|
||||||
|
 | |
| |
| |
| |
| 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 UBE4A |
 Gene summary |
| Gene information | Gene symbol | UBE4A | Gene ID | 9354 |
| Gene name | ubiquitination factor E4A | |
| Synonyms | E4|UBOX2|UFD2 | |
| Cytomap | 11q23.3 | |
| Type of gene | protein-coding | |
| Description | ubiquitin conjugation factor E4 ARING-type E3 ubiquitin transferase E4 Aubiquitination factor E4A (UFD2 homolog, yeast) | |
| Modification date | 20180523 | |
| UniProtAcc | Q14139 | |
| Context | PubMed: UBE4A [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 |
Top |
Exon skipping events across known transcript of Ensembl for UBE4A 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 UBE4A |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for UBE4A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_65517 | 11 | 118243221:118243381:118243800:118244003:118244208:118244400 | 118243800:118244003 | ENSG00000110344.5 | ENST00000252108.3 |
| exon_skip_65520 | 11 | 118244208:118244400:118245610:118245944:118247288:118247409 | 118245610:118245944 | ENSG00000110344.5 | ENST00000252108.3,ENST00000431736.2 |
| exon_skip_65527 | 11 | 118255349:118255450:118255546:118255660:118257152:118257327 | 118255546:118255660 | ENSG00000110344.5 | ENST00000545354.1,ENST00000252108.3,ENST00000431736.2 |
| exon_skip_65528 | 11 | 118257152:118257327:118260439:118260620:118261371:118261519 | 118260439:118260620 | ENSG00000110344.5 | ENST00000545354.1,ENST00000252108.3,ENST00000431736.2 |
| exon_skip_65531 | 11 | 118261371:118261519:118263452:118263610:118267028:118267222 | 118263452:118263610 | ENSG00000110344.5 | ENST00000545354.1,ENST00000252108.3,ENST00000431736.2 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for UBE4A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_65517 | 11 | 118243221:118243381:118243800:118244003:118244208:118244400 | 118243800:118244003 | ENSG00000110344.5 | ENST00000252108.3 |
| exon_skip_65520 | 11 | 118244208:118244400:118245610:118245944:118247288:118247409 | 118245610:118245944 | ENSG00000110344.5 | ENST00000252108.3,ENST00000431736.2 |
| exon_skip_65527 | 11 | 118255349:118255450:118255546:118255660:118257152:118257327 | 118255546:118255660 | ENSG00000110344.5 | ENST00000252108.3,ENST00000431736.2,ENST00000545354.1 |
| exon_skip_65528 | 11 | 118257152:118257327:118260439:118260620:118261371:118261519 | 118260439:118260620 | ENSG00000110344.5 | ENST00000252108.3,ENST00000431736.2,ENST00000545354.1 |
| exon_skip_65531 | 11 | 118261371:118261519:118263452:118263610:118267028:118267222 | 118263452:118263610 | ENSG00000110344.5 | ENST00000252108.3,ENST00000431736.2,ENST00000545354.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for UBE4A |
| 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 |
| ENST00000252108 | 118243800 | 118244003 | Frame-shift |
| ENST00000252108 | 118245610 | 118245944 | Frame-shift |
| ENST00000252108 | 118260439 | 118260620 | Frame-shift |
| ENST00000252108 | 118263452 | 118263610 | Frame-shift |
| ENST00000252108 | 118255546 | 118255660 | 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 |
| ENST00000252108 | 118243800 | 118244003 | Frame-shift |
| ENST00000252108 | 118245610 | 118245944 | Frame-shift |
| ENST00000252108 | 118260439 | 118260620 | Frame-shift |
| ENST00000252108 | 118263452 | 118263610 | Frame-shift |
| ENST00000252108 | 118255546 | 118255660 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for UBE4A |
| 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 |
| ENST00000252108 | 6120 | 1066 | 118255546 | 118255660 | 2430 | 2543 | 766 | 804 |
| 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 |
| ENST00000252108 | 6120 | 1066 | 118255546 | 118255660 | 2430 | 2543 | 766 | 804 |
| 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 |
| Q14139 | 766 | 804 | 1 | 1066 | Chain | ID=PRO_0000194990;Note=Ubiquitin conjugation factor E4 A |
| 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 |
| Q14139 | 766 | 804 | 1 | 1066 | Chain | ID=PRO_0000194990;Note=Ubiquitin conjugation factor E4 A |
Top |
SNVs in the skipped exons for UBE4A |
| - 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-G3-A3CJ-01 | exon_skip_65520 | 118245611 | 118245944 | 118245630 | 118245630 | Frame_Shift_Del | A | - | p.E379fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_65520 | 118245611 | 118245944 | 118245702 | 118245702 | Frame_Shift_Del | T | - | p.L403fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_65528 | 118260440 | 118260620 | 118260540 | 118260540 | Frame_Shift_Del | A | - | p.L896fs |
| UCEC | TCGA-AX-A05Z-01 | exon_skip_65517 | 118243801 | 118244003 | 118243914 | 118243914 | Nonsense_Mutation | C | T | p.R286* |
| READ | TCGA-F5-6814-01 | exon_skip_65520 | 118245611 | 118245944 | 118245674 | 118245674 | Nonsense_Mutation | G | T | p.E401X |
| BLCA | TCGA-DK-AA6S-01 | exon_skip_65520 | 118245611 | 118245944 | 118245786 | 118245786 | Nonsense_Mutation | C | G | p.S431* |
| KIRC | TCGA-A3-3380-01 | exon_skip_65520 | 118245611 | 118245944 | 118245844 | 118245844 | Nonsense_Mutation | C | A | p.C450* |
| LUAD | TCGA-73-4658-01 | exon_skip_65531 | 118263453 | 118263610 | 118263480 | 118263480 | Nonsense_Mutation | G | T | p.E982* |
| HNSC | TCGA-BA-6871-01 | exon_skip_65528 | 118260440 | 118260620 | 118260439 | 118260439 | Splice_Site | G | A | p.E863_splice |
| - 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 |
| AN3CA_ENDOMETRIUM | 118245611 | 118245944 | 118245926 | 118245926 | Frame_Shift_Del | A | - | p.K485fs |
| HEC108_ENDOMETRIUM | 118243801 | 118244003 | 118243849 | 118243849 | Missense_Mutation | T | C | p.I264T |
| MCC13_SKIN | 118243801 | 118244003 | 118243890 | 118243890 | Missense_Mutation | C | T | p.P278S |
| SW13_ADRENAL_CORTEX | 118243801 | 118244003 | 118243957 | 118243957 | Missense_Mutation | A | C | p.Y300S |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118245611 | 118245944 | 118245672 | 118245672 | Missense_Mutation | C | T | p.P400L |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118245611 | 118245944 | 118245686 | 118245686 | Missense_Mutation | T | A | p.C405S |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 118245611 | 118245944 | 118245696 | 118245696 | Missense_Mutation | C | T | p.S408F |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118245611 | 118245944 | 118245696 | 118245696 | Missense_Mutation | C | T | p.S408F |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118245611 | 118245944 | 118245701 | 118245701 | Missense_Mutation | C | T | p.L410F |
| MORCPR_LUNG | 118245611 | 118245944 | 118245729 | 118245729 | Missense_Mutation | G | A | p.G419D |
| HEC59_ENDOMETRIUM | 118245611 | 118245944 | 118245778 | 118245778 | Missense_Mutation | G | A | p.M435I |
| OAW28_OVARY | 118245611 | 118245944 | 118245860 | 118245860 | Missense_Mutation | C | T | p.R463W |
| SW684_SOFT_TISSUE | 118245611 | 118245944 | 118245878 | 118245878 | Missense_Mutation | C | T | p.P469S |
| SNGM_ENDOMETRIUM | 118245611 | 118245944 | 118245939 | 118245939 | Missense_Mutation | T | C | p.M489T |
| JHUEM7_ENDOMETRIUM | 118255547 | 118255660 | 118255570 | 118255570 | Missense_Mutation | G | T | p.K781N |
| MFE319_ENDOMETRIUM | 118255547 | 118255660 | 118255617 | 118255617 | Missense_Mutation | T | C | p.L797P |
| SUPT11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118255547 | 118255660 | 118255652 | 118255652 | Missense_Mutation | G | A | p.A809T |
| JHUEM7_ENDOMETRIUM | 118260440 | 118260620 | 118260482 | 118260482 | Missense_Mutation | T | C | p.I884T |
| OE21_OESOPHAGUS | 118260440 | 118260620 | 118260595 | 118260595 | Missense_Mutation | A | T | p.I922F |
| PK1_PANCREAS | 118263453 | 118263610 | 118263525 | 118263525 | Missense_Mutation | A | G | p.M1004V |
| MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118260440 | 118260620 | 118260508 | 118260508 | Nonsense_Mutation | C | T | p.Q893* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for UBE4A |
| 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 UBE4A |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for UBE4A |
Top |
RelatedDrugs for UBE4A |
| 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 UBE4A |
| 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)
|