Clec4d C-type lectin domain family 4, member D [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clec4dprovided by RGD
Official Full Name: C-type lectin domain family 4, member Dprovided by RGD
Primary source: RGD:1303339
See related: EnsemblRapid:ENSRNOG00000067848 AllianceGenome:RGD:1303339
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: Mcl; Clecsf8
Summary: Predicted to enable D-mannose binding activity; immunoglobulin receptor binding activity; and pattern recognition receptor activity. Predicted to be involved in antifungal innate immune response; positive regulation of canonical NF-kappaB signal transduction; and positive regulation of myeloid dendritic cell activation. Predicted to act upstream of or within several processes, including Fc-gamma receptor signaling pathway; T cell differentiation involved in immune response; and defense response to other organism. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC4D (C-type lectin domain family 4 member D). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 39.3), Lung (RPKM 39.2) and 7 other tissues See more
Orthologs: human mouse all
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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 (158275287..158286978)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (156589591..156599279)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (156253084..156264766)

Chromosome 4 - NC_086022.1 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: 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?

C-type lectin receptors Mcl and Mincle control development of multiple sclerosis-like neuroinflammation.
Title: C-type lectin receptors Mcl and Mincle control development of multiple sclerosis-like neuroinflammation.
The results presented in this paper suggest that the Mincle/MCL/FcepsilonRI-gamma complex is the functionally optimal form for these C-type lectin receptors on the surface of myeloid cells.
Title: Mincle, the receptor for mycobacterial cord factor, forms a functional receptor complex with MCL and FcεRI-γ.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables D-mannose binding	IEA Inferred from Electronic Annotation more info
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 carbohydrate binding	IBA Inferred from Biological aspect of Ancestor more info
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables immunoglobulin receptor binding	IEA Inferred from Electronic Annotation more info
enables immunoglobulin receptor binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables pattern recognition receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables pattern recognition receptor activity	IEA Inferred from Electronic Annotation more info
enables pattern recognition receptor activity	ISO Inferred from Sequence Orthology more info
enables pattern recognition receptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Fc-gamma receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Fc-gamma receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in T cell differentiation involved in immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within T cell differentiation involved in immune response	ISO Inferred from Sequence Orthology more info
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within adaptive immune response	ISO Inferred from Sequence Orthology more info
involved_in antifungal innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in antifungal innate immune response	IEA Inferred from Electronic Annotation more info
involved_in antifungal innate immune response	ISO Inferred from Sequence Orthology more info
involved_in antifungal innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to bacterium	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within defense response to bacterium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within innate immune response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of myeloid dendritic cell activation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of myeloid dendritic cell activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of myeloid dendritic cell activation	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 plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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

Names: C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 8; C-type lectin superfamily member 8; macrophage C-type 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_001003707.2 → NP_001003707.2 C-type lectin domain family 4 member D

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q2TUL6, Q69FH1

UniProtKB/TrEMBL

A6ILH2, G3V7B1

Related

ENSRNOP00000108621.1, ENSRNOT00000135922.1

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

158275287..158286978

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063286350.1 → XP_063142420.1 C-type lectin domain family 4 member D isoform X4
XM_039107890.2 → XP_038963818.1 C-type lectin domain family 4 member D isoform X3

UniProtKB/Swiss-Prot

Q2TUL6, Q69FH1

Conserved Domains (1) summary

cd03590
Location:46 → 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)
XM_006237322.5 → XP_006237384.1 C-type lectin domain family 4 member D isoform X1

UniProtKB/Swiss-Prot

Q2TUL6, Q69FH1

Conserved Domains (1) summary

cd03590
Location:81 → 205

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_017592704.3 → XP_017448193.1 C-type lectin domain family 4 member D isoform X2

UniProtKB/Swiss-Prot

Q2TUL6, Q69FH1