|
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 BARD1 |
Gene summary |
Gene information | Gene symbol | BARD1 | Gene ID | 580 |
Gene name | BRCA1 associated RING domain 1 | |
Synonyms | - | |
Cytomap | 2q35 | |
Type of gene | protein-coding | |
Description | BRCA1-associated RING domain protein 1BRCA1-associated RING domain gene 1RING-type E3 ubiquitin transferase BARD1 | |
Modification date | 20200322 | |
UniProtAcc | A0A087WZ19, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
BARD1 | GO:0046826 | negative regulation of protein export from nucleus | 15265711 |
BARD1 | GO:0085020 | protein K6-linked ubiquitination | 12890688|20351172 |
Top |
Gene structures and expression levels for BARD1 |
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 |
PG | UP | ENST00000455743.5 | BARD1-204:nonsense_mediated_decay:BARD1 | 5.557441e+01 | 8.475397e-01 | 4.776490e-04 | 8.542693e-03 |
TC | UP | ENST00000650978.1 | BARD1-215:nonsense_mediated_decay:BARD1 | 5.346794e+00 | 9.923737e-01 | 5.005898e-08 | 3.477305e-06 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for BARD1 |
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_174882 | chr2 | 214780968:214781509:214797061:214797117:214809412:214809597 | 214797061:214797117 |
exon_skip_219120 | chr2 | 214769232:214769312:214780968:214781509:214792297:214792445 | 214780968:214781509 |
exon_skip_34070 | chr2 | 214792297:214792445:214797061:214797117:214809412:214809642 | 214797061:214797117 |
exon_skip_36549 | chr2 | 214780560:214781509:214792297:214792445:214797061:214797117 | 214792297:214792445 |
exon_skip_50787 | chr2 | 214780968:214781509:214792297:214792445:214797061:214797117 | 214792297:214792445 |
exon_skip_68924 | chr2 | 214769232:214769312:214780560:214781509:214792297:214792445 | 214780560:214781509 |
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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for BARD1 |
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 |
ENST00000260947 | 214780560 | 214781509 | Frame-shift |
ENST00000260947 | 214792297 | 214792445 | 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 |
ENST00000260947 | 214780560 | 214781509 | Frame-shift |
ENST00000260947 | 214792297 | 214792445 | 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 |
ENST00000260947 | 214780560 | 214781509 | Frame-shift |
ENST00000260947 | 214792297 | 214792445 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for BARD1 |
p-ENSG00000138376_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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in BARD1 |
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 |
Top |
SNVs in the skipped exons for BARD1 |
- 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 |
Top |
AD stage-associated exon skippint events for BARD1 |
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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BARD1 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for BARD1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for BARD1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for BARD1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |