Nlrc3 NLR family, CARD domain containing 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nlrc3provided by MGI
Official Full Name: NLR family, CARD domain containing 3provided by MGI
Primary source: MGI:MGI:2444070
See related: Ensembl:ENSMUSG00000049871 AllianceGenome:MGI:2444070
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: CLR16.2; mFLJ00348; D230007K08Rik
Summary: Enables phosphatidylinositol 3-kinase regulatory subunit binding activity. Involved in several processes, including negative regulation of cell population proliferation; negative regulation of cytokine production; and negative regulation of defense response. Acts upstream of or within negative regulation of I-kappaB kinase/NF-kappaB signaling; regulation of protein ubiquitination; and response to lipopolysaccharide. Predicted to be located in centriolar satellite; intracellular membrane-bounded organelle; and perinuclear region of cytoplasm. Predicted to be active in cytosol. Orthologous to human NLRC3 (NLR family CARD domain containing 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in thymus adult (RPKM 24.8), spleen adult (RPKM 10.4) and 5 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 A1; 16 2.32 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (3762871..3796881, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (3943807..3979017, complement)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dynamic bidirectional regulation of NLRC3 and gammaherpesviruses during viral latency in B lymphocytes.
Title: Dynamic bidirectional regulation of NLRC3 and gammaherpesviruses during viral latency in B lymphocytes.
NLRC3 deficiency promotes hypoxia-induced pulmonary hypertension development via IKK/NF-kappaB p65/HIF-1alpha pathway.
Title: NLRC3 deficiency promotes hypoxia-induced pulmonary hypertension development via IKK/NF-κB p65/HIF-1α pathway.
NLRC3 Participates in Inhibiting the Pulmonary Inflammatory Response of Sepsis-Induced Acute Lung Injury.
Title: NLRC3 Participates in Inhibiting the Pulmonary Inflammatory Response of Sepsis-Induced Acute Lung Injury.
NLRC3 expression in macrophage impairs glycolysis and host immune defense by modulating the NF-kappaB-NFAT5 complex during septic immunosuppression.
Title: NLRC3 expression in macrophage impairs glycolysis and host immune defense by modulating the NF-κB-NFAT5 complex during septic immunosuppression.
NLRC3 deficiency promotes cutaneous wound healing due to the inhibition of p53 signaling.
Title: NLRC3 deficiency promotes cutaneous wound healing due to the inhibition of p53 signaling.
Nlrc3 Knockout Mice Showed Renal Pathological Changes After HTNV Infection.
Title: Nlrc3 Knockout Mice Showed Renal Pathological Changes After HTNV Infection.
NLRC3 Delays the Progression of AD in APP/PS1 Mice via Inhibiting PI3K Activation.
Title: NLRC3 Delays the Progression of AD in APP/PS1 Mice via Inhibiting PI3K Activation.
NLRC3 alleviates hypoxia/reoxygenation induced inflammation in RAW264.7 cells by inhibiting K63-linked ubiquitination of TRAF6.
Title: NLRC3 alleviates hypoxia/reoxygenation induced inflammation in RAW264.7 cells by inhibiting K63-linked ubiquitination of TRAF6.
Results revealed that NLRC3 attenuates the antigen-presenting function of dendritic cells (DCs) and their ability to activate and polarize naive CD4+ T cells into Th1 and Th17 subsets and thereby restricts experimental autoimmune encephalomyelitis (EAE) progression. NLRC3 has a negative effect via regulating p38 signal pathway in DCs.
Title: NLRC3 expression in dendritic cells attenuates CD4(+) T cell response and autoimmunity.
By NLRC3 diminishes its interaction with STING.
Title: Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Variation

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Alleles

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

Targeted (4) 1 citation
Endonuclease-mediated (7) 1 citation

General gene information

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Markers

D9Mit34.1 (e-PCR), detects polymorphism
- UniSTS:131903

PMC133845P3 (e-PCR)
- UniSTS:270670

PMC152246P1 (e-PCR)
- UniSTS:271203

D16Mit32 (e-PCR), detects polymorphism
- UniSTS:116444

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables molecular function inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol 3-kinase regulatory subunit binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in T cell activation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in intracellular signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of NF-kappaB transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of NLRP3 inflammasome complex assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical NF-kappaB signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of canonical NF-kappaB signal transduction	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cytokine production involved in inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of fibroblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interferon-alpha production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interferon-beta production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-1 beta production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-12 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of non-canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to lipopolysaccharide	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in centriolar satellite	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: protein NLRC3

Names: caterpillar 16.2

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_001081280.2 → NP_001074749.1 protein NLRC3 isoform 1

See identical proteins and their annotated locations for NP_001074749.1

Status: VALIDATED

Description

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

Source sequence(s)

AC087900, AC129021

Consensus CDS

CCDS49747.1

UniProtKB/TrEMBL

J3QQ49

Related

ENSMUSP00000137628.2, ENSMUST00000177551.2

Conserved Domains (3) summary

cd00116
Location:792 → 1090

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:845 → 872

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:176 → 342

NACHT; NACHT domain
NM_175547.4 → NP_780756.1 protein NLRC3 isoform 2

See identical proteins and their annotated locations for NP_780756.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two alternate exons in the 5' coding region and uses an alternate downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC087900, AC129021, AK084199

Consensus CDS

CCDS70677.1

UniProtKB/Swiss-Prot

Q5DU56

Related

ENSMUSP00000137325.2, ENSMUST00000180200.8

Conserved Domains (3) summary

smart00368
Location:25 → 51

LRR_RI; Leucine rich repeat, ribonuclease inhibitor type

cd00116
Location:87 → 385

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:140 → 167

LRR_RI; leucine-rich repeat [structural motif]

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_000082.7 Reference GRCm39 C57BL/6J

Range

3762871..3796881 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030249121.2 → XP_030104981.1 protein NLRC3 isoform X8

Conserved Domains (2) summary

sd00033
Location:140 → 167

LRR_RI; leucine-rich repeat [structural motif]

cl39015
Location:5 → 290

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
XM_030249120.2 → XP_030104980.1 protein NLRC3 isoform X7

Conserved Domains (3) summary

smart00368
Location:25 → 51

LRR_RI; Leucine rich repeat, ribonuclease inhibitor type

sd00033
Location:28 → 55

LRR_RI; leucine-rich repeat [structural motif]

cl39015
Location:87 → 392

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
XM_030249119.2 → XP_030104979.1 protein NLRC3 isoform X6

Conserved Domains (2) summary

sd00033
Location:169 → 196

LRR_RI; leucine-rich repeat [structural motif]

cl39015
Location:116 → 414

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
XM_011245906.4 → XP_011244208.1 protein NLRC3 isoform X5

Conserved Domains (2) summary

sd00033
Location:57 → 84

LRR_RI; leucine-rich repeat [structural motif]

cl39015
Location:116 → 421

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
XM_011245903.3 → XP_011244205.1 protein NLRC3 isoform X2

Conserved Domains (5) summary

sd00033
Location:845 → 872

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:176 → 342

NACHT; NACHT domain

pfam17776
Location:492 → 617

NLRC4_HD2; NLRC4 helical domain HD2

pfam17779
Location:432 → 490

NOD2_WH; NOD2 winged helix domain

cl39015
Location:710 → 995

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
XM_011245902.3 → XP_011244204.1 protein NLRC3 isoform X1

Conserved Domains (5) summary

sd00033
Location:733 → 760

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:176 → 342

NACHT; NACHT domain

pfam17776
Location:492 → 617

NLRC4_HD2; NLRC4 helical domain HD2

pfam17779
Location:432 → 490

NOD2_WH; NOD2 winged helix domain

cl39015
Location:792 → 1097

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
XM_036159931.1 → XP_036015824.1 protein NLRC3 isoform X3

Conserved Domains (5) summary

sd00033
Location:673 → 704

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:176 → 342

NACHT; NACHT domain

pfam17776
Location:492 → 617

NLRC4_HD2; NLRC4 helical domain HD2

pfam17779
Location:432 → 490

NOD2_WH; NOD2 winged helix domain

cl39015
Location:662 → 820

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
XM_006522150.3 → XP_006522213.1 protein NLRC3 isoform X4

Conserved Domains (3) summary

pfam05729
Location:176 → 342

NACHT; NACHT domain

pfam17776
Location:492 → 617

NLRC4_HD2; NLRC4 helical domain HD2

pfam17779
Location:432 → 490

NOD2_WH; NOD2 winged helix domain