|
||||||
|
 | |
| |
| |
| |
| 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 NEDD4 |
 Gene summary |
| Gene information | Gene symbol | NEDD4 | Gene ID | 4734 |
| Gene name | neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase | |
| Synonyms | NEDD4-1|RPF1 | |
| Cytomap | 15q21.3 | |
| Type of gene | protein-coding | |
| Description | E3 ubiquitin-protein ligase NEDD4HECT-type E3 ubiquitin transferase NEDD4cell proliferation-inducing gene 53 proteinreceptor-potentiating factor 1 | |
| Modification date | 20180527 | |
| UniProtAcc | P46934 | |
| Context | PubMed: NEDD4 [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 |
| NEDD4 | GO:0006511 | ubiquitin-dependent protein catabolic process | 20086093 |
| NEDD4 | GO:0006622 | protein targeting to lysosome | 17116753 |
| NEDD4 | GO:0007041 | lysosomal transport | 18544533 |
| NEDD4 | GO:0010766 | negative regulation of sodium ion transport | 10642508 |
| NEDD4 | GO:0016567 | protein ubiquitination | 17996703|18305167|25631046|26280536 |
| NEDD4 | GO:0031623 | receptor internalization | 18544533 |
| NEDD4 | GO:0032801 | receptor catabolic process | 18544533 |
| NEDD4 | GO:0034765 | regulation of ion transmembrane transport | 17289006 |
| NEDD4 | GO:0042391 | regulation of membrane potential | 17289006 |
| NEDD4 | GO:0042921 | glucocorticoid receptor signaling pathway | 8649367 |
| NEDD4 | GO:0045732 | positive regulation of protein catabolic process | 14973438 |
| NEDD4 | GO:0046824 | positive regulation of nucleocytoplasmic transport | 17218261 |
| NEDD4 | GO:0050847 | progesterone receptor signaling pathway | 8649367 |
| NEDD4 | GO:1901016 | regulation of potassium ion transmembrane transporter activity | 17289006 |
| NEDD4 | GO:2000650 | negative regulation of sodium ion transmembrane transporter activity | 10642508 |
Top |
Exon skipping events across known transcript of Ensembl for NEDD4 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. |
 |
Top |
Gene isoform structures and expression levels for NEDD4 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for NEDD4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_127413 | 15 | 56125205:56125302:56126235:56126343:56126424:56126484 | 56126235:56126343 | ENSG00000069869.11 | ENST00000506154.1,ENST00000338963.2,ENST00000435532.3,ENST00000508871.1,ENST00000508342.1 |
| exon_skip_127417 | 15 | 56126235:56126343:56126424:56126484:56129986:56130047 | 56126424:56126484 | ENSG00000069869.11 | ENST00000506154.1,ENST00000338963.2,ENST00000435532.3,ENST00000508871.1,ENST00000508342.1 |
| exon_skip_127419 | 15 | 56130304:56130378:56130706:56130802:56132644:56132715 | 56130706:56130802 | ENSG00000069869.11 | ENST00000506154.1,ENST00000338963.2,ENST00000435532.3,ENST00000508871.1,ENST00000508342.1,ENST00000503468.1 |
| exon_skip_127420 | 15 | 56134131:56134361:56139166:56139232:56140569:56140628 | 56139166:56139232 | ENSG00000069869.11 | ENST00000506154.1,ENST00000338963.2,ENST00000435532.3,ENST00000508871.1,ENST00000508342.1,ENST00000503468.1 |
| exon_skip_127421 | 15 | 56144621:56144741:56148328:56148394:56152604:56152772 | 56148328:56148394 | ENSG00000069869.11 | ENST00000506154.1,ENST00000338963.2,ENST00000435532.3,ENST00000508871.1,ENST00000508342.1,ENST00000503468.1 |
| exon_skip_127422 | 15 | 56155185:56155277:56161776:56161879:56164612:56164674 | 56161776:56161879 | ENSG00000069869.11 | ENST00000514893.1,ENST00000435532.3,ENST00000502612.1,ENST00000507063.1,ENST00000508871.1,ENST00000508342.1 |
| exon_skip_127423 | 15 | 56155185:56155277:56161776:56161879:56207481:56208667 | 56161776:56161879 | ENSG00000069869.11 | ENST00000503468.1 |
| exon_skip_127427 | 15 | 56161776:56161879:56164612:56164674:56166155:56166206 | 56164612:56164674 | ENSG00000069869.11 | ENST00000514893.1,ENST00000506154.1,ENST00000435532.3,ENST00000502612.1,ENST00000507063.1,ENST00000508342.1 |
| exon_skip_127431 | 15 | 56164612:56164674:56166155:56166206:56207481:56207852 | 56166155:56166206 | ENSG00000069869.11 | ENST00000506154.1,ENST00000508342.1 |
| exon_skip_127432 | 15 | 56164612:56164674:56166155:56166206:56216843:56216897 | 56166155:56166206 | ENSG00000069869.11 | ENST00000514893.1,ENST00000435532.3,ENST00000502612.1 |
| exon_skip_127433 | 15 | 56166155:56166206:56197409:56197479:56216843:56216897 | 56197409:56197479 | ENSG00000069869.11 | ENST00000507063.1 |
| exon_skip_127437 | 15 | 56216843:56216897:56226890:56226952:56243573:56243598 | 56226890:56226952 | ENSG00000069869.11 | ENST00000513957.1 |
| exon_skip_127438 | 15 | 56216843:56216897:56243573:56243612:56258670:56258744 | 56243573:56243612 | ENSG00000069869.11 | ENST00000502612.1 |
| exon_skip_127439 | 15 | 56243573:56243612:56243708:56243787:56258670:56258744 | 56243708:56243787 | ENSG00000069869.11 | ENST00000513957.1,ENST00000435532.3 |
| exon_skip_127440 | 15 | 56243708:56243787:56258670:56258744:56285708:56285746 | 56258670:56258744 | ENSG00000069869.11 | ENST00000435532.3 |
| exon_skip_127442 | 15 | 56279928:56280199:56284123:56284203:56285708:56285746 | 56284123:56284203 | ENSG00000069869.11 | ENST00000508075.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for NEDD4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_127413 | 15 | 56125205:56125302:56126235:56126343:56126424:56126484 | 56126235:56126343 | ENSG00000069869.11 | ENST00000508871.1,ENST00000338963.2,ENST00000508342.1,ENST00000435532.3,ENST00000506154.1 |
| exon_skip_127417 | 15 | 56126235:56126343:56126424:56126484:56129986:56130047 | 56126424:56126484 | ENSG00000069869.11 | ENST00000508871.1,ENST00000338963.2,ENST00000508342.1,ENST00000435532.3,ENST00000506154.1 |
| exon_skip_127419 | 15 | 56130304:56130378:56130706:56130802:56132644:56132715 | 56130706:56130802 | ENSG00000069869.11 | ENST00000508871.1,ENST00000503468.1,ENST00000338963.2,ENST00000508342.1,ENST00000435532.3,ENST00000506154.1 |
| exon_skip_127420 | 15 | 56134131:56134361:56139166:56139232:56140569:56140628 | 56139166:56139232 | ENSG00000069869.11 | ENST00000508871.1,ENST00000503468.1,ENST00000338963.2,ENST00000508342.1,ENST00000435532.3,ENST00000506154.1 |
| exon_skip_127421 | 15 | 56144621:56144741:56148328:56148394:56152604:56152772 | 56148328:56148394 | ENSG00000069869.11 | ENST00000508871.1,ENST00000503468.1,ENST00000338963.2,ENST00000508342.1,ENST00000435532.3,ENST00000506154.1 |
| exon_skip_127422 | 15 | 56155185:56155277:56161776:56161879:56164612:56164674 | 56161776:56161879 | ENSG00000069869.11 | ENST00000508871.1,ENST00000508342.1,ENST00000435532.3,ENST00000502612.1,ENST00000514893.1,ENST00000507063.1 |
| exon_skip_127423 | 15 | 56155185:56155277:56161776:56161879:56207481:56208667 | 56161776:56161879 | ENSG00000069869.11 | ENST00000503468.1 |
| exon_skip_127427 | 15 | 56161776:56161879:56164612:56164674:56166155:56166206 | 56164612:56164674 | ENSG00000069869.11 | ENST00000508342.1,ENST00000435532.3,ENST00000506154.1,ENST00000502612.1,ENST00000514893.1,ENST00000507063.1 |
| exon_skip_127431 | 15 | 56164612:56164674:56166155:56166206:56207481:56207852 | 56166155:56166206 | ENSG00000069869.11 | ENST00000508342.1,ENST00000506154.1 |
| exon_skip_127432 | 15 | 56164612:56164674:56166155:56166206:56216843:56216897 | 56166155:56166206 | ENSG00000069869.11 | ENST00000435532.3,ENST00000502612.1,ENST00000514893.1 |
| exon_skip_127433 | 15 | 56166155:56166206:56197409:56197479:56216843:56216897 | 56197409:56197479 | ENSG00000069869.11 | ENST00000507063.1 |
| exon_skip_127438 | 15 | 56216843:56216897:56243573:56243612:56258670:56258744 | 56243573:56243612 | ENSG00000069869.11 | ENST00000502612.1 |
| exon_skip_127439 | 15 | 56243573:56243612:56243708:56243787:56258670:56258744 | 56243708:56243787 | ENSG00000069869.11 | ENST00000435532.3,ENST00000513957.1 |
| exon_skip_127442 | 15 | 56279928:56280199:56284123:56284203:56285708:56285746 | 56284123:56284203 | ENSG00000069869.11 | ENST00000508075.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for NEDD4 |
| 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 |
| ENST00000508342 | 56161776 | 56161879 | Frame-shift |
| ENST00000508342 | 56164612 | 56164674 | Frame-shift |
| ENST00000508342 | 56126235 | 56126343 | In-frame |
| ENST00000508342 | 56126424 | 56126484 | In-frame |
| ENST00000508342 | 56130706 | 56130802 | In-frame |
| ENST00000508342 | 56139166 | 56139232 | In-frame |
| ENST00000508342 | 56148328 | 56148394 | In-frame |
| ENST00000508342 | 56166155 | 56166206 | 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 |
| ENST00000508342 | 56161776 | 56161879 | Frame-shift |
| ENST00000508342 | 56164612 | 56164674 | Frame-shift |
| ENST00000508342 | 56126235 | 56126343 | In-frame |
| ENST00000508342 | 56126424 | 56126484 | In-frame |
| ENST00000508342 | 56130706 | 56130802 | In-frame |
| ENST00000508342 | 56139166 | 56139232 | In-frame |
| ENST00000508342 | 56148328 | 56148394 | In-frame |
| ENST00000508342 | 56166155 | 56166206 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for NEDD4 |
| 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 |
| ENST00000508342 | 7252 | 1319 | 56166155 | 56166206 | 1849 | 1899 | 516 | 533 |
| ENST00000508342 | 7252 | 1319 | 56148328 | 56148394 | 2518 | 2583 | 739 | 761 |
| ENST00000508342 | 7252 | 1319 | 56139166 | 56139232 | 3100 | 3165 | 933 | 955 |
| ENST00000508342 | 7252 | 1319 | 56130706 | 56130802 | 3589 | 3684 | 1096 | 1128 |
| ENST00000508342 | 7252 | 1319 | 56126424 | 56126484 | 3820 | 3879 | 1173 | 1193 |
| ENST00000508342 | 7252 | 1319 | 56126235 | 56126343 | 3880 | 3987 | 1193 | 1229 |
| 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 |
| ENST00000508342 | 7252 | 1319 | 56166155 | 56166206 | 1849 | 1899 | 516 | 533 |
| ENST00000508342 | 7252 | 1319 | 56148328 | 56148394 | 2518 | 2583 | 739 | 761 |
| ENST00000508342 | 7252 | 1319 | 56139166 | 56139232 | 3100 | 3165 | 933 | 955 |
| ENST00000508342 | 7252 | 1319 | 56130706 | 56130802 | 3589 | 3684 | 1096 | 1128 |
| ENST00000508342 | 7252 | 1319 | 56126424 | 56126484 | 3820 | 3879 | 1173 | 1193 |
| ENST00000508342 | 7252 | 1319 | 56126235 | 56126343 | 3880 | 3987 | 1193 | 1229 |
| 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 |
Top |
SNVs in the skipped exons for NEDD4 |
| - 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-A39Y-01 | exon_skip_127421 | 56148329 | 56148394 | 56148353 | 56148353 | Frame_Shift_Del | A | - | p.F753fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_127427 | 56164613 | 56164674 | 56164667 | 56164667 | Frame_Shift_Del | T | - | p.N536fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_127439 | 56243709 | 56243787 | 56243720 | 56243720 | Frame_Shift_Del | T | - | p.T63fs |
| LUAD | TCGA-73-4677-01 | exon_skip_127439 | 56243709 | 56243787 | 56243739 | 56243739 | Frame_Shift_Del | A | - | p.L56fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_127439 | 56243709 | 56243787 | 56243742 | 56243742 | Frame_Shift_Del | A | - | p.V55fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_127439 | 56243709 | 56243787 | 56243745 | 56243745 | Frame_Shift_Del | T | - | p.G54fs |
| UCEC | TCGA-AX-A0J0-01 | exon_skip_127419 | 56130707 | 56130802 | 56130751 | 56130751 | Nonsense_Mutation | C | A | p.E1042* |
| - 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 |
| SNU175_LARGE_INTESTINE | 56126236 | 56126343 | 56126257 | 56126257 | Missense_Mutation | C | A | p.Q1222H |
| MCC26_SKIN | 56126236 | 56126343 | 56126316 | 56126316 | Missense_Mutation | C | T | p.D1203N |
| SNU175_LARGE_INTESTINE | 56126425 | 56126484 | 56126429 | 56126429 | Missense_Mutation | A | G | p.L1192P |
| HEC251_ENDOMETRIUM | 56126425 | 56126484 | 56126445 | 56126445 | Missense_Mutation | A | C | p.F1187V |
| HEC251_ENDOMETRIUM | 56126425 | 56126484 | 56126479 | 56126479 | Missense_Mutation | G | T | p.F1175L |
| JHUEM7_ENDOMETRIUM | 56126425 | 56126484 | 56126479 | 56126479 | Missense_Mutation | G | T | p.F1175L |
| CL14_LARGE_INTESTINE | 56130707 | 56130802 | 56130730 | 56130730 | Missense_Mutation | T | C | p.I1121V |
| 59M_OVARY | 56130707 | 56130802 | 56130758 | 56130758 | Missense_Mutation | G | T | p.D1111E |
| MFE319_ENDOMETRIUM | 56139167 | 56139232 | 56139199 | 56139199 | Missense_Mutation | A | G | p.Y945H |
| HT115_LARGE_INTESTINE | 56139167 | 56139232 | 56139204 | 56139204 | Missense_Mutation | C | A | p.R943I |
| NCIH2227_LUNG | 56161777 | 56161879 | 56161850 | 56161850 | Missense_Mutation | C | T | p.R564K |
| HS343T_FIBROBLAST | 56164613 | 56164674 | 56164646 | 56164646 | Missense_Mutation | T | C | p.Y543C |
| LC1F_LUNG | 56164613 | 56164674 | 56164652 | 56164652 | Missense_Mutation | C | T | p.R541K |
| LC1SQSF_LUNG | 56164613 | 56164674 | 56164652 | 56164652 | Missense_Mutation | C | T | p.R541K |
| LC1SQ_LUNG | 56164613 | 56164674 | 56164652 | 56164652 | Missense_Mutation | C | T | p.R541K |
| SNU520_STOMACH | 56164613 | 56164674 | 56164652 | 56164652 | Missense_Mutation | C | T | p.R541K |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 56164613 | 56164674 | 56164659 | 56164659 | Missense_Mutation | A | T | p.L539M |
| S117_SOFT_TISSUE | 56164613 | 56164674 | 56164659 | 56164659 | Missense_Mutation | A | T | p.L539M |
| NB1_AUTONOMIC_GANGLIA | 56243709 | 56243787 | 56243725 | 56243725 | Missense_Mutation | G | A | p.T61I |
| RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 56139167 | 56139232 | 56139168 | 56139168 | Splice_Site | T | C | p.Q955R |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NEDD4 |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NEDD4 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NEDD4 |
Top |
RelatedDrugs for NEDD4 |
| 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 |
Top |
RelatedDiseases for NEDD4 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| NEDD4 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| NEDD4 | C0022548 | Keloid | 1 | CTD_human |
| NEDD4 | C0038325 | Stevens-Johnson Syndrome | 1 | CTD_human |
| NEDD4 | C0151744 | Myocardial Ischemia | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|