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

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 AllianceGenome:MGI:1861231
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
Summary: Enables carbohydrate binding activity and pattern recognition receptor activity. Involved in several processes, including positive regulation of I-kappaB kinase/NF-kappaB signaling; positive regulation of immune response; and response to fungus. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in external side of plasma membrane. Is expressed in bone marrow; embryo; lung; spleen; and thymus. Orthologous to human CLEC6A (C-type lectin domain containing 6A). [provided by Alliance of Genome Resources, Apr 2022]
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

Location:: 6 F2; 6 58.3 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	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)

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?

The intestinal commensal fungus Wallemia mellicola enhances asthma in mice through Dectin-2.
Title: The intestinal commensal fungus Wallemia mellicola enhances asthma in mice through Dectin-2.
Dectin-2 Deficiency Promotes Proinflammatory Cytokine Release From Macrophages and Impairs Insulin Secretion.
Title: Dectin-2 Deficiency Promotes Proinflammatory Cytokine Release From Macrophages and Impairs Insulin Secretion.
Dectin-2 is critical for phagocyte function and resistance to Paracoccidioides brasiliensis in mice.
Title: Dectin-2 is critical for phagocyte function and resistance to Paracoccidioides brasiliensis in mice.
The C-Type Lectin Receptor Dectin-2 Is a Receptor for Aspergillus fumigatus Galactomannan.
Title: The C-Type Lectin Receptor Dectin-2 Is a Receptor for Aspergillus fumigatus Galactomannan.
Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice.
Title: Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice.
Dectin-2-mediated initiation of immune responses caused by influenza virus hemagglutinin.
Title: Dectin-2-mediated initiation of immune responses caused by influenza virus hemagglutinin.
Dectin-2 mediates phagocytosis of Lactobacillus paracasei KW3110 and IL-10 production by macrophages.
Title: Dectin-2 mediates phagocytosis of Lactobacillus paracasei KW3110 and IL-10 production by macrophages.
CARD9-Associated Dectin-1 and Dectin-2 Are Required for Protective Immunity of a Multivalent Vaccine against Coccidioides posadasii Infection.
Title: CARD9-Associated Dectin-1 and Dectin-2 Are Required for Protective Immunity of a Multivalent Vaccine against Coccidioides posadasii Infection.
Association of modulation of pro-inflammatory responses by dectin-2 with preterm delivery: An experimental model.
Title: Association of modulation of pro-inflammatory responses by dectin-2 with preterm delivery: An experimental model.
Deletion of hematopoietic Dectin-2 or CARD9 does not protect against atherosclerotic plaque formation in hyperlipidemic mice.
Title: Deletion of hematopoietic Dectin-2 or CARD9 does not protect against atherosclerotic plaque formation in hyperlipidemic mice.

Submit: New GeneRIF Correction See all GeneRIFs (42)

Variation

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Alleles

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

Targeted (4) 1 citation
Endonuclease-mediated (5)

General gene information

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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
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
involved_in antifungal innate immune response	IMP Inferred from Mutant Phenotype 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
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 T-helper 17 type immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay 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
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

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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)

NM_001190320.1 → NP_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:49 → 174

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_001190321.1 → NP_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:45 → 170

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_020001.2 → NP_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

Q9JKF2, Q9JKF3, Q9JKF4

UniProtKB/TrEMBL

Q3V2N1

Related

ENSMUSP00000024118.5, ENSMUST00000024118.11

Conserved Domains (1) summary

cd03590
Location:79 → 204

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)