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

Gene ID: 268857, updated on 8-Feb-2024

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
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Genomic context

See Nlrc3 in Genome Data Viewer
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_000082.7Genomic Context describing neighboring genes Neighboring gene clusterin associated protein 1 Neighboring gene predicted gene 15539 Neighboring gene predicted gene, 57636 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:3976439-3976665 Neighboring gene SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae) Neighboring gene STARR-seq mESC enhancer starr_39914 Neighboring gene deoxyribonuclease I Neighboring gene TNF receptor-associated protein 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

General gene information

Markers

Clone Names

  • FLJ00348, MGC161259

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

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)

  1. NM_001081280.2NP_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:7921090
    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:845872
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:176342
    NACHT; NACHT domain
  2. NM_175547.4NP_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:2551
    LRR_RI; Leucine rich repeat, ribonuclease inhibitor type
    cd00116
    Location:87385
    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:140167
    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

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    3762871..3796881 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030249121.2XP_030104981.1  protein NLRC3 isoform X8

    Conserved Domains (2) summary
    sd00033
    Location:140167
    LRR_RI; leucine-rich repeat [structural motif]
    cl39015
    Location:5290
    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 ...
  2. XM_030249120.2XP_030104980.1  protein NLRC3 isoform X7

    Conserved Domains (3) summary
    smart00368
    Location:2551
    LRR_RI; Leucine rich repeat, ribonuclease inhibitor type
    sd00033
    Location:2855
    LRR_RI; leucine-rich repeat [structural motif]
    cl39015
    Location:87392
    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 ...
  3. XM_030249119.2XP_030104979.1  protein NLRC3 isoform X6

    Conserved Domains (2) summary
    sd00033
    Location:169196
    LRR_RI; leucine-rich repeat [structural motif]
    cl39015
    Location:116414
    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 ...
  4. XM_011245906.4XP_011244208.1  protein NLRC3 isoform X5

    Conserved Domains (2) summary
    sd00033
    Location:5784
    LRR_RI; leucine-rich repeat [structural motif]
    cl39015
    Location:116421
    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 ...
  5. XM_011245903.3XP_011244205.1  protein NLRC3 isoform X2

    Conserved Domains (5) summary
    sd00033
    Location:845872
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:176342
    NACHT; NACHT domain
    pfam17776
    Location:492617
    NLRC4_HD2; NLRC4 helical domain HD2
    pfam17779
    Location:432490
    NOD2_WH; NOD2 winged helix domain
    cl39015
    Location:710995
    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 ...
  6. XM_011245902.3XP_011244204.1  protein NLRC3 isoform X1

    Conserved Domains (5) summary
    sd00033
    Location:733760
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:176342
    NACHT; NACHT domain
    pfam17776
    Location:492617
    NLRC4_HD2; NLRC4 helical domain HD2
    pfam17779
    Location:432490
    NOD2_WH; NOD2 winged helix domain
    cl39015
    Location:7921097
    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 ...
  7. XM_036159931.1XP_036015824.1  protein NLRC3 isoform X3

    Conserved Domains (5) summary
    sd00033
    Location:673704
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:176342
    NACHT; NACHT domain
    pfam17776
    Location:492617
    NLRC4_HD2; NLRC4 helical domain HD2
    pfam17779
    Location:432490
    NOD2_WH; NOD2 winged helix domain
    cl39015
    Location:662820
    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 ...
  8. XM_006522150.3XP_006522213.1  protein NLRC3 isoform X4

    Conserved Domains (3) summary
    pfam05729
    Location:176342
    NACHT; NACHT domain
    pfam17776
    Location:492617
    NLRC4_HD2; NLRC4 helical domain HD2
    pfam17779
    Location:432490
    NOD2_WH; NOD2 winged helix domain

RNA

  1. XR_875809.4 RNA Sequence