Clec4a2 C-type lectin domain family 4, member a2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clec4a2provided by MGI
Official Full Name: C-type lectin domain family 4, member a2provided by MGI
Primary source: MGI:MGI:1349412
See related: Ensembl:ENSMUSG00000030148 AllianceGenome:MGI:1349412
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: DCIR; Dcir1; Clec4a; Clecsf6
Summary: Predicted to enable D-mannose binding activity; calcium ion binding activity; and pattern recognition receptor activity. Predicted to be involved in several processes, including antifungal innate immune response; negative regulation of tumor necrosis factor production; and plasmacytoid dendritic cell antigen processing and presentation. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC4A (C-type lectin domain family 4 member A). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in liver E18 (RPKM 3.2), bladder adult (RPKM 1.3) and 13 other tissues See more
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 6 F2; 6 58.18 cM

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (123099627..123119891)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (123122690..123143999)

Chromosome 6 - NC_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The C-type lectin DCIR contributes to the immune response and pathogenesis of colorectal cancer.
Title: The C-type lectin DCIR contributes to the immune response and pathogenesis of colorectal cancer.
DCIR suppresses osteoclastic proliferation and resorption by downregulating M-CSF and RANKL signaling.
Title: DCIR suppresses osteoclastic proliferation and resorption by downregulating M-CSF and RANKL signaling.
Blocking DCIR mitigates colitis and prevents colorectal tumors by enhancing the GM-CSF-STAT5 pathway.
Title: Blocking DCIR mitigates colitis and prevents colorectal tumors by enhancing the GM-CSF-STAT5 pathway.
C-type lectin receptor CLEC4A2 promotes tissue adaptation of macrophages and protects against atherosclerosis.
Title: C-type lectin receptor CLEC4A2 promotes tissue adaptation of macrophages and protects against atherosclerosis.
DCIR and its ligand asialo-biantennary N-glycan regulate DC function and osteoclastogenesis.
Title: DCIR and its ligand asialo-biantennary N-glycan regulate DC function and osteoclastogenesis.
DCIR modulates immunity to M. tuberculosis through sustaining type I IFN signaling in DCs, which reduces IL-12-p70 production and Th1 expansion. As a consequence, DCIR-deficient mice control M. tuberculosis infection better than their WT counterparts but also develop more immunopathology in the lungs.
Title: C-type lectin receptor DCIR modulates immunity to tuberculosis by sustaining type I interferon signaling in dendritic cells.
this study shows that upon injection of d-galactosamine and lipopolysaccharide, Dcir1-/- mice show decreased mortality rates and serum levels of alanine aminotransferase
Title: Absence of DCIR1 reduces the mortality rate of endotoxemic hepatitis in mice.
Dcir1 enhances the pathogenesis of DSS colitis by altering neutrophil recruitment and their functions.
Title: Dendritic cell immunoreceptor 1 alters neutrophil responses in the development of experimental colitis.
While DCIR1 was ubiquitously expressed on myeloid cells in various immune organs, significant expression of DCAR2 was detected only on subpopulations of conventional dendritic cells from bone marrow and skin-draining lymph nodes.
Title: Ubiquitous versus restricted expression of the two mouse dendritic cell C-type lectin receptors, DCIR1 and DCAR2, among myeloid cells.
MCL-/- as well as DCIR-/- mice exhibited only a slightly increased severity of disease compared to wild-type mice indicating a limited role for MCL and DCIR in the regulation of intestinal immunity.
Title: Role of the C-type lectin receptors MCL and DCIR in experimental colitis.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Variation

Go to the top of the page Help

Alleles

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

Endonuclease-mediated (4)
Targeted (3) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

NoName (e-PCR)
- UniSTS:235554

BE200183 (e-PCR)
- UniSTS:208028

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 calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables carbohydrate binding	IBA Inferred from Biological aspect of Ancestor more info
enables carbohydrate binding	ISO Inferred from Sequence Orthology more info
enables carbohydrate binding	ISS Inferred from Sequence or Structural Similarity more info
enables carbohydrate binding	TAS Traceable Author Statement more info	PubMed
enables pattern recognition receptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in CD8-positive, alpha-beta T cell activation	ISO Inferred from Sequence Orthology more info
involved_in CD8-positive, alpha-beta T cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in 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 antigen processing and presentation of exogenous peptide antigen via MHC class I	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class I	ISS Inferred from Sequence or Structural Similarity more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cytokine production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of tumor necrosis factor production	ISS Inferred from Sequence or Structural Similarity more info
involved_in plasmacytoid dendritic cell antigen processing and presentation	ISO Inferred from Sequence Orthology more info
involved_in plasmacytoid dendritic cell antigen processing and presentation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

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

Names: C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 6; C-type lectin superfamily member 6; dendritic cell immunoreceptor

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001170332.2 → NP_001163803.1 C-type lectin domain family 4 member A isoform b

See identical proteins and their annotated locations for NP_001163803.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform (b).

Source sequence(s)

AC164111

Consensus CDS

CCDS20510.1

UniProtKB/Swiss-Prot

Q4VA33, Q9QZ15

Related

ENSMUSP00000124615.2, ENSMUST00000161365.8

Conserved Domains (1) summary

cd03590
Location:107 → 233

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_001170333.2 → NP_001163804.1 C-type lectin domain family 4 member A isoform a

See identical proteins and their annotated locations for NP_001163804.1

Status: VALIDATED

Description

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

Source sequence(s)

AC164111

Consensus CDS

CCDS51894.1

UniProtKB/TrEMBL

Q923C7

Related

ENSMUSP00000032248.8, ENSMUST00000032248.8

Conserved Domains (1) summary

cd03590
Location:131 → 257

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_001410583.1 → NP_001397512.1 C-type lectin domain family 4 member A isoform c

Status: VALIDATED

Source sequence(s)

AC164111
NM_001410584.1 → NP_001397513.1 C-type lectin domain family 4 member A isoform d

Status: VALIDATED

Source sequence(s)

AC164111
NM_011999.5 → NP_036129.1 C-type lectin domain family 4 member A isoform b

See identical proteins and their annotated locations for NP_036129.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform (b).

Source sequence(s)

AC164111

Consensus CDS

CCDS20510.1

UniProtKB/Swiss-Prot

Q4VA33, Q9QZ15

Related

ENSMUSP00000045781.7, ENSMUST00000041779.13

Conserved Domains (1) summary

cd03590
Location:107 → 233

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)

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

123099627..123119891

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011241364.4 → XP_011239666.1 C-type lectin domain family 4 member A isoform X2

Conserved Domains (1) summary

cl02432
Location:131 → 177

CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
XM_030255403.2 → XP_030111263.1 C-type lectin domain family 4 member A isoform X3

Conserved Domains (1) summary

cl02432
Location:107 → 153

CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain