is displayed at high levels on nearly all hematopoietic cells, in a pattern that is similar to that of class I MHC molecules.
    Title: Missing self-recognition of Ocil/Clr-b by inhibitory NKR-P1 natural killer cell receptors.
  10. Data show that osteoclast inhibitory lectin (OCIL) binds a range of physiologically important glycosaminoglycans, and this property may modulate OCIL actions upon other cells.
    Title: Characterization of sugar binding by osteoclast inhibitory lectin.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

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Markers

Homology

Clone Names

  • MGC123478

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables carbohydrate binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transmembrane signaling receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cellular defense response TAS
Traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within negative regulation of osteoclast differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within protection from natural killer cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within protection from natural killer cell mediated cytotoxicity IGI
Inferred from Genetic Interaction
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
C-type lectin domain family 2 member D
Names
C lectin-related protein B
C-type lectin-domain family 2 member D
C-type lectin-related protein B
lectin-like transmembrane protein
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_053109.3 → NP_444339.1  C-type lectin domain family 2 member D

    See identical proteins and their annotated locations for NP_444339.1

    Status: VALIDATED

    Source sequence(s)
    AW987086, AY320031
    Consensus CDS
    CCDS20581.1
    UniProtKB/Swiss-Prot
    Q1AFZ3, Q8VI19, Q8VI20, Q91V08
    UniProtKB/TrEMBL
    F5BFH0
    Related
    ENSMUSP00000032260.6, ENSMUST00000032260.6
    Conserved Domains (3) summary
    cd03593
    Location:80 → 192
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
    PHA02867
    Location:39 → 196
    PHA02867; C-type lectin protein; Provisional
    pfam05473
    Location:3 → 144
    Herpes_UL45; UL45 protein

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
    129157578..129163498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006506805.5 → XP_006506868.1  C-type lectin domain family 2 member D isoform X1

    Conserved Domains (1) summary
    PHA02642
    Location:1 → 143
    PHA02642; C-type lectin-like protein; Provisional
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q91V08.1 GenPept UniProtKB/Swiss-Prot:Q91V08

Gene LinkOut

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

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