|
||||||
|
 | |
| |
| |
| 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 MDH2 |
 Gene summary |
| Gene information | Gene symbol | MDH2 | Gene ID | 4191 |
| Gene name | malate dehydrogenase 2 | |
| Synonyms | EIEE51|M-MDH|MDH|MGC:3559|MOR1 | |
| Cytomap | 7q11.23 | |
| Type of gene | protein-coding | |
| Description | malate dehydrogenase, mitochondrialmalate dehydrogenase 2, NAD (mitochondrial)testicular tissue protein Li 120 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 21623795(Up-regulation of the mitochondrial malate dehydrogenase by oxidative stress is mediated by miR-743a) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| MDH2 | GO:0006108 | malate metabolic process | 16740313 |
| MDH2 | GO:0006475 | internal protein amino acid acetylation | 20167786 |
| MDH2 | GO:0009060 | aerobic respiration | 27989324 |
Top |
Gene structures and expression levels for MDH2 |
| 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. |
 |
ENSG00000146701
| 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 |
| STG | UP | ENST00000461665.5 | MDH2-206:retained_intron:MDH2 | 1.285459e+01 | 2.238329e+00 | 1.222924e-03 | 4.262126e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for MDH2 |
| 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_134487 | chr7 | 76048161:76048226:76054830:76054998:76057410:76057447 | 76054830:76054998 |
| exon_skip_160041 | chr7 | 76048193:76048226:76054830:76054998:76057410:76057447 | 76054830:76054998 |
| exon_skip_201566 | chr7 | 76048161:76048226:76057410:76057493:76057969:76058078 | 76057410:76057493 |
| exon_skip_253695 | chr7 | 76057969:76058078:76060373:76060498:76063515:76063592 | 76060373:76060498 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for MDH2 |
| 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 |
| ENST00000315758 | 76054830 | 76054998 | Frame-shift |
| ENST00000315758 | 76060373 | 76060498 | 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 |
| ENST00000315758 | 76054830 | 76054998 | Frame-shift |
| ENST00000315758 | 76060373 | 76060498 | 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 |
| ENST00000315758 | 76054830 | 76054998 | Frame-shift |
| ENST00000315758 | 76060373 | 76060498 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for MDH2 |
p-ENSG00000146701_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 |
| ENST00000315758 | 2226 | 338 | 76060373 | 76060498 | 525 | 649 | 143 | 185 |
| 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 |
| ENST00000315758 | 2226 | 338 | 76060373 | 76060498 | 525 | 649 | 143 | 185 |
| 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 |
| ENST00000315758 | 2226 | 338 | 76060373 | 76060498 | 525 | 649 | 143 | 185 |
| 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 |
| P40926 | 143 | 185 | 144 | 185 | Alternative sequence | ID=VSP_055312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P40926 | 143 | 185 | 165 | 168 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 176 | 176 | Binding site | Note=Substrate;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU10004,ECO:0000269|Ref.16 |
| P40926 | 143 | 185 | 25 | 338 | Chain | ID=PRO_0000018628;Note=Malate dehydrogenase%2C mitochondrial |
| P40926 | 143 | 185 | 144 | 157 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 171 | 185 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 165 | 165 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P40926 | 143 | 185 | 185 | 185 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:19608861,ECO:0000269|PubMed:20167786;Dbxref=PMID:19608861,PMID:20167786 |
| P40926 | 143 | 185 | 185 | 185 | Modified residue | Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P08249 |
| P40926 | 143 | 185 | 185 | 185 | Mutagenesis | Note=No activation of enzyme activity on treatment with TSA or NAM%3B when associated with R-301%3B R-307 and R-314. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20167786;Dbxref=PMID:20167786 |
| 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 |
| P40926 | 143 | 185 | 144 | 185 | Alternative sequence | ID=VSP_055312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P40926 | 143 | 185 | 165 | 168 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 176 | 176 | Binding site | Note=Substrate;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU10004,ECO:0000269|Ref.16 |
| P40926 | 143 | 185 | 25 | 338 | Chain | ID=PRO_0000018628;Note=Malate dehydrogenase%2C mitochondrial |
| P40926 | 143 | 185 | 144 | 157 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 171 | 185 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 165 | 165 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P40926 | 143 | 185 | 185 | 185 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:19608861,ECO:0000269|PubMed:20167786;Dbxref=PMID:19608861,PMID:20167786 |
| P40926 | 143 | 185 | 185 | 185 | Modified residue | Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P08249 |
| P40926 | 143 | 185 | 185 | 185 | Mutagenesis | Note=No activation of enzyme activity on treatment with TSA or NAM%3B when associated with R-301%3B R-307 and R-314. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20167786;Dbxref=PMID:20167786 |
| 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 |
| P40926 | 143 | 185 | 144 | 185 | Alternative sequence | ID=VSP_055312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P40926 | 143 | 185 | 165 | 168 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 176 | 176 | Binding site | Note=Substrate;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU10004,ECO:0000269|Ref.16 |
| P40926 | 143 | 185 | 25 | 338 | Chain | ID=PRO_0000018628;Note=Malate dehydrogenase%2C mitochondrial |
| P40926 | 143 | 185 | 144 | 157 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 171 | 185 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2DFD |
| P40926 | 143 | 185 | 165 | 165 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P40926 | 143 | 185 | 185 | 185 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:19608861,ECO:0000269|PubMed:20167786;Dbxref=PMID:19608861,PMID:20167786 |
| P40926 | 143 | 185 | 185 | 185 | Modified residue | Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P08249 |
| P40926 | 143 | 185 | 185 | 185 | Mutagenesis | Note=No activation of enzyme activity on treatment with TSA or NAM%3B when associated with R-301%3B R-307 and R-314. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20167786;Dbxref=PMID:20167786 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in MDH2 |
| 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 |
Top |
SNVs in the skipped exons for MDH2 |
| - 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 |
Top |
AD stage-associated exon skippint events for MDH2 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MDH2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for MDH2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_134487 | -4.074600e-01 | 9.794814e-08 |
| CB | TRA2A | exon_skip_134487 | -4.175887e-01 | 4.341961e-08 |
Top |
RelatedDrugs for MDH2 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P40926 | approved|nutraceutical|vet_approved | DB04272 | Citric Acid | small molecule | P40926 |
| P40926 | approved|withdrawn | DB09092 | Xanthinol | small molecule | P40926 |
Top |
RelatedDiseases for MDH2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|