Clec4a3 C-type lectin domain family 4, member A3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clec4a3provided by RGD
Official Full Name: C-type lectin domain family 4, member A3provided by RGD
Primary source: RGD:1359528
See related: Ensembl:ENSRNOG00000010018 AllianceGenome:RGD:1359528
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Dcir3
Summary: Predicted to enable calcium ion binding activity and mannose binding 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 integral component of 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, Apr 2022]
Expression: Biased expression in Spleen (RPKM 255.1), Lung (RPKM 71.0) and 8 other tissues See more
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Genomic context

Location:: 4q42

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (157885899..157896728)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (156214030..156224818)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (155913366..155923079, complement)

Chromosome 4 - NC_086022.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

APLEC influences innate immunity and responses to infectious agents.
Title: The rat antigen-presenting lectin-like receptor complex influences innate immunity and development of infectious diseases.
Rat APLEC is associated with susceptibility to polyarthritis.
Title: Association of arthritis with a gene complex encoding C-type lectin-like receptors.

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General gene information

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Gene Ontology Provided by RGD

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	ISO Inferred from Sequence Orthology more info
enables mannose binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in CD8-positive, alpha-beta T cell activation	ISO Inferred from Sequence Orthology 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 negative regulation of cytokine production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in plasmacytoid dendritic cell antigen processing and presentation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: C-type lectin domain family 4, member A3

Names: antigen-presenting cell lectin-like receptor complex APLEC; dendritic cell inhibitory receptor 3

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_001005891.1 → NP_001005891.1 C-type lectin domain family 4, member A3

See identical proteins and their annotated locations for NP_001005891.1

Status: PROVISIONAL

Source sequence(s)

AY397671

UniProtKB/TrEMBL

A6ILG4, Q2TUL9, Q5YIS0

Related

ENSRNOP00000013308.3, ENSRNOT00000013308.6

Conserved Domains (1) summary

cd03590
Location:107 → 231

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_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

157885899..157896728

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039107889.2 → XP_038963817.1 C-type lectin domain family 4, member A3 isoform X1

UniProtKB/TrEMBL

E9PT25

Conserved Domains (1) summary

cd03590
Location:107 → 231

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)