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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 CDH12 |
Gene summary |
Gene information | Gene symbol | CDH12 | Gene ID | 1010 |
Gene name | cadherin 12 | |
Synonyms | CDHB | |
Cytomap | 5p14.3 | |
Type of gene | protein-coding | |
Description | cadherin-12Br-cadherinN-cadherin 2brain-cadherincadherin, neural type, 2neural type cadherin 2neuronal cadherin 2 | |
Modification date | 20200313 | |
UniProtAcc | P55289, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for CDH12 |
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 | ENST00000382254.6 | CDH12-201:protein_coding:CDH12 | 1.029953e+02 | -8.467583e-01 | 5.481383e-04 | 9.417967e-03 |
PG | DOWN | ENST00000518209.1 | CDH12-204:lncRNA:CDH12 | 4.211370e+00 | -9.350199e-01 | 3.206254e-03 | 3.335365e-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 CDH12 |
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_268000 | chr5 | 21842161:21842328:21854671:21854790:21975091:21975121 | 21854671:21854790 |
exon_skip_44447 | chr5 | 21842161:21842328:21854671:21854790:21975091:21975385 | 21854671:21854790 |
exon_skip_50331 | chr5 | 22212498:22212643:22405257:22405351:22505270:22505364 | 22405257:22405351 |
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 CDH12 |
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 |
ENST00000382254 | 22405257 | 22405351 | 3UTR-3UTR |
ENST00000382254 | 21854671 | 21854790 | In-frame |
ENST00000504376 | 21854671 | 21854790 | In-frame |
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 |
ENST00000382254 | 22405257 | 22405351 | 3UTR-3UTR |
ENST00000382254 | 21854671 | 21854790 | In-frame |
ENST00000504376 | 21854671 | 21854790 | In-frame |
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 |
ENST00000382254 | 22405257 | 22405351 | 3UTR-3UTR |
ENST00000382254 | 21854671 | 21854790 | In-frame |
ENST00000504376 | 21854671 | 21854790 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CDH12 |
p-ENSG00000154162_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 |
ENST00000382254 | 4181 | 794 | 21854671 | 21854790 | 1614 | 1732 | 175 | 215 |
ENST00000504376 | 4177 | 794 | 21854671 | 21854790 | 1238 | 1356 | 175 | 215 |
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 |
ENST00000382254 | 4181 | 794 | 21854671 | 21854790 | 1614 | 1732 | 175 | 215 |
ENST00000504376 | 4177 | 794 | 21854671 | 21854790 | 1238 | 1356 | 175 | 215 |
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 |
ENST00000382254 | 4181 | 794 | 21854671 | 21854790 | 1614 | 1732 | 175 | 215 |
ENST00000504376 | 4177 | 794 | 21854671 | 21854790 | 1238 | 1356 | 175 | 215 |
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 |
P55289 | 175 | 215 | 176 | 215 | Alternative sequence | ID=VSP_056449;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P55289 | 175 | 215 | 176 | 215 | Alternative sequence | ID=VSP_056449;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P55289 | 175 | 215 | 55 | 794 | Chain | ID=PRO_0000003792;Note=Cadherin-12 |
P55289 | 175 | 215 | 55 | 794 | Chain | ID=PRO_0000003792;Note=Cadherin-12 |
P55289 | 175 | 215 | 161 | 269 | Domain | Note=Cadherin 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
P55289 | 175 | 215 | 161 | 269 | Domain | Note=Cadherin 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
P55289 | 175 | 215 | 55 | 609 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
P55289 | 175 | 215 | 55 | 609 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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 |
P55289 | 175 | 215 | 176 | 215 | Alternative sequence | ID=VSP_056449;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P55289 | 175 | 215 | 176 | 215 | Alternative sequence | ID=VSP_056449;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P55289 | 175 | 215 | 55 | 794 | Chain | ID=PRO_0000003792;Note=Cadherin-12 |
P55289 | 175 | 215 | 55 | 794 | Chain | ID=PRO_0000003792;Note=Cadherin-12 |
P55289 | 175 | 215 | 161 | 269 | Domain | Note=Cadherin 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
P55289 | 175 | 215 | 161 | 269 | Domain | Note=Cadherin 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
P55289 | 175 | 215 | 55 | 609 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
P55289 | 175 | 215 | 55 | 609 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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 |
P55289 | 175 | 215 | 176 | 215 | Alternative sequence | ID=VSP_056449;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P55289 | 175 | 215 | 176 | 215 | Alternative sequence | ID=VSP_056449;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
P55289 | 175 | 215 | 55 | 794 | Chain | ID=PRO_0000003792;Note=Cadherin-12 |
P55289 | 175 | 215 | 55 | 794 | Chain | ID=PRO_0000003792;Note=Cadherin-12 |
P55289 | 175 | 215 | 161 | 269 | Domain | Note=Cadherin 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
P55289 | 175 | 215 | 161 | 269 | Domain | Note=Cadherin 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
P55289 | 175 | 215 | 55 | 609 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
P55289 | 175 | 215 | 55 | 609 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CDH12 |
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 |
Mayo | ENST00000382254 | 22405257 | 22405351 | hsa-miR-7847-3p | chr5:22405312-22405319 | 8mer-1a | chr5:22405299-22405319 | 150.00 | -16.83 |
Mayo | ENST00000382254 | 22405257 | 22405351 | hsa-miR-4693-5p | chr5:22405316-22405323 | 8mer-1a | chr5:22405301-22405323 | 151.00 | -9.36 |
Mayo | ENST00000382254 | 22405257 | 22405351 | hsa-miR-4318 | chr5:22405315-22405322 | 8mer-1a | chr5:22405301-22405323 | 151.00 | -9.36 |
Mayo | ENST00000382254 | 22405257 | 22405351 | hsa-miR-320e | chr5:22405284-22405291 | 8mer-1a | chr5:22405274-22405291 | 160.00 | -17.54 |
Mayo | ENST00000382254 | 22405257 | 22405351 | hsa-miR-1825 | chr5:22405336-22405343 | 8mer-1a | chr5:22405327-22405348 | 150.00 | -16.29 |
Mayo | ENST00000382254 | 22405257 | 22405351 | hsa-miR-219b-5p | chr5:22405341-22405348 | 8mer-1a | chr5:22405327-22405348 | 150.00 | -16.29 |
MSBB | ENST00000382254 | 22405257 | 22405351 | hsa-miR-7847-3p | chr5:22405312-22405319 | 8mer-1a | chr5:22405299-22405319 | 150.00 | -16.83 |
MSBB | ENST00000382254 | 22405257 | 22405351 | hsa-miR-4693-5p | chr5:22405316-22405323 | 8mer-1a | chr5:22405301-22405323 | 151.00 | -9.36 |
MSBB | ENST00000382254 | 22405257 | 22405351 | hsa-miR-4318 | chr5:22405315-22405322 | 8mer-1a | chr5:22405301-22405323 | 151.00 | -9.36 |
MSBB | ENST00000382254 | 22405257 | 22405351 | hsa-miR-320e | chr5:22405284-22405291 | 8mer-1a | chr5:22405274-22405291 | 160.00 | -17.54 |
MSBB | ENST00000382254 | 22405257 | 22405351 | hsa-miR-1825 | chr5:22405336-22405343 | 8mer-1a | chr5:22405327-22405348 | 150.00 | -16.29 |
MSBB | ENST00000382254 | 22405257 | 22405351 | hsa-miR-219b-5p | chr5:22405341-22405348 | 8mer-1a | chr5:22405327-22405348 | 150.00 | -16.29 |
ROSMAP | ENST00000382254 | 22405257 | 22405351 | hsa-miR-7847-3p | chr5:22405312-22405319 | 8mer-1a | chr5:22405299-22405319 | 150.00 | -16.83 |
ROSMAP | ENST00000382254 | 22405257 | 22405351 | hsa-miR-4693-5p | chr5:22405316-22405323 | 8mer-1a | chr5:22405301-22405323 | 151.00 | -9.36 |
ROSMAP | ENST00000382254 | 22405257 | 22405351 | hsa-miR-4318 | chr5:22405315-22405322 | 8mer-1a | chr5:22405301-22405323 | 151.00 | -9.36 |
ROSMAP | ENST00000382254 | 22405257 | 22405351 | hsa-miR-320e | chr5:22405284-22405291 | 8mer-1a | chr5:22405274-22405291 | 160.00 | -17.54 |
ROSMAP | ENST00000382254 | 22405257 | 22405351 | hsa-miR-1825 | chr5:22405336-22405343 | 8mer-1a | chr5:22405327-22405348 | 150.00 | -16.29 |
ROSMAP | ENST00000382254 | 22405257 | 22405351 | hsa-miR-219b-5p | chr5:22405341-22405348 | 8mer-1a | chr5:22405327-22405348 | 150.00 | -16.29 |
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SNVs in the skipped exons for CDH12 |
- 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 CDH12 |
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 CDH12 |
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 CDH12 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for CDH12 |
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 CDH12 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |