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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for DEPDC4 |
 Gene summary |
| Gene information | Gene symbol | DEPDC4 | Gene ID | 120863 |
| Gene name | DEP domain containing 4 | |
| Synonyms | DEP.4 | |
| Cytomap | 12q23.1 | |
| Type of gene | protein-coding | |
| Description | DEP domain-containing protein 4 | |
| Modification date | 20180403 | |
| UniProtAcc | Q8N2C3 | |
| Context | PubMed: DEPDC4 [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 |
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Exon skipping events across known transcript of Ensembl for DEPDC4 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 DEPDC4 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for DEPDC4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_95590 | 12 | 100631745:100631895:100635420:100635623:100636263:100636347 | 100635420:100635623 | ENSG00000166153.12 | ENST00000378244.2 |
| exon_skip_95594 | 12 | 100646257:100646314:100647266:100647493:100649826:100650004 | 100647266:100647493 | ENSG00000166153.12 | ENST00000550587.1,ENST00000549249.1,ENST00000299185.8 |
| exon_skip_95595 | 12 | 100649826:100650004:100655507:100655546:100656041:100656134 | 100655507:100655546 | ENSG00000166153.12 | ENST00000548313.1,ENST00000549249.1 |
| exon_skip_95596 | 12 | 100649826:100650004:100656041:100656187:100657274:100657470 | 100656041:100656187 | ENSG00000166153.12 | ENST00000550587.1,ENST00000551642.1,ENST00000416321.1,ENST00000378244.2 |
| exon_skip_95597 | 12 | 100649826:100650004:100656041:100656187:100660697:100660833 | 100656041:100656187 | ENSG00000166153.12 | ENST00000549341.1,ENST00000299185.8 |
| exon_skip_95601 | 12 | 100656041:100656187:100657274:100657671:100660697:100660833 | 100657274:100657671 | ENSG00000166153.12 | ENST00000550587.1,ENST00000551642.1,ENST00000416321.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for DEPDC4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_95590 | 12 | 100631745:100631895:100635420:100635623:100636263:100636347 | 100635420:100635623 | ENSG00000166153.12 | ENST00000378244.2 |
| exon_skip_95594 | 12 | 100646257:100646314:100647266:100647493:100649826:100650004 | 100647266:100647493 | ENSG00000166153.12 | ENST00000550587.1,ENST00000549249.1,ENST00000299185.8 |
| exon_skip_95595 | 12 | 100649826:100650004:100655507:100655546:100656041:100656134 | 100655507:100655546 | ENSG00000166153.12 | ENST00000548313.1,ENST00000549249.1 |
| exon_skip_95596 | 12 | 100649826:100650004:100656041:100656187:100657274:100657470 | 100656041:100656187 | ENSG00000166153.12 | ENST00000378244.2,ENST00000416321.1,ENST00000550587.1,ENST00000551642.1 |
| exon_skip_95597 | 12 | 100649826:100650004:100656041:100656187:100660697:100660833 | 100656041:100656187 | ENSG00000166153.12 | ENST00000299185.8,ENST00000549341.1 |
| exon_skip_95600 | 12 | 100656041:100656187:100657274:100657470:100660697:100660833 | 100657274:100657470 | ENSG00000166153.12 | ENST00000549249.1 |
| exon_skip_95601 | 12 | 100656041:100656187:100657274:100657671:100660697:100660833 | 100657274:100657671 | ENSG00000166153.12 | ENST00000416321.1,ENST00000550587.1,ENST00000551642.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for DEPDC4 |
| 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 |
| ENST00000416321 | 100656041 | 100656187 | Frame-shift |
| ENST00000416321 | 100657274 | 100657671 | Frame-shift |
| 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 |
| ENST00000416321 | 100656041 | 100656187 | Frame-shift |
| ENST00000416321 | 100657274 | 100657671 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for DEPDC4 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 DEPDC4 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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-A39Y-01 | exon_skip_95601 | 100657275 | 100657671 | 100657315 | 100657315 | Frame_Shift_Del | T | - | p.R172fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_95601 | 100657275 | 100657671 | 100657315 | 100657315 | Frame_Shift_Del | T | - | p.R172fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_95601 | 100657275 | 100657671 | 100657397 | 100657397 | Frame_Shift_Del | T | - | p.K144fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_95601 | 100657275 | 100657671 | 100657655 | 100657655 | Frame_Shift_Del | A | - | p.F58fs |
| COAD | TCGA-AZ-4315-01 | exon_skip_95597 exon_skip_95596 | 100656042 | 100656187 | 100656045 | 100656045 | Nonsense_Mutation | C | A | p.E233X |
| LGG | TCGA-DB-A4XF-01 | exon_skip_95597 exon_skip_95596 | 100656042 | 100656187 | 100656178 | 100656178 | Nonsense_Mutation | A | C | p.Y188* |
| LGG | TCGA-DB-A4XF-01 | exon_skip_95597 exon_skip_95596 | 100656042 | 100656187 | 100656178 | 100656178 | Nonsense_Mutation | A | C | p.Y188X |
| COAD | TCGA-CA-6717-01 | exon_skip_95601 | 100657275 | 100657671 | 100657285 | 100657285 | Nonsense_Mutation | C | A | p.E182X |
| HNSC | TCGA-BA-5152-01 | exon_skip_95601 | 100657275 | 100657671 | 100657384 | 100657384 | Nonsense_Mutation | C | A | p.E149* |
| - 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 |
| NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100657275 | 100657671 | 100657663 | 100657664 | Frame_Shift_Del | CA | - | p.G56fs |
| SNU1040_LARGE_INTESTINE | 100657275 | 100657671 | 100657391 | 100657392 | Frame_Shift_Ins | - | T | p.K146fs |
| SNU1_STOMACH | 100657275 | 100657671 | 100657403 | 100657404 | Frame_Shift_Ins | - | A | p.F142fs |
| PC3_PROSTATE | 100657275 | 100657671 | 100657317 | 100657317 | Missense_Mutation | T | C | p.K171R |
| PC3JPC3_LUNG | 100657275 | 100657671 | 100657317 | 100657317 | Missense_Mutation | T | C | p.K171R |
| SNU475_LIVER | 100657275 | 100657671 | 100657339 | 100657339 | Missense_Mutation | T | C | p.K164E |
| LS180_LARGE_INTESTINE | 100657275 | 100657671 | 100657515 | 100657515 | Missense_Mutation | A | G | p.M105T |
| KYSE70_OESOPHAGUS | 100657275 | 100657671 | 100657603 | 100657603 | Missense_Mutation | C | T | p.E76K |
| SNU1040_LARGE_INTESTINE | 100657275 | 100657671 | 100657637 | 100657637 | Missense_Mutation | C | A | p.W64C |
| KYSE70_OESOPHAGUS | 100656042 | 100656187 | 100656050 | 100656050 | Nonsense_Mutation | G | C | p.S231* |
| NCIH650_LUNG | 100656042 | 100656187 | 100656150 | 100656151 | Nonsense_Mutation | CC | AT | p.E198* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for DEPDC4 |
| 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 DEPDC4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for DEPDC4 |
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RelatedDrugs for DEPDC4 |
| 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 DEPDC4 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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