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NOD2 nucleotide binding oligomerization domain containing 2 [ Homo sapiens (human) ]

Gene ID: 64127, updated on 14-Mar-2020

Summary

Official Symbol
NOD2provided by HGNC
Official Full Name
nucleotide binding oligomerization domain containing 2provided by HGNC
Primary source
HGNC:HGNC:5331
See related
Ensembl:ENSG00000167207 MIM:605956
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
CD; ACUG; BLAU; IBD1; YAOS; BLAUS; NLRC2; NOD2B; CARD15; CLR16.3; PSORAS1
Summary
This gene is a member of the Nod1/Apaf-1 family and encodes a protein with two caspase recruitment (CARD) domains and six leucine-rich repeats (LRRs). The protein is primarily expressed in the peripheral blood leukocytes. It plays a role in the immune response to intracellular bacterial lipopolysaccharides (LPS) by recognizing the muramyl dipeptide (MDP) derived from them and activating the NFKB protein. Mutations in this gene have been associated with Crohn disease and Blau syndrome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
Expression
Broad expression in bone marrow (RPKM 3.3), appendix (RPKM 2.5) and 16 other tissues See more
Orthologs

Genomic context

See NOD2 in Genome Data Viewer
Location:
16q12.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (50693587..50733077)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (50727507..50766990)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NKD inhibitor of WNT signaling pathway 1 Neighboring gene uncharacterized LOC101927272 Neighboring gene sorting nexin 20 Neighboring gene uncharacterized LOC102724907 Neighboring gene microRNA 3181 Neighboring gene CYLD lysine 63 deubiquitinase Neighboring gene uncharacterized LOC105371251 Neighboring gene long intergenic non-protein coding RNA 2168

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?

Phenotypes

Associated conditions

Description Tests
Blau syndrome
MedGen: C1861303 OMIM: 186580 GeneReviews: Not available
Compare labs
Inflammatory bowel disease 1
MedGen: C0678202 OMIM: 266600 GeneReviews: Not available
Compare labs
Yao syndrome
MedGen: C4310620 OMIM: 617321 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study identifies IL23R as an inflammatory bowel disease gene.
NHGRI GWA Catalog
A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300.
NHGRI GWA Catalog
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
NHGRI GWA Catalog
Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy.
NHGRI GWA Catalog
Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.
NHGRI GWA Catalog
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
NHGRI GWA Catalog
Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci.
NHGRI GWA Catalog
Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis.
NHGRI GWA Catalog
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Genomewide association study of leprosy.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease.
NHGRI GWA Catalog
Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4.
NHGRI GWA Catalog
Systematic association mapping identifies NELL1 as a novel IBD disease gene.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr upregulates the gene expression of NOD2 in human monocyte-derived dendritic cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
CARD domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
Hsp70 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Hsp90 protein binding IDA
Inferred from Direct Assay
more info
PubMed 
actin binding IDA
Inferred from Direct Assay
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
muramyl dipeptide binding IDA
Inferred from Direct Assay
more info
PubMed 
peptidoglycan binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
JNK cascade TAS
Traceable Author Statement
more info
 
activation of MAPK activity TAS
Traceable Author Statement
more info
 
cellular response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to muramyl dipeptide IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to muramyl dipeptide IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
 
cellular response to peptidoglycan IEA
Inferred from Electronic Annotation
more info
 
cytokine production involved in immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytokine secretion involved in immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
defense response TAS
Traceable Author Statement
more info
PubMed 
defense response to bacterium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
defense response to bacterium IDA
Inferred from Direct Assay
more info
PubMed 
detection of bacterium IDA
Inferred from Direct Assay
more info
PubMed 
detection of biotic stimulus TAS
Traceable Author Statement
more info
PubMed 
detection of muramyl dipeptide IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response NAS
Non-traceable Author Statement
more info
PubMed 
interleukin-1-mediated signaling pathway TAS
Traceable Author Statement
more info
 
intracellular signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
maintenance of gastrointestinal epithelium IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of macrophage apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleotide-binding oligomerization domain containing 2 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
nucleotide-binding oligomerization domain containing signaling pathway TAS
Traceable Author Statement
more info
 
positive regulation of B cell activation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of JNK cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of MAP kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity TAS
Traceable Author Statement
more info
 
positive regulation of NIK/NF-kappaB signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of Notch signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cytokine production involved in inflammatory response IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of dendritic cell antigen processing and presentation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of dendritic cell cytokine production IEA
Inferred from Electronic Annotation
more info
 
positive regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of gamma-delta T cell activation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-1 beta production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-1 beta secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-10 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-17 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-8 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of nitric-oxide synthase biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of oxidoreductase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of phosphatidylinositol 3-kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of prostaglandin-E synthase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of prostaglandin-endoperoxide synthase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein K63-linked ubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of stress-activated MAPK cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of tumor necrosis factor production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of tumor necrosis factor production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of type 2 immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of inflammatory response IC
Inferred by Curator
more info
PubMed 
response to muramyl dipeptide IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to muramyl dipeptide IDA
Inferred from Direct Assay
more info
PubMed 
response to muramyl dipeptide IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to nutrient IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
basolateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytoskeleton 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
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
nucleotide-binding oligomerization domain-containing protein 2
Names
NLR family, CARD domain containing 2
NOD-like receptor C2
caspase recruitment domain family, member 15
caspase recruitment domain protein 15
caspase recruitment domain-containing protein 15
inflammatory bowel disease protein 1
nucleotide-binding oligomerization domain 2
nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2

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_007508.1 RefSeqGene

    Range
    5001..40939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_177

mRNA and Protein(s)

  1. NM_001293557.2NP_001280486.1  nucleotide-binding oligomerization domain-containing protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001280486.1

    Status: REVIEWED

    Source sequence(s)
    AC007608, AC007728
    Consensus CDS
    CCDS86525.1
    UniProtKB/Swiss-Prot
    Q9HC29
    Conserved Domains (6) summary
    cd08788
    Location:107187
    CARD_NOD2_2_CARD15; Caspase activation and recruitment domain of NOD2, repeat 2
    sd00033
    Location:793817
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:737764
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:266436
    NACHT; NACHT domain
    cl14633
    Location:792
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl29113
    Location:7401005
    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. NM_001370466.1NP_001357395.1  nucleotide-binding oligomerization domain-containing protein 2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC007608, AC007728
    Related
    ENSP00000495993.1, ENST00000647318.1
    Conserved Domains (6) summary
    cd08788
    Location:107187
    CARD_NOD2_2_CARD15; Caspase activation and recruitment domain of NOD2, repeat 2
    sd00033
    Location:793817
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:737764
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:266436
    NACHT; NACHT domain
    cl14633
    Location:792
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl29113
    Location:7401005
    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. NM_022162.3NP_071445.1  nucleotide-binding oligomerization domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_071445.1

    Status: REVIEWED

    Source sequence(s)
    AC007608, AC007728
    Consensus CDS
    CCDS10746.1
    UniProtKB/Swiss-Prot
    Q9HC29
    Related
    ENSP00000300589.2, ENST00000300589.6
    Conserved Domains (7) summary
    COG4886
    Location:7951040
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    cd00116
    Location:7671032
    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 ...
    cd08788
    Location:134214
    CARD_NOD2_2_CARD15; Caspase activation and recruitment domain of NOD2, repeat 2
    sd00033
    Location:820844
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:764791
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:293463
    NACHT; NACHT domain
    cl14633
    Location:34119
    DD; Death Domain Superfamily of protein-protein interaction domains

RNA

  1. NR_163434.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC007608, AC007728
    Related
    ENST00000646677.1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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
    50693587..50733077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023536.1XP_016879025.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X4

    Conserved Domains (4) summary
    cd00116
    Location:545810
    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:598622
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:542569
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:71241
    NACHT; NACHT domain
  2. XM_017023537.1XP_016879026.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X4

    Conserved Domains (4) summary
    cd00116
    Location:545810
    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:598622
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:542569
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:71241
    NACHT; NACHT domain
  3. XM_006721242.4XP_006721305.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X2

    Conserved Domains (7) summary
    COG4886
    Location:768985
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    cd00116
    Location:753977
    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 ...
    cd08788
    Location:107187
    CARD_NOD2_2_CARD15; Caspase activation and recruitment domain of NOD2, repeat 2
    sd00033
    Location:793817
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:737752
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:266436
    NACHT; NACHT domain
    cl14633
    Location:792
    DD; Death Domain Superfamily of protein-protein interaction domains
  4. XM_011523260.3XP_011521562.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X6

    See identical proteins and their annotated locations for XP_011521562.1

    UniProtKB/TrEMBL
    A0A286YF65
    Conserved Domains (3) summary
    cd08787
    Location:792
    CARD_NOD2_1_CARD15; Caspase activation and recruitment domain of NOD2, repeat 1
    cd08788
    Location:107187
    CARD_NOD2_2_CARD15; Caspase activation and recruitment domain of NOD2, repeat 2
    pfam05729
    Location:266436
    NACHT; NACHT domain
  5. XM_006721243.4XP_006721306.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X5

    See identical proteins and their annotated locations for XP_006721306.1

    UniProtKB/TrEMBL
    A0A286YF65
    Related
    ENSP00000493088.1, ENST00000641284.1
    Conserved Domains (3) summary
    cd08787
    Location:792
    CARD_NOD2_1_CARD15; Caspase activation and recruitment domain of NOD2, repeat 1
    cd08788
    Location:107187
    CARD_NOD2_2_CARD15; Caspase activation and recruitment domain of NOD2, repeat 2
    pfam05729
    Location:266436
    NACHT; NACHT domain
  6. XM_011523261.2XP_011521563.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X7

    See identical proteins and their annotated locations for XP_011521563.1

    UniProtKB/TrEMBL
    A0A286YF65
    Conserved Domains (3) summary
    cd08787
    Location:792
    CARD_NOD2_1_CARD15; Caspase activation and recruitment domain of NOD2, repeat 1
    cd08788
    Location:107187
    CARD_NOD2_2_CARD15; Caspase activation and recruitment domain of NOD2, repeat 2
    pfam05729
    Location:266436
    NACHT; NACHT domain
  7. XM_011523259.2XP_011521561.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X4

    Conserved Domains (4) summary
    cd00116
    Location:545810
    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:598622
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:542569
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:71241
    NACHT; NACHT domain
  8. XM_017023538.1XP_016879027.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X4

    Conserved Domains (4) summary
    cd00116
    Location:545810
    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:598622
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:542569
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:71241
    NACHT; NACHT domain
  9. XM_017023535.1XP_016879024.1  nucleotide-binding oligomerization domain-containing protein 2 isoform X3

RNA

  1. XR_933387.2 RNA Sequence

  2. XR_429725.3 RNA Sequence

  3. XR_429726.3 RNA Sequence

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