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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 NDUFS2 |
Gene summary |
Gene information | Gene symbol | NDUFS2 | Gene ID | 4720 |
Gene name | NADH:ubiquinone oxidoreductase core subunit S2 | |
Synonyms | CI-49|MC1DN6 | |
Cytomap | 1q23.3 | |
Type of gene | protein-coding | |
Description | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialCI-49kDNADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)NADH-ubiquinone oxidoreductase 49 kDa subunitNADH-ubiquinone oxidoreductase NDUFS2 subunitcomp | |
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 |
NDUFS2 | GO:0006979 | response to oxidative stress | 12857734 |
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Gene structures and expression levels for NDUFS2 |
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 |
CB | UP | ENST00000392179.4 | NDUFS2-202:protein_coding:NDUFS2 | 3.314408e+02 | 1.747715e+00 | 9.853146e-04 | 5.100354e-03 |
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 NDUFS2 |
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_101495 | chr1 | 161209865:161209931:161210111:161210188:161210304:161210389 | 161210111:161210188 |
exon_skip_103968 | chr1 | 161212351:161212480:161212592:161212654:161213380:161213412 | 161212592:161212654 |
exon_skip_120730 | chr1 | 161212403:161212480:161213090:161213182:161213380:161213412 | 161213090:161213182 |
exon_skip_139953 | chr1 | 161212351:161212480:161213090:161213182:161213380:161213412 | 161213090:161213182 |
exon_skip_153267 | chr1 | 161210111:161210188:161210304:161210389:161210591:161210696 | 161210304:161210389 |
exon_skip_16251 | chr1 | 161206409:161206597:161209193:161209313:161209483:161209516 | 161209193:161209313 |
exon_skip_166199 | chr1 | 161212403:161212480:161212592:161212654:161213380:161213412 | 161212592:161212654 |
exon_skip_206649 | chr1 | 161203437:161203543:161203787:161203837:161206407:161206597 | 161203787:161203837 |
exon_skip_216240 | chr1 | 161210695:161210710:161212351:161212480:161213380:161213412 | 161212351:161212480 |
exon_skip_22954 | chr1 | 161202376:161202480:161203437:161203543:161206407:161206593 | 161203437:161203543 |
exon_skip_233359 | chr1 | 161202376:161202480:161203437:161203543:161206407:161206559 | 161203437:161203543 |
exon_skip_285638 | chr1 | 161209483:161209595:161209857:161209931:161210111:161210188 | 161209857:161209931 |
exon_skip_57754 | chr1 | 161212436:161212480:161212592:161212654:161213380:161213412 | 161212592:161212654 |
exon_skip_62579 | chr1 | 161210675:161210710:161212351:161212480:161213380:161213412 | 161212351:161212480 |
exon_skip_70832 | chr1 | 161203437:161203543:161206407:161206597:161209193:161209306 | 161206407:161206597 |
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 NDUFS2 |
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 |
ENST00000367993 | 161203437 | 161203543 | Frame-shift |
ENST00000367993 | 161206407 | 161206597 | Frame-shift |
ENST00000367993 | 161210304 | 161210389 | Frame-shift |
ENST00000367993 | 161212351 | 161212480 | Frame-shift |
ENST00000367993 | 161210111 | 161210188 | 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 |
ENST00000367993 | 161203437 | 161203543 | Frame-shift |
ENST00000367993 | 161210111 | 161210188 | 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 |
ENST00000367993 | 161203437 | 161203543 | Frame-shift |
ENST00000367993 | 161206407 | 161206597 | Frame-shift |
ENST00000367993 | 161209193 | 161209313 | Frame-shift |
ENST00000367993 | 161210304 | 161210389 | Frame-shift |
ENST00000367993 | 161212351 | 161212480 | Frame-shift |
ENST00000367993 | 161209857 | 161209931 | In-frame |
ENST00000367993 | 161210111 | 161210188 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NDUFS2 |
p-ENSG00000158864_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 |
ENST00000367993 | 2059 | 463 | 161210111 | 161210188 | 1152 | 1228 | 234 | 260 |
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 |
ENST00000367993 | 2059 | 463 | 161210111 | 161210188 | 1152 | 1228 | 234 | 260 |
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 |
ENST00000367993 | 2059 | 463 | 161209857 | 161209931 | 1077 | 1150 | 209 | 234 |
ENST00000367993 | 2059 | 463 | 161210111 | 161210188 | 1152 | 1228 | 234 | 260 |
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 |
O75306 | 234 | 260 | 231 | 234 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 34 | 463 | Chain | ID=PRO_0000019981;Note=NADH dehydrogenase [ubiquinone] iron-sulfur protein 2%2C mitochondrial |
O75306 | 234 | 260 | 240 | 249 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 251 | 259 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 260 | 264 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
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 |
O75306 | 234 | 260 | 231 | 234 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 34 | 463 | Chain | ID=PRO_0000019981;Note=NADH dehydrogenase [ubiquinone] iron-sulfur protein 2%2C mitochondrial |
O75306 | 234 | 260 | 240 | 249 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 251 | 259 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 260 | 264 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
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 |
O75306 | 209 | 234 | 219 | 223 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 209 | 234 | 231 | 234 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 209 | 234 | 34 | 463 | Chain | ID=PRO_0000019981;Note=NADH dehydrogenase [ubiquinone] iron-sulfur protein 2%2C mitochondrial |
O75306 | 209 | 234 | 198 | 218 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 209 | 234 | 224 | 224 | Natural variant | ID=VAR_071891;Note=A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21057504;Dbxref=PMID:21057504 |
O75306 | 209 | 234 | 228 | 228 | Natural variant | ID=VAR_019535;Note=In MT-C1D. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11220739;Dbxref=dbSNP:rs121434427,PMID:11220739 |
O75306 | 209 | 234 | 229 | 229 | Natural variant | ID=VAR_034151;Note=P->A;Dbxref=dbSNP:rs16827493 |
O75306 | 209 | 234 | 229 | 229 | Natural variant | ID=VAR_019536;Note=In MT-C1D. P->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11220739;Dbxref=dbSNP:rs121434428,PMID:11220739 |
O75306 | 234 | 260 | 231 | 234 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 34 | 463 | Chain | ID=PRO_0000019981;Note=NADH dehydrogenase [ubiquinone] iron-sulfur protein 2%2C mitochondrial |
O75306 | 234 | 260 | 240 | 249 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 251 | 259 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
O75306 | 234 | 260 | 260 | 264 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XTB |
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3'-UTR located exon skipping events that lost miRNA binding sites in NDUFS2 |
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 |
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SNVs in the skipped exons for NDUFS2 |
- 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 NDUFS2 |
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 |
CDR | MSBB | IFG | exon_skip_22954 | -3.860443e-01 | 4.245355e-02 | chr1 | + | 161202376 | 161202480 | 161203437 | 161203543 | 161206407 | 161206593 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NDUFS2 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
TC | exon_skip_233359 | rs4073054 | chr1:161230697 | 1.390712e-04 | 2.124339e-02 |
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Correlation with RNA binding proteins (RBPs) for NDUFS2 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | ZNF638 | exon_skip_22954 | -5.362491e-01 | 3.221054e-13 |
CB | TRA2A | exon_skip_22954 | -4.519834e-01 | 2.225419e-09 |
CB | NUP42 | exon_skip_22954 | 6.000468e-01 | 6.346276e-17 |
FL | HNRNPH2 | exon_skip_22954 | 4.233013e-01 | 5.190051e-10 |
IFG | ILF2 | exon_skip_22954 | 4.584149e-01 | 1.415229e-02 |
IFG | HNRNPK | exon_skip_22954 | 5.034822e-01 | 6.308623e-03 |
IFG | HNRNPH2 | exon_skip_22954 | 4.667095e-01 | 1.229215e-02 |
IFG | EIF4B | exon_skip_22954 | 5.112239e-01 | 5.430965e-03 |
IFG | ESRP2 | exon_skip_22954 | -4.081002e-01 | 3.109386e-02 |
PG | HNRNPH2 | exon_skip_22954 | 4.450556e-01 | 3.857969e-10 |
STG | HNRNPH2 | exon_skip_22954 | 4.325328e-01 | 1.854734e-05 |
TC | NUP42 | exon_skip_233359 | 4.747609e-01 | 2.258326e-10 |
TC | HNRNPH2 | exon_skip_233359 | 5.252951e-01 | 9.933325e-13 |
TC | ESRP1 | exon_skip_233359 | 4.934582e-01 | 3.361021e-11 |
TC | NOVA1 | exon_skip_233359 | 4.214029e-01 | 2.869665e-08 |
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RelatedDrugs for NDUFS2 |
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 NDUFS2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |