Clec4m C-type lectin domain family 4 member M [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clec4mprovided by RGD
Official Full Name: C-type lectin domain family 4 member Mprovided by RGD
Primary source: RGD:1561466
See related: EnsemblRapid:ENSRNOG00000029881 AllianceGenome:RGD:1561466
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cd209b
Summary: Predicted to enable several functions, including (1->3)-beta-D-glucan binding activity; mannose binding activity; and virus receptor activity. Predicted to be involved in immune response and viral entry into host cell. Predicted to act upstream of or within several processes, including detection of other organism; phagocytosis, recognition; and positive regulation of tumor necrosis factor production. Predicted to be integral component of membrane. Predicted to be active in external side of plasma membrane. Human ortholog(s) of this gene implicated in Coronavirus infectious disease (multiple); aspergillosis; dengue disease (multiple); human immunodeficiency virus infectious disease (multiple); and tuberculosis (multiple). Orthologous to several human genes including CD209 (CD209 molecule). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 284.2), Thymus (RPKM 56.0) and 1 other tissue See more
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Genomic context

Location:: 12p12

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (6713795..6722414, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (1915902..1924529, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (2817633..2826303, complement)

Chromosome 12 - NC_086030.1 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 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?

Rat CD209b and SIGN-R1 on microglia mediate the SIGN-R1 complement activation pathway against S. pneumoniae, and thereby plays an important role in the pathogenesis of pneumococcal meningitis.
Title: The C-type lectin CD209b is expressed on microglia and it mediates the uptake of capsular polysaccharides of Streptococcus pneumoniae.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables (1->3)-beta-D-glucan binding	ISO Inferred from Sequence Orthology more info
enables D-mannose binding	IBA Inferred from Biological aspect of Ancestor more info
enables D-mannose binding	ISO Inferred from Sequence Orthology more info
enables calcium-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables pattern recognition receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables polysaccharide binding	ISO Inferred from Sequence Orthology more info
enables virus receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within detection of bacterium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within detection of yeast	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endocytosis	ISO Inferred from Sequence Orthology more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within phagocytosis, recognition	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of phagocytosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in receptor-mediated virion attachment to host cell	ISO Inferred from Sequence Orthology more info
involved_in symbiont entry into host cell	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 external side of plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: CD209b antigen

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_001170397.1 → NP_001163868.1 CD209b antigen

Status: VALIDATED

Source sequence(s)

BC091252

UniProtKB/TrEMBL

F1LM87

Related

ENSRNOP00000058462.4, ENSRNOT00000061749.6

Conserved Domains (2) summary

cd03590
Location:189 → 311

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)

cl00173
Location:78 → 164

VIP2; VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of ...

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_086030.1 Reference GRCr8

Range

6713795..6722414 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039089146.2 → XP_038945074.1 CD209b antigen isoform X1

UniProtKB/TrEMBL

A0A8I6ANB8, F1LM87

Conserved Domains (1) summary

cd03590
Location:206 → 328

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)