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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for NOD1 |
Gene summary |
Gene information | Gene symbol | NOD1 | Gene ID | 10392 |
Gene name | nucleotide binding oligomerization domain containing 1 | |
Synonyms | CARD4|CLR7.1|NLRC1 | |
Cytomap | 7p14.3 | |
Type of gene | protein-coding | |
Description | nucleotide-binding oligomerization domain-containing protein 1NLR family, CARD domain containing 1caspase recruitment domain family, member 4caspase recruitment domain-containing protein 4nucleotide-binding oligomerization domain, leucine rich repeat | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
NOD1 | GO:0006919 | activation of cysteine-type endopeptidase activity involved in apoptotic process | 10329646 |
NOD1 | GO:0016045 | detection of bacterium | 15653568 |
NOD1 | GO:0035556 | intracellular signal transduction | 15653568 |
NOD1 | GO:0042228 | interleukin-8 biosynthetic process | 15653568 |
NOD1 | GO:0042742 | defense response to bacterium | 15653568 |
NOD1 | GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB signaling | 10329646 |
NOD1 | GO:0043280 | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 10329646 |
NOD1 | GO:0051092 | positive regulation of NF-kappaB transcription factor activity | 17054981|19043560 |
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Gene structures and expression levels for NOD1 |
Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NOD1 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_103355 | chr7 | 30436001:30436081:30437573:30437656:30446141:30446224 | 30437573:30437656 |
exon_skip_115297 | chr7 | 30448298:30448381:30451216:30453040:30455137:30455311 | 30451216:30453040 |
exon_skip_11863 | chr7 | 30425209:30425710:30428504:30428609:30429374:30429457 | 30428504:30428609 |
exon_skip_130517 | chr7 | 30424530:30425710:30428504:30428609:30429374:30429457 | 30428504:30428609 |
exon_skip_246691 | chr7 | 30435998:30436081:30437573:30437656:30446141:30446224 | 30437573:30437656 |
exon_skip_277917 | chr7 | 30425209:30425710:30429374:30429457:30446141:30446224 | 30429374:30429457 |
exon_skip_699 | chr7 | 30429374:30429457:30433096:30433179:30435998:30436081 | 30433096:30433179 |
exon_skip_90546 | chr7 | 30456785:30457042:30459152:30459240:30459901:30460041 | 30459152:30459240 |
exon_skip_9755 | chr7 | 30459901:30460041:30463609:30463698:30478606:30478636 | 30463609:30463698 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for NOD1 |
Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000222823 | 30459152 | 30459240 | 3UTR-3UTR |
ENST00000222823 | 30451216 | 30453040 | Frame-shift |
ENST00000222823 | 30433096 | 30433179 | In-frame |
ENST00000222823 | 30437573 | 30437656 | In-frame |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000222823 | 30459152 | 30459240 | 3UTR-3UTR |
ENST00000222823 | 30451216 | 30453040 | Frame-shift |
ENST00000222823 | 30437573 | 30437656 | In-frame |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000222823 | 30459152 | 30459240 | 3UTR-3UTR |
ENST00000222823 | 30451216 | 30453040 | Frame-shift |
ENST00000222823 | 30433096 | 30433179 | In-frame |
ENST00000222823 | 30437573 | 30437656 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NOD1 |
p-ENSG00000106100_img4.png |
Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000222823 | 4516 | 953 | 30437573 | 30437656 | 2980 | 3062 | 818 | 845 |
ENST00000222823 | 4516 | 953 | 30433096 | 30433179 | 3148 | 3230 | 874 | 901 |
Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000222823 | 4516 | 953 | 30437573 | 30437656 | 2980 | 3062 | 818 | 845 |
Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000222823 | 4516 | 953 | 30437573 | 30437656 | 2980 | 3062 | 818 | 845 |
ENST00000222823 | 4516 | 953 | 30433096 | 30433179 | 3148 | 3230 | 874 | 901 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
Q9Y239 | 818 | 845 | 250 | 953 | Alternative sequence | ID=VSP_055826;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q9Y239 | 818 | 845 | 1 | 953 | Chain | ID=PRO_0000144077;Note=Nucleotide-binding oligomerization domain-containing protein 1 |
Q9Y239 | 818 | 845 | 839 | 862 | Repeat | Note=LRR 6 |
Q9Y239 | 874 | 901 | 250 | 953 | Alternative sequence | ID=VSP_055826;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q9Y239 | 874 | 901 | 1 | 953 | Chain | ID=PRO_0000144077;Note=Nucleotide-binding oligomerization domain-containing protein 1 |
Q9Y239 | 874 | 901 | 877 | 877 | Mutagenesis | Note=Does not associate with cell membrane. Q->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17970764;Dbxref=PMID:17970764 |
Q9Y239 | 874 | 901 | 867 | 891 | Repeat | Note=LRR 7 |
Q9Y239 | 874 | 901 | 895 | 918 | Repeat | Note=LRR 8 |
Lost protein functional features of individual exon skipping events in MSBB. |
UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
Q9Y239 | 818 | 845 | 250 | 953 | Alternative sequence | ID=VSP_055826;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q9Y239 | 818 | 845 | 1 | 953 | Chain | ID=PRO_0000144077;Note=Nucleotide-binding oligomerization domain-containing protein 1 |
Q9Y239 | 818 | 845 | 839 | 862 | Repeat | Note=LRR 6 |
Lost protein functional features of individual exon skipping events in Mayo. |
UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
Q9Y239 | 818 | 845 | 250 | 953 | Alternative sequence | ID=VSP_055826;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q9Y239 | 818 | 845 | 1 | 953 | Chain | ID=PRO_0000144077;Note=Nucleotide-binding oligomerization domain-containing protein 1 |
Q9Y239 | 818 | 845 | 839 | 862 | Repeat | Note=LRR 6 |
Q9Y239 | 874 | 901 | 250 | 953 | Alternative sequence | ID=VSP_055826;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q9Y239 | 874 | 901 | 1 | 953 | Chain | ID=PRO_0000144077;Note=Nucleotide-binding oligomerization domain-containing protein 1 |
Q9Y239 | 874 | 901 | 877 | 877 | Mutagenesis | Note=Does not associate with cell membrane. Q->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17970764;Dbxref=PMID:17970764 |
Q9Y239 | 874 | 901 | 867 | 891 | Repeat | Note=LRR 7 |
Q9Y239 | 874 | 901 | 895 | 918 | Repeat | Note=LRR 8 |
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3'-UTR located exon skipping events that lost miRNA binding sites in NOD1 |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
Mayo | ENST00000222823 | 30459152 | 30459240 | hsa-miR-4699-5p | chr7:30459211-30459218 | 8mer-1a | chr7:30459198-30459218 | 150.00 | -9.87 |
Mayo | ENST00000222823 | 30459152 | 30459240 | hsa-miR-9902 | chr7:30459231-30459238 | 8mer-1a | chr7:30459217-30459238 | 145.00 | -13.99 |
MSBB | ENST00000222823 | 30459152 | 30459240 | hsa-miR-4699-5p | chr7:30459211-30459218 | 8mer-1a | chr7:30459198-30459218 | 150.00 | -9.87 |
MSBB | ENST00000222823 | 30459152 | 30459240 | hsa-miR-9902 | chr7:30459231-30459238 | 8mer-1a | chr7:30459217-30459238 | 145.00 | -13.99 |
ROSMAP | ENST00000222823 | 30459152 | 30459240 | hsa-miR-4699-5p | chr7:30459211-30459218 | 8mer-1a | chr7:30459198-30459218 | 150.00 | -9.87 |
ROSMAP | ENST00000222823 | 30459152 | 30459240 | hsa-miR-9902 | chr7:30459231-30459238 | 8mer-1a | chr7:30459217-30459238 | 145.00 | -13.99 |
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SNVs in the skipped exons for NOD1 |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- Non-synonymous mutations located in the skipped exons in CCLE. |
Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for NOD1 |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NOD1 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for NOD1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for NOD1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for NOD1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |