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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 SDHA |
Gene summary |
Gene information | Gene symbol | SDHA | Gene ID | 6389 |
Gene name | succinate dehydrogenase complex flavoprotein subunit A | |
Synonyms | CMD1GG|FP|PGL5|SDH1|SDH2|SDHF | |
Cytomap | 5p15.33 | |
Type of gene | protein-coding | |
Description | succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialflavoprotein subunit of complex IIsuccinate dehydrogenase complex, subunit A, flavoprotein (Fp) | |
Modification date | 20200313 | |
UniProtAcc | ||
Context | - 18460208(Identification of Valid Reference Genes for the Normalization of RT qPCR Gene Expression Data in Human Brain Tissue) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SDHA | GO:0006105 | succinate metabolic process | 7550341 |
SDHA | GO:0022904 | respiratory electron transport chain | 7550341 |
SDHA | GO:0055114 | oxidation-reduction process | 7550341 |
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Gene structures and expression levels for SDHA |
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 |
STG | UP | ENST00000505555.5 | SDHA-206:retained_intron:SDHA | 4.794172e+01 | 8.212335e-01 | 3.462099e-04 | 2.231169e-02 |
CB | UP | ENST00000505555.5 | SDHA-206:retained_intron:SDHA | 8.954639e+01 | 9.202282e-01 | 1.793441e-10 | 1.033720e-08 |
CB | DOWN | ENST00000509564.1 | SDHA-211:protein_coding:SDHA | 7.728225e+01 | -1.128160e+00 | 2.625273e-06 | 3.405088e-05 |
CB | UP | ENST00000504824.5 | SDHA-205:retained_intron:SDHA | 1.714191e+01 | 1.312030e+00 | 9.695528e-04 | 5.032961e-03 |
CB | DOWN | ENST00000509082.1 | SDHA-209:lncRNA:SDHA | 9.062563e+01 | -2.575105e+00 | 1.563046e-03 | 7.510642e-03 |
TC | DOWN | ENST00000509564.1 | SDHA-211:protein_coding:SDHA | 6.844294e+01 | -1.136831e+00 | 6.598344e-07 | 2.877748e-05 |
TC | DOWN | ENST00000509082.1 | SDHA-209:lncRNA:SDHA | 9.323988e+01 | -1.530021e+00 | 2.584625e-03 | 2.038477e-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 SDHA |
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_168185 | chr5 | 224360:224521:225419:225562:225883:226047 | 225419:225562 |
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 SDHA |
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 |
ENST00000264932 | 225419 | 225562 | 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 |
ENST00000264932 | 225419 | 225562 | 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 |
ENST00000264932 | 225419 | 225562 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SDHA |
p-ENSG00000073578_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 |
ENST00000264932 | 2407 | 664 | 225419 | 225562 | 429 | 571 | 104 | 152 |
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 |
ENST00000264932 | 2407 | 664 | 225419 | 225562 | 429 | 571 | 104 | 152 |
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 |
ENST00000264932 | 2407 | 664 | 225419 | 225562 | 429 | 571 | 104 | 152 |
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 |
P31040 | 104 | 152 | 105 | 152 | Alternative sequence | ID=VSP_055077;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P31040 | 104 | 152 | 126 | 270 | Alternative sequence | ID=VSP_055078;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
P31040 | 104 | 152 | 43 | 664 | Chain | ID=PRO_0000010335;Note=Succinate dehydrogenase [ubiquinone] flavoprotein subunit%2C mitochondrial |
P31040 | 104 | 152 | 91 | 106 | Nucleotide binding | Note=FAD;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q0QF01 |
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 |
P31040 | 104 | 152 | 105 | 152 | Alternative sequence | ID=VSP_055077;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P31040 | 104 | 152 | 126 | 270 | Alternative sequence | ID=VSP_055078;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
P31040 | 104 | 152 | 43 | 664 | Chain | ID=PRO_0000010335;Note=Succinate dehydrogenase [ubiquinone] flavoprotein subunit%2C mitochondrial |
P31040 | 104 | 152 | 91 | 106 | Nucleotide binding | Note=FAD;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q0QF01 |
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 |
P31040 | 104 | 152 | 105 | 152 | Alternative sequence | ID=VSP_055077;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P31040 | 104 | 152 | 126 | 270 | Alternative sequence | ID=VSP_055078;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
P31040 | 104 | 152 | 43 | 664 | Chain | ID=PRO_0000010335;Note=Succinate dehydrogenase [ubiquinone] flavoprotein subunit%2C mitochondrial |
P31040 | 104 | 152 | 91 | 106 | Nucleotide binding | Note=FAD;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q0QF01 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SDHA |
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 SDHA |
- 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 SDHA |
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 SDHA |
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 SDHA |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SDHA |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
P31040 | approved|investigational|nutraceutical | DB09270 | Ubidecarenone | small molecule | P31040 |
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RelatedDiseases for SDHA |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |