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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for MDH1 |
 Gene summary |
| Gene information | Gene symbol | MDH1 | Gene ID | 4190 |
| Gene name | malate dehydrogenase 1 | |
| Synonyms | HEL-S-32|MDH-s|MDHA|MGC:1375|MOR2 | |
| Cytomap | 2p15 | |
| Type of gene | protein-coding | |
| Description | malate dehydrogenase, cytoplasmicmalate dehydrogenase, peroxisomalcytosolic malate dehydrogenasediiodophenylpyruvate reductaseepididymis secretory protein Li 32malate dehydrogenase 1, NAD (soluble)soluble malate dehydrogenase | |
| Modification date | 20200313 | |
| UniProtAcc | A0A5K1VW95, | |
| Context | - 28966679(Dynamical Differential Networks and Modules Inferring Disrupted Genes Associated With the Progression of Alzheimer's Disease) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for MDH1 |
| 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. |
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ENSG00000014641
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PCC | UP | ENST00000409476.5 | MDH1-202:protein_coding:MDH1 | 8.894411e+00 | 9.756933e-01 | 2.682157e-03 | 4.684707e-02 |
| PG | DOWN | ENST00000495083.1 | MDH1-214:retained_intron:MDH1 | 6.696047e+00 | -1.216808e+00 | 1.414042e-04 | 3.541109e-03 |
| CB | DOWN | ENST00000495083.1 | MDH1-214:retained_intron:MDH1 | 1.821384e+02 | -2.382900e+00 | 2.795222e-16 | 2.105218e-13 |
| CB | DOWN | ENST00000409908.5 | MDH1-203:protein_coding:MDH1 | 2.664285e+01 | -4.790159e+00 | 1.441092e-06 | 2.044085e-05 |
| TC | DOWN | ENST00000495083.1 | MDH1-214:retained_intron:MDH1 | 2.527189e+02 | -2.185839e+00 | 2.864280e-13 | 1.258782e-10 |
| TC | DOWN | ENST00000409908.5 | MDH1-203:protein_coding:MDH1 | 5.250658e+01 | -4.412059e+00 | 1.458183e-04 | 2.177397e-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 MDH1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_100286 | chr2 | 63588998:63589046:63599170:63599292:63604696:63604810 | 63599170:63599292 |
| exon_skip_110875 | chr2 | 63588998:63589046:63594488:63594586:63595423:63595519 | 63594488:63594586 |
| exon_skip_112760 | chr2 | 63597548:63597574:63599170:63599292:63604696:63604810 | 63599170:63599292 |
| exon_skip_115884 | chr2 | 63594488:63594586:63595423:63595519:63597399:63597574 | 63595423:63595519 |
| exon_skip_147971 | chr2 | 63588958:63589046:63599170:63599292:63604696:63604872 | 63599170:63599292 |
| exon_skip_163595 | chr2 | 63588998:63589046:63594488:63594586:63597399:63597538 | 63594488:63594586 |
| exon_skip_178321 | chr2 | 63599214:63599292:63604696:63604872:63605280:63605393 | 63604696:63604872 |
| exon_skip_194234 | chr2 | 63599170:63599292:63604696:63604872:63605280:63605393 | 63604696:63604872 |
| exon_skip_194648 | chr2 | 63594488:63594586:63595423:63595519:63597399:63597411 | 63595423:63595519 |
| exon_skip_210612 | chr2 | 63595423:63595519:63597399:63597574:63599170:63599288 | 63597399:63597574 |
| exon_skip_231376 | chr2 | 63588998:63589046:63594488:63594586:63597399:63597416 | 63594488:63594586 |
| exon_skip_276047 | chr2 | 63604696:63604872:63605280:63605393:63605939:63606028 | 63605280:63605393 |
| exon_skip_279683 | chr2 | 63588958:63589046:63599170:63599292:63604696:63604795 | 63599170:63599292 |
| exon_skip_28106 | chr2 | 63588997:63589046:63593440:63593628:63594488:63594586 | 63593440:63593628 |
| exon_skip_284220 | chr2 | 63588982:63589046:63589961:63590084:63594488:63594586 | 63589961:63590084 |
| exon_skip_290629 | chr2 | 63588998:63589046:63593124:63593628:63594488:63594586 | 63593124:63593628 |
| exon_skip_293503 | chr2 | 63594488:63594586:63595423:63595519:63597399:63597433 | 63595423:63595519 |
| exon_skip_35168 | chr2 | 63594488:63594586:63595423:63595519:63597399:63597538 | 63595423:63595519 |
| exon_skip_36280 | chr2 | 63605280:63605393:63605939:63606028:63606862:63607091 | 63605939:63606028 |
| exon_skip_5562 | chr2 | 63594488:63594586:63597399:63597574:63599170:63599288 | 63597399:63597574 |
| exon_skip_75849 | chr2 | 63588998:63589046:63594488:63594586:63597399:63597574 | 63594488:63594586 |
| exon_skip_77345 | chr2 | 63604835:63604872:63605280:63605393:63605939:63606028 | 63605280:63605393 |
| exon_skip_85602 | chr2 | 63588997:63589046:63593440:63593628:63594488:63594575 | 63593440:63593628 |
| exon_skip_8795 | chr2 | 63588998:63589046:63593124:63593628:63594488:63594575 | 63593124:63593628 |
| exon_skip_90995 | chr2 | 63594502:63594586:63597399:63597574:63599170:63599288 | 63597399:63597574 |
| 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 MDH1 |
| 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 |
| ENST00000233114 | 63595423 | 63595519 | Frame-shift |
| ENST00000233114 | 63597399 | 63597574 | Frame-shift |
| ENST00000233114 | 63594488 | 63594586 | In-frame |
| ENST00000233114 | 63604696 | 63604872 | In-frame |
| ENST00000233114 | 63605280 | 63605393 | In-frame |
| ENST00000233114 | 63605939 | 63606028 | 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 |
| ENST00000233114 | 63595423 | 63595519 | Frame-shift |
| 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 |
| ENST00000233114 | 63595423 | 63595519 | Frame-shift |
| ENST00000233114 | 63597399 | 63597574 | Frame-shift |
| ENST00000233114 | 63594488 | 63594586 | In-frame |
| ENST00000233114 | 63599170 | 63599292 | In-frame |
| ENST00000233114 | 63604696 | 63604872 | In-frame |
| ENST00000233114 | 63605280 | 63605393 | In-frame |
| ENST00000233114 | 63605939 | 63606028 | In-frame |
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Infer the effects of exon skipping event on protein functional features for MDH1 |
p-ENSG00000014641_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 |
| ENST00000233114 | 1667 | 334 | 63594488 | 63594586 | 440 | 537 | 1 | 34 |
| ENST00000233114 | 1667 | 334 | 63604696 | 63604872 | 935 | 1110 | 166 | 225 |
| ENST00000233114 | 1667 | 334 | 63605280 | 63605393 | 1112 | 1224 | 225 | 263 |
| ENST00000233114 | 1667 | 334 | 63605939 | 63606028 | 1226 | 1314 | 263 | 293 |
| 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 |
| 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 |
| ENST00000233114 | 1667 | 334 | 63594488 | 63594586 | 440 | 537 | 1 | 34 |
| ENST00000233114 | 1667 | 334 | 63599170 | 63599292 | 812 | 933 | 125 | 166 |
| ENST00000233114 | 1667 | 334 | 63604696 | 63604872 | 935 | 1110 | 166 | 225 |
| ENST00000233114 | 1667 | 334 | 63605280 | 63605393 | 1112 | 1224 | 225 | 263 |
| ENST00000233114 | 1667 | 334 | 63605939 | 63606028 | 1226 | 1314 | 263 | 293 |
| 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 |
| P40925 | 1 | 34 | 1 | 89 | Alternative sequence | ID=VSP_042661;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P40925 | 1 | 34 | 1 | 1 | Alternative sequence | ID=VSP_045847;Note=In isoform 3. M->MRRCSYFPKDVTVFDKDDK;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P40925 | 1 | 34 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| P40925 | 1 | 34 | 1 | 1 | Initiator methionine | Note=Removed;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:25944712,ECO:0000269|Ref.8;Dbxref=PMID:25944712 |
| P40925 | 1 | 34 | 2 | 2 | Modified residue | Note=N-acetylserine;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:25944712,ECO:0000269|Ref.8;Dbxref=PMID:25944712 |
| P40925 | 1 | 34 | 11 | 17 | Nucleotide binding | Note=NAD;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P40925 | 1 | 34 | 15 | 15 | Sequence conflict | Note=Q->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P40925 | 166 | 225 | 187 | 187 | Active site | Note=Proton acceptor;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P40925 | 166 | 225 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| P40925 | 166 | 225 | 214 | 214 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P14152 |
| P40925 | 166 | 225 | 217 | 217 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P14152 |
| P40925 | 225 | 263 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| P40925 | 225 | 263 | 230 | 230 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P14152 |
| P40925 | 225 | 263 | 241 | 241 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| P40925 | 263 | 293 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| 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 |
| 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 |
| P40925 | 1 | 34 | 1 | 89 | Alternative sequence | ID=VSP_042661;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P40925 | 1 | 34 | 1 | 1 | Alternative sequence | ID=VSP_045847;Note=In isoform 3. M->MRRCSYFPKDVTVFDKDDK;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P40925 | 1 | 34 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| P40925 | 1 | 34 | 1 | 1 | Initiator methionine | Note=Removed;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:25944712,ECO:0000269|Ref.8;Dbxref=PMID:25944712 |
| P40925 | 1 | 34 | 2 | 2 | Modified residue | Note=N-acetylserine;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:25944712,ECO:0000269|Ref.8;Dbxref=PMID:25944712 |
| P40925 | 1 | 34 | 11 | 17 | Nucleotide binding | Note=NAD;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P40925 | 1 | 34 | 15 | 15 | Sequence conflict | Note=Q->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P40925 | 125 | 166 | 131 | 131 | Binding site | Note=Substrate;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P40925 | 125 | 166 | 162 | 162 | Binding site | Note=Substrate |
| P40925 | 125 | 166 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| P40925 | 125 | 166 | 129 | 131 | Nucleotide binding | Note=NAD;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P40925 | 166 | 225 | 187 | 187 | Active site | Note=Proton acceptor;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P40925 | 166 | 225 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| P40925 | 166 | 225 | 214 | 214 | Modified residue | Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P14152 |
| P40925 | 166 | 225 | 217 | 217 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P14152 |
| P40925 | 225 | 263 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
| P40925 | 225 | 263 | 230 | 230 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P14152 |
| P40925 | 225 | 263 | 241 | 241 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| P40925 | 263 | 293 | 2 | 334 | Chain | ID=PRO_0000113409;Note=Malate dehydrogenase%2C cytoplasmic |
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3'-UTR located exon skipping events that lost miRNA binding sites in MDH1 |
| 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 MDH1 |
| - 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 MDH1 |
| 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 MDH1 |
| 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 MDH1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for MDH1 |
| 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 MDH1 |
| 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)
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