|
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 PFDN1 |
Gene summary |
Gene information | Gene symbol | PFDN1 | Gene ID | 5201 |
Gene name | prefoldin subunit 1 | |
Synonyms | PDF|PFD1 | |
Cytomap | 5q31.3 | |
Type of gene | protein-coding | |
Description | prefoldin subunit 1prefoldin 1 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context | - 28183528(Transethnic Genome-Wide Scan Identifies Novel Alzheimer's Disease Loci) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for PFDN1 |
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 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PFDN1 |
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_105165 | chr5 | 140245552:140246057:140281449:140281533:140303041:140303083 | 140281449:140281533 |
exon_skip_168401 | chr5 | 140245552:140246057:140281449:140281533:140300416:140300582 | 140281449:140281533 |
exon_skip_88029 | chr5 | 140281449:140281533:140300416:140300582:140303041:140303083 | 140300416:140300582 |
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 PFDN1 |
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 |
ENST00000261813 | 140281449 | 140281533 | 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 |
ENST00000261813 | 140281449 | 140281533 | 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 |
ENST00000261813 | 140281449 | 140281533 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for PFDN1 |
p-ENSG00000113068_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 PFDN1 |
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 PFDN1 |
- 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 PFDN1 |
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 PFDN1 |
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 PFDN1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | TARDBP | exon_skip_88029 | -4.115655e-01 | 7.066305e-08 |
CB | CNOT4 | exon_skip_88029 | -4.749604e-01 | 2.523793e-10 |
CB | RBM3 | exon_skip_88029 | 4.835647e-01 | 1.070578e-10 |
CB | TRA2A | exon_skip_88029 | -5.503356e-01 | 5.711649e-14 |
CB | FUBP1 | exon_skip_88029 | -4.106497e-01 | 7.603065e-08 |
CB | RBM45 | exon_skip_88029 | 7.016521e-01 | 6.974470e-25 |
CB | NUP42 | exon_skip_88029 | 4.745274e-01 | 2.633450e-10 |
DLPFC | RBFOX2 | exon_skip_88029 | 4.798310e-01 | 5.574005e-21 |
FL | RBM3 | exon_skip_88029 | 4.063421e-01 | 8.682654e-09 |
HCC | RBFOX2 | exon_skip_88029 | 4.512739e-01 | 4.210454e-15 |
IFG | PABPN1L | exon_skip_88029 | -4.804764e-01 | 9.655528e-03 |
PCC | RBFOX2 | exon_skip_88029 | 5.818640e-01 | 7.085870e-21 |
PCC | RBM3 | exon_skip_88029 | 4.803565e-01 | 8.238190e-14 |
PCC | KHSRP | exon_skip_88029 | 4.352412e-01 | 2.377750e-11 |
STG | RBM3 | exon_skip_88029 | 4.778763e-01 | 8.440352e-06 |
TC | RBFOX2 | exon_skip_88029 | 5.972677e-01 | 7.658202e-17 |
TC | RBM3 | exon_skip_88029 | 5.940096e-01 | 1.238274e-16 |
TC | MATR3 | exon_skip_88029 | 5.549821e-01 | 2.629507e-14 |
TC | NUP42 | exon_skip_88029 | 5.369891e-01 | 2.478536e-13 |
Top |
RelatedDrugs for PFDN1 |
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 PFDN1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |