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    Nlrc4 NLR family, CARD domain containing 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 298784, updated on 18-Sep-2024

    Summary

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    Official Symbol
    Nlrc4provided by RGD
    Official Full Name
    NLR family, CARD domain containing 4provided by RGD
    Primary source
    RGD:1309831
    See related
    EnsemblRapid:ENSRNOG00000005810 AllianceGenome:RGD:1309831
    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
    Ipaf; Card12
    Summary
    Predicted to enable several functions, including ATP binding activity; caspase binding activity; and protein homodimerization activity. Predicted to be involved in several processes, including positive regulation of proteolysis; regulation of gene expression; and response to bacterium. Predicted to act upstream of or within regulation of apoptotic process and regulation of cysteine-type endopeptidase activity involved in apoptotic process. Predicted to be located in cytosol. Predicted to be part of IPAF inflammasome complex. Human ortholog(s) of this gene implicated in familial cold autoinflammatory syndrome 4. Orthologous to human NLRC4 (NLR family CARD domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 61.9), Lung (RPKM 28.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Nlrc4 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (26743658..26771783)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (20991785..21018254)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (22167874..22194755)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134479107 Neighboring gene Yip1 domain family, member 4 Neighboring gene solute carrier family 30 member 6 Neighboring gene uncharacterized LOC103692563 Neighboring gene spastin

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. The pivotal role of the NLRC4 inflammasome in neuroinflammation after intracerebral hemorrhage in rats. Gan H, et al. Exp Mol Med, 2021 Nov. PMID 34848837, Free PMC Article
    2. Gonadal Hormones E2 and P Mitigate Cerebral Ischemia-Induced Upregulation of the AIM2 and NLRC4 Inflammasomes in Rats. Habib P, et al. Int J Mol Sci, 2020 Jul 7. PMID 32645874, Free PMC Article
    3. Cryoelectron Tomography of the NAIP5/NLRC4 Inflammasome: Implications for NLR Activation. Diebolder CA, et al. Structure, 2015 Dec 1. PMID 26585513
    4. Structural and biochemical basis for induced self-propagation of NLRC4. Hu Z, et al. Science, 2015 Oct 23. PMID 26449475
    5. NLRC4-driven production of IL-1β discriminates between pathogenic and commensal bacteria and promotes host intestinal defense. Franchi L, et al. Nat Immunol, 2012 May. PMID 22484733, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The pivotal role of the NLRC4 inflammasome in neuroinflammation after intracerebral hemorrhage in rats.
      Title: The pivotal role of the NLRC4 inflammasome in neuroinflammation after intracerebral hemorrhage in rats.
    2. Gonadal Hormones E2 and P Mitigate Cerebral Ischemia-Induced Upregulation of the AIM2 and NLRC4 Inflammasomes in Rats.
      Title: Gonadal Hormones E2 and P Mitigate Cerebral Ischemia-Induced Upregulation of the AIM2 and NLRC4 Inflammasomes in Rats.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables caspase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables endopeptidase activator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in activation of cysteine-type endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in activation of cysteine-type endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in activation of innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in activation of innate immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in defense response to bacterium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in defense response to bacterium ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in defense response to bacterium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in detection of bacterium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in detection of bacterium ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in detection of bacterium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of NF-kappaB transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of NF-kappaB transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interleukin-1 beta production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interleukin-1 beta production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of protein processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein homooligomerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein homooligomerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in pyroptotic inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in pyroptotic inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of cysteine-type endopeptidase activity involved in apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of IPAF inflammasome complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of IPAF inflammasome complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in intracellular membrane-bounded organelle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    NLR family CARD domain-containing protein 4
    Names
    caspase recruitment domain family, member 12
    ice protease-activating factor

    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_001309432.1 → NP_001296361.1  NLR family CARD domain-containing protein 4

      See identical proteins and their annotated locations for NP_001296361.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000006
      UniProtKB/Swiss-Prot
      F1M649
      UniProtKB/TrEMBL
      A6H9Y2
      Conserved Domains (4) summary
      cd00116
      Location:736 → 1008
      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 ...
      sd00034
      Location:663 → 688
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam00619
      Location:1 → 86
      CARD; Caspase recruitment domain
      cl21455
      Location:163 → 316
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    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

    1. NC_086024.1 Reference GRCr8

      Range
      26743658..26771783
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008764491.4 → XP_008762713.1  NLR family CARD domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_008762713.1

      UniProtKB/Swiss-Prot
      F1M649
      UniProtKB/TrEMBL
      A6H9Y2
      Related
      ENSRNOP00000007655.6, ENSRNOT00000007655.9
      Conserved Domains (4) summary
      cd00116
      Location:736 → 1008
      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 ...
      sd00034
      Location:663 → 688
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam00619
      Location:1 → 86
      CARD; Caspase recruitment domain
      cl21455
      Location:163 → 316
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. XM_063261611.1 → XP_063117681.1  NLR family CARD domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A6H9Y2

    3. XM_063261612.1 → XP_063117682.1  NLR family CARD domain-containing protein 4 isoform X3

      UniProtKB/TrEMBL
      A6H9Y2

    RNA

    1. XR_592891.2 RNA Sequence

    2. XR_010052054.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001106707.1: Suppressed sequence

      Description
      NM_001106707.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F1M649.2 GenPept UniProtKB/Swiss-Prot:F1M649

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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