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NLRC3 NLR family CARD domain containing 3 [ Homo sapiens (human) ]

Gene ID: 197358, updated on 11-Sep-2019

Summary

Official Symbol
NLRC3provided by HGNC
Official Full Name
NLR family CARD domain containing 3provided by HGNC
Primary source
HGNC:HGNC:29889
See related
Ensembl:ENSG00000167984 MIM:615648
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NOD3; CLR16.2
Summary
This gene encodes a NOD-like receptor family member. The encoded protein is a cytosolic regulator of innate immunity. This protein directly interacts with stimulator of interferon genes (STING), to prevent its proper trafficking, resulting in disruption of STING-dependent activation of the innate immune response. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
Expression
Broad expression in lymph node (RPKM 6.9), spleen (RPKM 4.9) and 23 other tissues See more
Orthologs

Genomic context

See NLRC3 in Genome Data Viewer
Location:
16p13.3
Exon count:
26
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (3539033..3577782, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (3589033..3627392, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene N(alpha)-acetyltransferase 60, NatF catalytic subunit Neighboring gene microRNA 6126 Neighboring gene chromosome 16 open reading frame 90 Neighboring gene ribosomal protein L18 pseudogene 12 Neighboring gene clusterin associated protein 1 Neighboring gene uncharacterized LOC101929732 Neighboring gene uncharacterized LOC105371060 Neighboring gene SLX4 structure-specific endonuclease subunit Neighboring gene deoxyribonuclease 1 Neighboring gene TNF receptor associated protein 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of NLR family, CARD domain containing 3 (NLRC3) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cytosolic sensors of pathogen-associated DNA, organism-specific biosystem (from REACTOME)
    Cytosolic sensors of pathogen-associated DNA, organism-specific biosystemPresence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon ...
  • IRF3-mediated induction of type I IFN, organism-specific biosystem (from REACTOME)
    IRF3-mediated induction of type I IFN, organism-specific biosystemTANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) are central regulators of type-I interferon induction during bacterial or viral infection. TBK1 was found to form complexes with...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • STING mediated induction of host immune responses, organism-specific biosystem (from REACTOME)
    STING mediated induction of host immune responses, organism-specific biosystemSTING (stimulator of IFN genes; also known as MITA/ERIS/MPYS/TMEM173) is an endoplasmic reticulum (ER) resident, which is required for effective type I IFN production in response to nucleic acids. In...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ00348

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
phosphatidylinositol 3-kinase regulatory subunit binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
I-kappaB kinase/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
T cell activation IEP
Inferred from Expression Pattern
more info
PubMed 
intracellular signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of I-kappaB kinase/NF-kappaB signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of NIK/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of NLRP3 inflammasome complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cytokine production involved in inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of fibroblast proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of inflammatory response IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of innate immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of interferon-alpha production ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of interferon-beta production ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-6 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of phosphatidylinositol 3-kinase signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of tumor necrosis factor production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of tumor necrosis factor production IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
microtubule organizing center IDA
Inferred from Direct Assay
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
NLR family CARD domain-containing protein 3
Names
CARD15-like protein
NACHT, LRR and CARD domains-containing protein 3
NOD-like receptor C3
caterpiller protein 16.2
nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_033123.1 RefSeqGene

    Range
    4989..43359
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_178844.4NP_849172.2  NLR family CARD domain-containing protein 3

    See identical proteins and their annotated locations for NP_849172.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the protein.
    Source sequence(s)
    AK090431, AK090476, AW271824, AY601811, BC027864, FJ889357
    Consensus CDS
    CCDS73817.1
    UniProtKB/Swiss-Prot
    Q7RTR2
    UniProtKB/TrEMBL
    C3VPR7, Q8NF06
    Related
    ENSP00000352039.6, ENST00000359128.10
    Conserved Domains (4) summary
    cd00116
    Location:7661053
    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:808833
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05729
    Location:139305
    NACHT; NACHT domain
    pfam13855
    Location:9741042
    LRR_8; Leucine rich repeat

RNA

  1. NR_075083.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in a 5' exon and contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK090431, AK090476, AW271824, AY601811, BC027864, FJ889357
    Related
    ENST00000615877.4

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    3539033..3577782 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023036.2XP_016878525.1  NLR family CARD domain-containing protein 3 isoform X1

  2. XM_017023038.2XP_016878527.1  NLR family CARD domain-containing protein 3 isoform X3

  3. XM_017023037.2XP_016878526.1  NLR family CARD domain-containing protein 3 isoform X2

  4. XM_017023027.2XP_016878516.1  NLR family CARD domain-containing protein 3 isoform X1

  5. XM_017023031.2XP_016878520.1  NLR family CARD domain-containing protein 3 isoform X1

  6. XM_017023035.2XP_016878524.1  NLR family CARD domain-containing protein 3 isoform X1

  7. XM_017023034.2XP_016878523.1  NLR family CARD domain-containing protein 3 isoform X1

  8. XM_017023028.2XP_016878517.1  NLR family CARD domain-containing protein 3 isoform X1

  9. XM_017023033.2XP_016878522.1  NLR family CARD domain-containing protein 3 isoform X1

  10. XM_017023029.2XP_016878518.1  NLR family CARD domain-containing protein 3 isoform X1

  11. XM_017023030.2XP_016878519.1  NLR family CARD domain-containing protein 3 isoform X1

  12. XM_017023039.1XP_016878528.1  NLR family CARD domain-containing protein 3 isoform X4

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