Clec4a C-type lectin domain family 4, member A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clec4aprovided by RGD
Official Full Name: C-type lectin domain family 4, member Aprovided by RGD
Primary source: RGD:1359662
See related: EnsemblRapid:ENSRNOG00000010045 AllianceGenome:RGD:1359662
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: Dcir1; 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 positive regulation of immune response; regulation of cytokine production; and response to fungus. 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, Dec 2024]
Expression: Biased expression in Spleen (RPKM 91.9), Thymus (RPKM 32.1) and 9 other tissues See more
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Genomic context

Location:: 4q42

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (158026138..158119904)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (156340439..156434212)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (156049800..156069260)

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?

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables D-mannose binding	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation 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 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

Process	Evidence Code	Pubs
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 antifungal innate immune response	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 defense response to fungus	ISO Inferred from Sequence Orthology more info
involved_in detection of yeast	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	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	ISS Inferred from Sequence or Structural Similarity more info
involved_in plasmacytoid dendritic cell antigen processing and presentation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T-helper 17 type immune response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of intracellular signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of positive regulation of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in response to yeast	ISO Inferred from Sequence Orthology more info
involved_in stimulatory C-type lectin receptor signaling pathway	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
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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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 inhibitory receptor 1

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_001005899.2 → NP_001005899.2 C-type lectin domain family 4 member A

See identical proteins and their annotated locations for NP_001005899.2

Status: PROVISIONAL

Source sequence(s)

AY581051

UniProtKB/Swiss-Prot

Q67EQ0

UniProtKB/TrEMBL

Q2TUM1, Q56TZ2

Related

ENSRNOP00000072877.2, ENSRNOT00000077840.4

Conserved Domains (1) summary

cd03590
Location:107 → 235

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

158026138..158119904

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039108012.1 → XP_038963940.1 C-type lectin domain family 4 member A isoform X3

Conserved Domains (1) summary

cd03590
Location:79 → 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)
XM_017592740.2 → XP_017448229.1 C-type lectin domain family 4 member A isoform X1

UniProtKB/Swiss-Prot

Q67EQ0

UniProtKB/TrEMBL

A0A0G2K425, Q2TUM1
XM_063286437.1 → XP_063142507.1 C-type lectin domain family 4 member A isoform X2

UniProtKB/Swiss-Prot

Q67EQ0

UniProtKB/TrEMBL

Q2TUM1
XM_017592741.2 → XP_017448230.1 C-type lectin domain family 4 member A isoform X2

UniProtKB/Swiss-Prot

Q67EQ0

UniProtKB/TrEMBL

Q2TUM1