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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 CHCHD3 |
 Gene summary |
| Gene information | Gene symbol | CHCHD3 | Gene ID | 54927 |
| Gene name | coiled-coil-helix-coiled-coil-helix domain containing 3 | |
| Synonyms | MICOS19|MINOS3|Mic19|PPP1R22 | |
| Cytomap | 7q32.3-q33 | |
| Type of gene | protein-coding | |
| Description | MICOS complex subunit MIC19coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrialmitochondrial contact site and cristae organizing system subunit 19mitochondrial inner membrane organizing system 3protein phosphatase 1, regulato | |
| Modification date | 20200327 | |
| 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 |
| CHCHD3 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 22567091 |
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Gene structures and expression levels for CHCHD3 |
| 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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ENSG00000106554
| 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 |
| 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 CHCHD3 |
| 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_105310 | chr7 | 132838399:132838469:132885662:132885745:132975169:132975286 | 132885662:132885745 |
| exon_skip_110689 | chr7 | 132785591:132785660:132796442:132796577:132838399:132838469 | 132796442:132796577 |
| exon_skip_119353 | chr7 | 132796563:132796577:132813425:132813561:132815475:132815628 | 132813425:132813561 |
| exon_skip_137733 | chr7 | 132975169:132975286:133022406:133022495:133024546:133024627 | 133022406:133022495 |
| exon_skip_177287 | chr7 | 132785525:132785660:132796442:132796577:132838399:132838469 | 132796442:132796577 |
| exon_skip_26889 | chr7 | 132885662:132885745:132886974:132886988:132975169:132975286 | 132886974:132886988 |
| exon_skip_287546 | chr7 | 132796442:132796577:132813425:132813561:132815475:132815628 | 132813425:132813561 |
| exon_skip_97043 | chr7 | 132796442:132796577:132838399:132838469:132885662:132885745 | 132838399:132838469 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_26889 | MSBB_STG | 6.090625e-01 | 7.166667e-01 | -1.076042e-01 | 4.921445e-02 |
| exon_skip_26889 | MSBB_PG | 5.038525e-01 | 6.669091e-01 | -1.630566e-01 | 2.295920e-02 |
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Open reading frame (ORF) annotation in the exon skipping event for CHCHD3 |
| 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 |
| ENST00000262570 | 132796442 | 132796577 | Frame-shift |
| 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 |
| ENST00000262570 | 132796442 | 132796577 | Frame-shift |
| ENST00000262570 | 132838399 | 132838469 | Frame-shift |
| ENST00000262570 | 132885662 | 132885745 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CHCHD3 |
p-ENSG00000106554_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 |
| 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 |
| ENST00000262570 | 1615 | 227 | 132885662 | 132885745 | 515 | 597 | 123 | 150 |
| 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 |
| 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 |
| Q9NX63 | 123 | 150 | 2 | 227 | Chain | ID=PRO_0000129163;Note=MICOS complex subunit MIC19 |
| Q9NX63 | 123 | 150 | 142 | 142 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CHCHD3 |
| 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 CHCHD3 |
| - 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 CHCHD3 |
| 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 CHCHD3 |
| 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 CHCHD3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | NUP42 | exon_skip_26889 | 5.329299e-01 | 4.786162e-13 |
| HCC | CNOT4 | exon_skip_26889 | -4.168430e-01 | 6.696457e-13 |
| PG | CNOT4 | exon_skip_26889 | 4.481843e-01 | 3.964022e-10 |
| PG | NUP42 | exon_skip_26889 | 4.886134e-01 | 5.215743e-12 |
| TC | NUP42 | exon_skip_26889 | 7.309909e-01 | 5.158855e-28 |
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RelatedDrugs for CHCHD3 |
| 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 CHCHD3 |
| 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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