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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 SDHD |
Gene summary |
Gene information | Gene symbol | SDHD | Gene ID | 6392 |
Gene name | succinate dehydrogenase complex subunit D | |
Synonyms | CBT1|CII-4|CWS3|PGL|PGL1|QPs3|SDH4|cybS | |
Cytomap | 11q23.1 | |
Type of gene | protein-coding | |
Description | succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrialsuccinate dehydrogenase complex subunit D integral membrane proteinsuccinate-ubiquinone oxidoreductase cytochrome b small subunitsuccinate-ubiquinone reductase membrane ancho | |
Modification date | 20200313 | |
UniProtAcc | A0A0S2Z4H7, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SDHD | GO:0006099 | tricarboxylic acid cycle | 9533030 |
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Gene structures and expression levels for SDHD |
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 | ENST00000528048.5 | SDHD-205:protein_coding:SDHD | 2.475765e+01 | 1.072835e+00 | 3.074382e-06 | 3.898092e-05 |
CB | UP | ENST00000525291.5 | SDHD-202:protein_coding:SDHD | 3.833292e+00 | 1.480064e+00 | 1.064126e-02 | 3.657683e-02 |
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 SDHD |
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_166988 | chr11 | 112086899:112086959:112087857:112087973:112088867:112089011 | 112087857:112087973 |
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 SDHD |
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 |
ENST00000375549 | 112087857 | 112087973 | 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 |
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 |
ENST00000375549 | 112087857 | 112087973 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SDHD |
p-ENSG00000204370_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 |
ENST00000375549 | 1456 | 159 | 112087857 | 112087973 | 189 | 304 | 18 | 56 |
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 |
ENST00000375549 | 1456 | 159 | 112087857 | 112087973 | 189 | 304 | 18 | 56 |
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 |
O14521 | 18 | 56 | 19 | 57 | Alternative sequence | ID=VSP_054744;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O14521 | 18 | 56 | 56 | 158 | Alternative sequence | ID=VSP_054745;Note=In isoform 3. HSGSKAASLHWTSERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWK->HWALDKLLLTMFMGMPCRKLPRQGFWHFQ;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O14521 | 18 | 56 | 50 | 50 | Natural variant | ID=VAR_017871;Note=Polymorphism that may increase susceptibility for developing paraganglioma%2C breast and thyroid carcinoma%3B may be involved in somatic Merkel cell carcinoma%3B associated with increased manganese superoxide dismutase expression%3B ass |
O14521 | 18 | 56 | 1 | 56 | Transit peptide | Note=Mitochondrion;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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 |
O14521 | 18 | 56 | 19 | 57 | Alternative sequence | ID=VSP_054744;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O14521 | 18 | 56 | 56 | 158 | Alternative sequence | ID=VSP_054745;Note=In isoform 3. HSGSKAASLHWTSERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWK->HWALDKLLLTMFMGMPCRKLPRQGFWHFQ;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O14521 | 18 | 56 | 50 | 50 | Natural variant | ID=VAR_017871;Note=Polymorphism that may increase susceptibility for developing paraganglioma%2C breast and thyroid carcinoma%3B may be involved in somatic Merkel cell carcinoma%3B associated with increased manganese superoxide dismutase expression%3B ass |
O14521 | 18 | 56 | 1 | 56 | Transit peptide | Note=Mitochondrion;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SDHD |
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 SDHD |
- 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 SDHD |
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 SDHD |
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 SDHD |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SDHD |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
O14521 | approved|withdrawn | DB00756 | Hexachlorophene | small molecule | O14521 |
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RelatedDiseases for SDHD |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |