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

Summary

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, Nov 2024]
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

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_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Endonuclease-mediated (7) 1 citation
Targeted (1) 1 citation

General gene information

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Markers

Clec2d (e-PCR), detects polymorphism
- UniSTS:528188

NoName (e-PCR)
- UniSTS:485309

MHAa87a3.seq (e-PCR)
- UniSTS:125410

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 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)

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

NC_000072.7 Reference GRCm39 C57BL/6J

Range

129157578..129163498

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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