Human Gene NLRC3 (uc010btn.3) Description and Page Index
  Description: Homo sapiens NLR family, CARD domain containing 3 (NLRC3), transcript variant 1, mRNA.
RefSeq Summary (NM_178844): 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].
Transcript (Including UTRs)
   Position: hg19 chr16:3,589,036-3,627,392 Size: 38,357 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr16:3,591,825-3,615,037 Size: 23,213 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:3,589,036-3,627,392)mRNA (may differ from genome)Protein (1065 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NLRC3_HUMAN
DESCRIPTION: RecName: Full=Protein NLRC3; AltName: Full=CARD15-like protein; AltName: Full=Caterpiller protein 16.2; Short=CLR16.2; AltName: Full=Nucleotide-binding oligomerization domain protein 3;
FUNCTION: May modulate T-cell activation. Decreases the transcription of genes that are normally up-regulated after T-cell stimulation. Delays degradation of NFKBIA/IKBA.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Detected in peripheral blood mononuclear cells.
INDUCTION: Down-regulated upon T-cell activation.
SIMILARITY: Belongs to the NLRP family.
SIMILARITY: Contains 16 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 NACHT domain.
SEQUENCE CAUTION: Sequence=BAC03412.1; Type=Erroneous initiation;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.27 RPKM in Spleen
Total median expression: 58.93 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -197.60411-0.481 Picture PostScript Text
3' UTR -914.382789-0.328 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007111 - NACHT_NTPase

Pfam Domains:
PF05729 - NACHT domain
PF13516 - Leucine Rich repeat

SCOP Domains:
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on Q7RTR2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003674 molecular_function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0036312 phosphatidylinositol 3-kinase regulatory subunit binding

Biological Process:
GO:0007249 I-kappaB kinase/NF-kappaB signaling
GO:0014067 negative regulation of phosphatidylinositol 3-kinase signaling
GO:0032088 negative regulation of NF-kappaB transcription factor activity
GO:0032687 negative regulation of interferon-alpha production
GO:0032688 negative regulation of interferon-beta production
GO:0032715 negative regulation of interleukin-6 production
GO:0032720 negative regulation of tumor necrosis factor production
GO:0042110 T cell activation
GO:0043124 negative regulation of I-kappaB kinase/NF-kappaB signaling
GO:0045824 negative regulation of innate immune response
GO:0048147 negative regulation of fibroblast proliferation
GO:0050680 negative regulation of epithelial cell proliferation
GO:0050728 negative regulation of inflammatory response
GO:1900016 negative regulation of cytokine production involved in inflammatory response
GO:1900226 negative regulation of NLRP3 inflammasome complex assembly
GO:1901223 negative regulation of NIK/NF-kappaB signaling

Cellular Component:
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC027864 - Homo sapiens cDNA clone IMAGE:5203014.
AY601811 - Homo sapiens caterpiller 16.2 mRNA, complete cds.
AK074109 - Homo sapiens mRNA for FLJ00180 protein.
AK090431 - Homo sapiens mRNA for FLJ00348 protein.
JD134057 - Sequence 115081 from Patent EP1572962.
JD339402 - Sequence 320426 from Patent EP1572962.
JD382483 - Sequence 363507 from Patent EP1572962.
JD440181 - Sequence 421205 from Patent EP1572962.
JD360419 - Sequence 341443 from Patent EP1572962.
JD512005 - Sequence 493029 from Patent EP1572962.
JD064728 - Sequence 45752 from Patent EP1572962.
JD146611 - Sequence 127635 from Patent EP1572962.
JD158316 - Sequence 139340 from Patent EP1572962.
JD113784 - Sequence 94808 from Patent EP1572962.
JD260039 - Sequence 241063 from Patent EP1572962.
JD421637 - Sequence 402661 from Patent EP1572962.
JD302788 - Sequence 283812 from Patent EP1572962.
JD114541 - Sequence 95565 from Patent EP1572962.
JD361595 - Sequence 342619 from Patent EP1572962.
JD064019 - Sequence 45043 from Patent EP1572962.
JD358122 - Sequence 339146 from Patent EP1572962.
JD334503 - Sequence 315527 from Patent EP1572962.
JD532123 - Sequence 513147 from Patent EP1572962.
JD495893 - Sequence 476917 from Patent EP1572962.
JD549041 - Sequence 530065 from Patent EP1572962.
JD342460 - Sequence 323484 from Patent EP1572962.
JD064563 - Sequence 45587 from Patent EP1572962.
JD487955 - Sequence 468979 from Patent EP1572962.
JD348676 - Sequence 329700 from Patent EP1572962.
JD397321 - Sequence 378345 from Patent EP1572962.
JD476865 - Sequence 457889 from Patent EP1572962.
JD489481 - Sequence 470505 from Patent EP1572962.
JD489482 - Sequence 470506 from Patent EP1572962.
JD371365 - Sequence 352389 from Patent EP1572962.
JD524782 - Sequence 505806 from Patent EP1572962.
JD352581 - Sequence 333605 from Patent EP1572962.
JD491331 - Sequence 472355 from Patent EP1572962.
JD106822 - Sequence 87846 from Patent EP1572962.
JD254694 - Sequence 235718 from Patent EP1572962.
JD519144 - Sequence 500168 from Patent EP1572962.
JD524796 - Sequence 505820 from Patent EP1572962.
JD352594 - Sequence 333618 from Patent EP1572962.
JD558577 - Sequence 539601 from Patent EP1572962.
JD358274 - Sequence 339298 from Patent EP1572962.
JD236311 - Sequence 217335 from Patent EP1572962.
JD302248 - Sequence 283272 from Patent EP1572962.
JD250278 - Sequence 231302 from Patent EP1572962.
JD370057 - Sequence 351081 from Patent EP1572962.
JD339520 - Sequence 320544 from Patent EP1572962.
JD173545 - Sequence 154569 from Patent EP1572962.
JD448091 - Sequence 429115 from Patent EP1572962.
FJ889357 - Homo sapiens NLRC3 (NLRC3) mRNA, complete cds.
BC169297 - Synthetic construct Homo sapiens clone IMAGE:9093249 NOD3 protein (NLRC3) gene, partial cds.
JD525223 - Sequence 506247 from Patent EP1572962.
JD061109 - Sequence 42133 from Patent EP1572962.
JD465356 - Sequence 446380 from Patent EP1572962.
JD317485 - Sequence 298509 from Patent EP1572962.
JD098288 - Sequence 79312 from Patent EP1572962.
JD497319 - Sequence 478343 from Patent EP1572962.
AF501291 - Homo sapiens CARD15-like protein mRNA, partial cds, alternatively spliced.
AF501292 - Homo sapiens CARD15-like protein mRNA, partial cds, alternatively spliced.
JD061890 - Sequence 42914 from Patent EP1572962.
JD343149 - Sequence 324173 from Patent EP1572962.
JD155654 - Sequence 136678 from Patent EP1572962.
JD067878 - Sequence 48902 from Patent EP1572962.
JD156073 - Sequence 137097 from Patent EP1572962.
BC169296 - Synthetic construct Homo sapiens clone IMAGE:9093240 NOD3 protein (NLRC3) gene, partial cds.
AK090476 - Homo sapiens mRNA for FLJ00398 protein.
JD095200 - Sequence 76224 from Patent EP1572962.
JD483259 - Sequence 464283 from Patent EP1572962.
JD157577 - Sequence 138601 from Patent EP1572962.
JD275968 - Sequence 256992 from Patent EP1572962.
JD067486 - Sequence 48510 from Patent EP1572962.
BC169295 - Synthetic construct Homo sapiens clone IMAGE:9093248 NOD3 protein (NLRC3) gene, partial cds.
JD050758 - Sequence 31782 from Patent EP1572962.
JD445960 - Sequence 426984 from Patent EP1572962.
JD404706 - Sequence 385730 from Patent EP1572962.
JD057035 - Sequence 38059 from Patent EP1572962.
JD265720 - Sequence 246744 from Patent EP1572962.
JD086166 - Sequence 67190 from Patent EP1572962.
JD257343 - Sequence 238367 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NLRC3_HUMAN, NM_178844, NOD3, NP_849172, Q5EY36, Q7RTR2, Q8NF48, Q8NI01, Q8NI02, Q8TEL3
UCSC ID: uc010btn.3
RefSeq Accession: NM_178844
Protein: Q7RTR2 (aka NLRC3_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178844.2
exon count: 21CDS single in 3' UTR: no RNA size: 6401
ORF size: 3199CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3719.50frame shift in genome: no % Coverage: 99.91
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.