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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 DENND4A |
 Gene summary |
| Gene information | Gene symbol | DENND4A | Gene ID | 10260 |
| Gene name | DENN domain containing 4A | |
| Synonyms | IRLB|MYCPBP | |
| Cytomap | 15q22.31 | |
| Type of gene | protein-coding | |
| Description | C-myc promoter-binding proteinDENN domain-containing protein 4ADENN/MADD domain containing 4Ac-myc promoter binding protein | |
| Modification date | 20180522 | |
| UniProtAcc | Q7Z401 | |
| Context | PubMed: DENND4A [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 DENND4A 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 DENND4A |
| 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 DENND4A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_128637 | 15 | 65960262:65960461:65962116:65962263:65962350:65962526 | 65962116:65962263 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2 |
| exon_skip_128639 | 15 | 65962350:65962526:65964129:65964224:65968782:65968972 | 65964129:65964224 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2 |
| exon_skip_128641 | 15 | 65989604:65989721:65992881:65993010:65993388:65993530 | 65992881:65993010 | ENSG00000174485.10 | ENST00000443035.3 |
| exon_skip_128643 | 15 | 65993388:65993530:65994099:65994228:65994642:65994849 | 65994099:65994228 | ENSG00000174485.10 | ENST00000443035.3,ENST00000564674.1,ENST00000431932.2 |
| exon_skip_128644 | 15 | 66010115:66010334:66015185:66015286:66021409:66021585 | 66015185:66015286 | ENSG00000174485.10 | ENST00000443035.3,ENST00000568515.1,ENST00000564674.1,ENST00000431932.2 |
| exon_skip_128645 | 15 | 66031043:66031213:66034052:66034122:66044716:66044966 | 66034052:66034122 | ENSG00000174485.10 | ENST00000443035.3,ENST00000568515.1,ENST00000564674.1,ENST00000431932.2 |
| exon_skip_128647 | 15 | 66034052:66034122:66044716:66044966:66048477:66048810 | 66044716:66044966 | ENSG00000174485.10 | ENST00000443035.3,ENST00000568515.1,ENST00000564674.1,ENST00000431932.2 |
| exon_skip_128649 | 15 | 66048477:66048810:66053697:66053776:66084347:66084462 | 66053697:66053776 | ENSG00000174485.10 | ENST00000443035.3,ENST00000568515.1,ENST00000564674.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for DENND4A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_128637 | 15 | 65960262:65960461:65962116:65962263:65962350:65962526 | 65962116:65962263 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2 |
| exon_skip_128639 | 15 | 65962350:65962526:65964129:65964224:65968782:65968972 | 65964129:65964224 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2 |
| exon_skip_128641 | 15 | 65989604:65989721:65992881:65993010:65993388:65993530 | 65992881:65993010 | ENSG00000174485.10 | ENST00000443035.3 |
| exon_skip_128643 | 15 | 65993388:65993530:65994099:65994228:65994642:65994849 | 65994099:65994228 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2,ENST00000564674.1 |
| exon_skip_128644 | 15 | 66010115:66010334:66015185:66015286:66021409:66021585 | 66015185:66015286 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2,ENST00000564674.1,ENST00000568515.1 |
| exon_skip_128645 | 15 | 66031043:66031213:66034052:66034122:66044716:66044966 | 66034052:66034122 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2,ENST00000564674.1,ENST00000568515.1 |
| exon_skip_128647 | 15 | 66034052:66034122:66044716:66044966:66048477:66048810 | 66044716:66044966 | ENSG00000174485.10 | ENST00000443035.3,ENST00000431932.2,ENST00000564674.1,ENST00000568515.1 |
| exon_skip_128649 | 15 | 66048477:66048810:66053697:66053776:66084347:66084462 | 66053697:66053776 | ENSG00000174485.10 | ENST00000443035.3,ENST00000564674.1,ENST00000568515.1 |
| exon_skip_128650 | 15 | 66048477:66048810:66053704:66053776:66084347:66084462 | 66053704:66053776 | ENSG00000174485.10 | ENST00000431932.2 |
| 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 DENND4A |
| 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 |
| ENST00000431932 | 65964129 | 65964224 | Frame-shift |
| ENST00000431932 | 66015185 | 66015286 | Frame-shift |
| ENST00000431932 | 66034052 | 66034122 | Frame-shift |
| ENST00000431932 | 66044716 | 66044966 | Frame-shift |
| ENST00000431932 | 65962116 | 65962263 | In-frame |
| ENST00000431932 | 65994099 | 65994228 | In-frame |
| 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 |
| ENST00000431932 | 66053704 | 66053776 | 3UTR-3UTR |
| ENST00000431932 | 65964129 | 65964224 | Frame-shift |
| ENST00000431932 | 66015185 | 66015286 | Frame-shift |
| ENST00000431932 | 66034052 | 66034122 | Frame-shift |
| ENST00000431932 | 66044716 | 66044966 | Frame-shift |
| ENST00000431932 | 65962116 | 65962263 | In-frame |
| ENST00000431932 | 65994099 | 65994228 | In-frame |
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Infer the effects of exon skipping event on protein functional features for DENND4A |
| 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 |
| ENST00000431932 | 5892 | 1863 | 65994099 | 65994228 | 2640 | 2768 | 810 | 853 |
| ENST00000431932 | 5892 | 1863 | 65962116 | 65962263 | 4718 | 4864 | 1503 | 1551 |
| 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 |
| ENST00000431932 | 5892 | 1863 | 65994099 | 65994228 | 2640 | 2768 | 810 | 853 |
| ENST00000431932 | 5892 | 1863 | 65962116 | 65962263 | 4718 | 4864 | 1503 | 1551 |
| 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 |
| Q7Z401 | 810 | 853 | 1 | 1863 | Chain | ID=PRO_0000223952;Note=C-myc promoter-binding protein |
| Q7Z401 | 810 | 853 | 809 | 843 | Repeat | Note=PPR 2 |
| Q7Z401 | 1503 | 1551 | 1 | 1863 | Chain | ID=PRO_0000223952;Note=C-myc promoter-binding protein |
| Q7Z401 | 1503 | 1551 | 1508 | 1508 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q7Z401 | 1503 | 1551 | 1532 | 1532 | Sequence conflict | Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q7Z401 | 810 | 853 | 1 | 1863 | Chain | ID=PRO_0000223952;Note=C-myc promoter-binding protein |
| Q7Z401 | 810 | 853 | 809 | 843 | Repeat | Note=PPR 2 |
| Q7Z401 | 1503 | 1551 | 1 | 1863 | Chain | ID=PRO_0000223952;Note=C-myc promoter-binding protein |
| Q7Z401 | 1503 | 1551 | 1508 | 1508 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q7Z401 | 1503 | 1551 | 1532 | 1532 | Sequence conflict | Note=T->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for DENND4A |
| - 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 |
| UCEC | TCGA-D1-A17Q-01 | 65994100 | 65994228 | 65994168 | 65994168 | Nonsense_Mutation | G | A | p.R831* | |
| BLCA | TCGA-GV-A3QH-01 | exon_skip_128644 | 66015186 | 66015286 | 66015201 | 66015201 | Nonsense_Mutation | G | A | p.Q525* |
| THYM | TCGA-XM-A8R8-01 | exon_skip_128647 | 66044717 | 66044966 | 66044868 | 66044868 | Nonsense_Mutation | G | T | p.S137X |
| PAAD | TCGA-IB-7651-01 | exon_skip_128637 | 65962117 | 65962263 | 65962264 | 65962264 | Splice_Site | C | A | . |
| - 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 |
| RL952_ENDOMETRIUM | 66044717 | 66044966 | 66044829 | 66044829 | Frame_Shift_Del | T | - | p.N150fs |
| HCC1833_LUNG | 65962117 | 65962263 | 65962151 | 65962151 | Missense_Mutation | C | A | p.A1541S |
| MCCAR_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 65962117 | 65962263 | 65962220 | 65962220 | Missense_Mutation | G | A | p.P1518S |
| LS411N_LARGE_INTESTINE | 65964130 | 65964224 | 65964134 | 65964134 | Missense_Mutation | A | C | p.M1443R |
| AU565_BREAST | 65964130 | 65964224 | 65964151 | 65964151 | Missense_Mutation | G | C | p.I1437M |
| SKBR3_BREAST | 65964130 | 65964224 | 65964151 | 65964151 | Missense_Mutation | G | C | p.I1437M |
| HEC108_ENDOMETRIUM | 65964130 | 65964224 | 65964167 | 65964167 | Missense_Mutation | G | A | p.A1432V |
| HT115_LARGE_INTESTINE | 65964130 | 65964224 | 65964221 | 65964221 | Missense_Mutation | G | T | p.S1414Y |
| SNU1040_LARGE_INTESTINE | 65994100 | 65994228 | 65994126 | 65994126 | Missense_Mutation | C | T | p.A845T |
| NH6_AUTONOMIC_GANGLIA | 66034053 | 66034122 | 66034109 | 66034109 | Missense_Mutation | A | G | p.V192A |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 66034053 | 66034122 | 66034109 | 66034109 | Missense_Mutation | A | G | p.V192A |
| LK2_LUNG | 66034053 | 66034122 | 66034109 | 66034109 | Missense_Mutation | A | G | p.V192A |
| MDAMB361_BREAST | 66044717 | 66044966 | 66044731 | 66044731 | Missense_Mutation | G | C | p.L183V |
| SNU407_LARGE_INTESTINE | 66044717 | 66044966 | 66044844 | 66044844 | Missense_Mutation | C | T | p.R145Q |
| LS180_LARGE_INTESTINE | 66044717 | 66044966 | 66044871 | 66044871 | Missense_Mutation | G | A | p.S136L |
| SNU1040_LARGE_INTESTINE | 66044717 | 66044966 | 66044877 | 66044877 | Missense_Mutation | C | T | p.S134N |
| SNU1040_LARGE_INTESTINE | 65994100 | 65994228 | 65994168 | 65994168 | Nonsense_Mutation | G | A | p.R831* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for DENND4A |
| 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 DENND4A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for DENND4A |
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RelatedDrugs for DENND4A |
| 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 DENND4A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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