Clec4d C-type lectin domain family 4, member d [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clec4dprovided by MGI
Official Full Name: C-type lectin domain family 4, member dprovided by MGI
Primary source: MGI:MGI:1298389
See related: Ensembl:ENSMUSG00000030144 AllianceGenome:MGI:1298389
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: mcl; Mpcl; Clecsf8
Summary: Enables immunoglobulin receptor binding activity. Involved in antifungal innate immune response; positive regulation of canonical NF-kappaB signal transduction; and positive regulation of myeloid dendritic cell activation. Acts upstream of or within several processes, including Fc-gamma receptor signaling pathway; T cell differentiation involved in immune response; and defense response to other organism. Located in plasma membrane. Is expressed in several structures, including heart; immune system; intestine; liver; and lung. Orthologous to human CLEC4D (C-type lectin domain family 4 member D). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in liver E18 (RPKM 1.3), lung adult (RPKM 0.5) and 12 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 F2; 6 58.33 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (123239066..123252227)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (123262107..123275268)

Chromosome 6 - NC_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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 expression is a hallmark of neutrophils infiltrating the skin in epidermolysis bullosa acquisita.
Title: C-type lectin receptor expression is a hallmark of neutrophils infiltrating the skin in epidermolysis bullosa acquisita.
C-type lectin Mincle-dependent and -independent activation of invariant NKT cells by exposure to Helicobacter pylori alpha-cholesteryl glucosides.
Title: C-type lectin Mincle-dependent and -independent activation of invariant NKT cells by exposure to Helicobacter pylori α-cholesteryl glucosides.
C-type lectin receptor Dectin3 deficiency balances the accumulation and function of FoxO1-mediated LOX-1(+) M-MDSCs in relieving lupus-like symptoms.
Title: C-type lectin receptor Dectin3 deficiency balances the accumulation and function of FoxO1-mediated LOX-1(+) M-MDSCs in relieving lupus-like symptoms.
The Ubiquitin-Modifying Enzyme A20 Terminates C-Type Lectin Receptor Signals and Is a Suppressor of Host Defense against Systemic Fungal Infection.
Title: The Ubiquitin-Modifying Enzyme A20 Terminates C-Type Lectin Receptor Signals and Is a Suppressor of Host Defense against Systemic Fungal Infection.
MCL (macrophage C-type lectin) plays a crucial role in killing bacteria during Escherichia coli-induced peritonitis. MCL-deficient mice with E. coli-induced sepsis showed lower survival rates and reduced bacterial clearance when compared with control mice, despite similar levels of proinflammatory cytokine production.
Title: Macrophage C-type lectin is essential for phagosome maturation and acidification during Escherichia coli-induced peritonitis.
Dectin-3 deficiency did not lead to increased susceptibility of mice to experimental pulmonary C. neoformans infection. Also, no significant differences in pulmonary leukocyte recruitment and cytokine production were observed in Dectin-3 deficient mice compared to wild type infected mice
Title: Dectin-3 Is Not Required for Protection against Cryptococcus neoformans Infection.
activation of CLRs Dectin-2 and Dectin-3 by fungi infections triggers them for ubiquitination and degradation in a Syk-dependent manner.
Title: E3 ubiquitin ligase Cbl-b negatively regulates C-type lectin receptor-mediated antifungal innate immunity.
The authors report that microbial stimulation triggers Mincle (Clec4e) expression through the myeloid differentiation primary response gene 88 (MyD88) pathway; a process that does not require MCL (Clecsf8, Clec4d). Conversely, they show that MCL is constitutively expressed but retained intracellularly until Mincle is induced, whereupon the receptors form heterodimers which are translocated to the cell surface.
Title: Signalling through MyD88 drives surface expression of the mycobacterial receptors MCL (Clecsf8, Clec4d) and Mincle (Clec4e) following microbial stimulation.
Data show that Mincle, the inducible receptor for mycobacterial cord factor, is the key switch for the transition of macrophages from cytokine expression to high nitric oxide production.
Title: Mincle-mediated translational regulation is required for strong nitric oxide production and inflammation resolution.
MCL regulates the development of vaccine-induced Th17 cells and protective immunity against lethal experimental infection with Blastomyces dermatitidis.
Title: The C-Type Lectin Receptor MCL Mediates Vaccine-Induced Immunity against Infection with Blastomyces dermatitidis.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Variation

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Alleles

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

Endonuclease-mediated (4)
Targeted (2) 1 citation

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables D-mannose binding	ISO Inferred from Sequence Orthology more info
enables D-mannose binding	ISS Inferred from Sequence or Structural Similarity more info
enables carbohydrate binding	IBA Inferred from Biological aspect of Ancestor more info
enables immunoglobulin receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables pattern recognition receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables pattern recognition receptor activity	ISO Inferred from Sequence Orthology more info
enables pattern recognition receptor activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Fc-gamma receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within T cell differentiation involved in immune response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within adaptive immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antifungal innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in antifungal innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antifungal innate immune response	ISO Inferred from Sequence Orthology more info
involved_in antifungal innate immune response	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within defense response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of myeloid dendritic cell activation	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
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: C-type lectin domain family 4 member D

Names: C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 8; C-type lectin, superfamily member 8; DC-associated C-type lectin 3; dectin-3; dendritic cell-associated C-type lectin 3; macrophage C-type lectin; macrophage-restricted C-type 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_001163161.1 → NP_001156633.1 C-type lectin domain family 4 member D isoform 2

See identical proteins and their annotated locations for NP_001156633.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region compared to variant 1. This results in a shorter isoform (2) compared to isoform 1.

Source sequence(s)

AC124563, AI390740, AK089500, AK150926

UniProtKB/TrEMBL

Q3UBK0

Conserved Domains (1) summary

cd03590
Location:82 → 206

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)
NM_010819.4 → NP_034949.3 C-type lectin domain family 4 member D isoform 1

See identical proteins and their annotated locations for NP_034949.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC124563, AI390740, AK089500, AK171409

Consensus CDS

CCDS20513.1

UniProtKB/Swiss-Prot

Q8C212, Q9Z2H6

UniProtKB/TrEMBL

Q4KL29

Related

ENSMUSP00000032240.3, ENSMUST00000032240.4

Conserved Domains (1) summary

cd03590
Location:83 → 207

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)