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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 ERCC3 |
Gene summary |
Gene information | Gene symbol | ERCC3 | Gene ID | 2071 |
Gene name | ERCC excision repair 3, TFIIH core complex helicase subunit | |
Synonyms | BTF2|GTF2H|RAD25|TFIIH|TTD2|XPB | |
Cytomap | 2q14.3 | |
Type of gene | protein-coding | |
Description | general transcription and DNA repair factor IIH helicase subunit XPBBTF2 p89DNA excision repair protein ERCC-3DNA repair helicaseDNA repair protein complementing XP-B cellsTFIIH 89 kDa subunitTFIIH basal transcription factor complex 89 kDa subunitT | |
Modification date | 20200327 | |
UniProtAcc | A0A2R8Y4R8, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
ERCC3 | GO:0006283 | transcription-coupled nucleotide-excision repair | 8663148 |
ERCC3 | GO:0006366 | transcription by RNA polymerase II | 9852112 |
ERCC3 | GO:0043065 | positive regulation of apoptotic process | 16914395 |
ERCC3 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 8692841 |
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Gene structures and expression levels for ERCC3 |
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 | ENST00000426778.5 | ERCC3-202:nonsense_mediated_decay:ERCC3 | 1.460037e+02 | 9.556687e-01 | 4.561174e-11 | 3.292617e-09 |
CB | DOWN | ENST00000646654.1 | ERCC3-219:nonsense_mediated_decay:ERCC3 | 2.664149e+02 | -1.344893e+00 | 1.614922e-05 | 1.582848e-04 |
CB | DOWN | ENST00000645736.1 | ERCC3-217:nonsense_mediated_decay:ERCC3 | 1.224959e+02 | -1.265785e+00 | 1.250540e-04 | 8.952877e-04 |
CB | UP | ENST00000494464.5 | ERCC3-209:retained_intron:ERCC3 | 8.830356e+00 | 1.383432e+00 | 5.168645e-03 | 2.022616e-02 |
TC | DOWN | ENST00000646654.1 | ERCC3-219:nonsense_mediated_decay:ERCC3 | 1.013293e+02 | -1.516502e+00 | 6.879406e-03 | 4.247296e-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 ERCC3 |
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_151487 | chr2 | 127289689:127289824:127290224:127290273:127292610:127292653 | 127290224:127290273 |
exon_skip_172042 | chr2 | 127271336:127271453:127272865:127272961:127279173:127279261 | 127272865:127272961 |
exon_skip_215613 | chr2 | 127289689:127289824:127290224:127290273:127291912:127292373 | 127290224:127290273 |
exon_skip_222560 | chr2 | 127259296:127259448:127261228:127261346:127271336:127271453 | 127261228:127261346 |
exon_skip_225459 | chr2 | 127280447:127280631:127284171:127284289:127286703:127286797 | 127284171:127284289 |
exon_skip_241150 | chr2 | 127261228:127261346:127271336:127271453:127272865:127272961 | 127271336:127271453 |
exon_skip_244694 | chr2 | 127279173:127279375:127280447:127280631:127286703:127286797 | 127280447:127280631 |
exon_skip_281803 | chr2 | 127289689:127289824:127290224:127290273:127292610:127292846 | 127290224:127290273 |
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 ERCC3 |
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 |
ENST00000285398 | 127271336 | 127271453 | Frame-shift |
ENST00000285398 | 127272865 | 127272961 | Frame-shift |
ENST00000285398 | 127280447 | 127280631 | Frame-shift |
ENST00000285398 | 127290224 | 127290273 | 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 |
ENST00000285398 | 127290224 | 127290273 | 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 |
ENST00000285398 | 127261228 | 127261346 | Frame-shift |
ENST00000285398 | 127271336 | 127271453 | Frame-shift |
ENST00000285398 | 127272865 | 127272961 | Frame-shift |
ENST00000285398 | 127280447 | 127280631 | Frame-shift |
ENST00000285398 | 127290224 | 127290273 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for ERCC3 |
p-ENSG00000163161_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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in ERCC3 |
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 ERCC3 |
- 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 ERCC3 |
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 ERCC3 |
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 ERCC3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for ERCC3 |
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 ERCC3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |