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Open reading frame (ORF) annotation in the exon skipping event | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon | |
Gene summary for FOXA2 |
Gene summary |
Gene information | Gene symbol | FOXA2 | Gene ID | 3170 |
Gene name | forkhead box A2 | |
Synonyms | HNF3B|TCF3B | |
Cytomap | 20p11.21 | |
Type of gene | protein-coding | |
Description | hepatocyte nuclear factor 3-betaHNF-3-betaHNF-3BTCF-3Bforkhead box protein A2hepatic nuclear factor-3-betatranscription factor 3B | |
Modification date | 20180527 | |
UniProtAcc | Q9Y261 | |
Context | PubMed: FOXA2 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
FOXA2 | GO:0006357 | regulation of transcription by RNA polymerase II | 12911579 |
FOXA2 | GO:0030193 | regulation of blood coagulation | 12911579 |
FOXA2 | GO:0031018 | endocrine pancreas development | 12124776 |
FOXA2 | GO:0045893 | positive regulation of transcription, DNA-templated | 9931457 |
FOXA2 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 12124776|20160041 |
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Exon skipping events across known transcript of Ensembl for FOXA2 from UCSC genome browser |
Skipped exons in TCGA and GTEx 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. |
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Gene isoform structures and expression levels for FOXA2 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for FOXA2 |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_355368 | 20 | 22561642:22563792:22564829:22564899:22565912:22566093 | 22564829:22564899 | ENSG00000125798.10 | ENST00000377115.4 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for FOXA2 |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_355368 | 20 | 22561642:22563792:22564829:22564899:22565912:22566093 | 22564829:22564899 | ENSG00000125798.10 | ENST00000377115.4 |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for FOXA2 |
Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000377115 | 22564829 | 22564899 | 3UTR-3CDS |
Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000377115 | 22564829 | 22564899 | 3UTR-3CDS |
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Infer the effects of exon skipping event on protein functional features for FOXA2 |
Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
Loci of skipped exons in TCGA 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 GTEx 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 TCGA. |
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 GTEx. |
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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SNVs in the skipped exons for FOXA2 |
- Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
- Differential PSIs between mutated versus non-mutated samples. |
- Non-synonymous mutations located in the skipped exons in TCGA. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
LIHC | TCGA-DD-A1EG-01 | exon_skip_355368 | 22564830 | 22564899 | 22564872 | 22564872 | Frame_Shift_Del | C | - | p.G9fs |
STAD | TCGA-HU-A4H2-01 | exon_skip_355368 | 22564830 | 22564899 | 22564868 | 22564868 | Nonsense_Mutation | C | A | p.E11* |
STAD | TCGA-HU-A4H2-01 | exon_skip_355368 | 22564830 | 22564899 | 22564868 | 22564868 | Nonsense_Mutation | C | A | p.E17X |
- Depth of coverage in the three exons composing exon skipping event |
Depth of coverage in three exons | Mutation description |
- 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 |
TOV21G_OVARY | 22564830 | 22564899 | 22564849 | 22564849 | Missense_Mutation | C | A | p.S17I |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FOXA2 |
sQTL information located at the skipped exons. |
Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FOXA2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FOXA2 |
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RelatedDrugs for FOXA2 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for FOXA2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |
FOXA2 | C0019284 | Diaphragmatic Hernia | 1 | CTD_human |
FOXA2 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
FOXA2 | C0024115 | Lung diseases | 1 | CTD_human |