|
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 CDH1 |
Gene summary |
Gene information | Gene symbol | CDH1 | Gene ID | 999 |
Gene name | cadherin 1 | |
Synonyms | Arc-1|BCDS1|CD324|CDHE|ECAD|LCAM|UVO | |
Cytomap | 16q22.1 | |
Type of gene | protein-coding | |
Description | cadherin-1CAM 120/80E-cadherin 1cadherin 1, E-cadherin (epithelial)cadherin 1, type 1, E-cadherin (epithelial)calcium-dependent adhesion protein, epithelialcell-CAM 120/80epididymis secretory sperm binding proteinepithelial cadherinuvomorulin | |
Modification date | 20200329 | |
UniProtAcc | A0A087WU43, A0A087WX17, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
CDH1 | GO:0042307 | positive regulation of protein import into nucleus | 16338932 |
CDH1 | GO:0045893 | positive regulation of transcription, DNA-templated | 16338932 |
CDH1 | GO:0071285 | cellular response to lithium ion | 12937339 |
CDH1 | GO:0071681 | cellular response to indole-3-methanol | 10868478 |
CDH1 | GO:0072659 | protein localization to plasma membrane | 17620337 |
CDH1 | GO:0098609 | cell-cell adhesion | 16338932|18593713 |
Top |
Gene structures and expression levels for CDH1 |
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 | DOWN | ENST00000357517.6 | PCDH1-202:lncRNA:PCDH1 | 1.416224e+02 | -8.814526e-01 | 2.507191e-03 | 2.803354e-02 |
CB | DOWN | ENST00000503492.5 | PCDH1-204:protein_coding:PCDH1 | 4.821794e+01 | -9.601113e-01 | 1.679062e-10 | 9.766087e-09 |
CB | UP | ENST00000505937.2 | PCDH1-205:nonsense_mediated_decay:PCDH1 | 4.843172e+00 | 1.345284e+00 | 3.535959e-10 | 1.854661e-08 |
TC | DOWN | ENST00000503492.5 | PCDH1-204:protein_coding:PCDH1 | 7.869025e+01 | -9.142930e-01 | 1.452312e-06 | 5.428647e-05 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CDH1 |
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_116723 | chr16 | 68808693:68808848:68810197:68810341:68811684:68811859 | 68810197:68810341 |
exon_skip_219757 | chr16 | 68815515:68815759:68819280:68819425:68822001:68822119 | 68819280:68819425 |
exon_skip_275082 | chr16 | 68815515:68815759:68819280:68819425:68822001:68822225 | 68819280:68819425 |
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 CDH1 |
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 |
ENST00000261769 | 68819280 | 68819425 | 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 |
ENST00000261769 | 68810197 | 68810341 | Frame-shift |
ENST00000261769 | 68819280 | 68819425 | 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 |
ENST00000261769 | 68810197 | 68810341 | Frame-shift |
ENST00000261769 | 68819280 | 68819425 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for CDH1 |
p-ENSG00000039068_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 CDH1 |
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 CDH1 |
- 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 CDH1 |
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 CDH1 |
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 CDH1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for CDH1 |
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 CDH1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |