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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for UBR4 |
 Gene summary |
| Gene information | Gene symbol | UBR4 | Gene ID | 23352 |
| Gene name | ubiquitin protein ligase E3 component n-recognin 4 | |
| Synonyms | RBAF600|ZUBR1|p600 | |
| Cytomap | 1p36.13 | |
| Type of gene | protein-coding | |
| Description | E3 ubiquitin-protein ligase UBR4N-recognin-4RING-type E3 ubiquitin transferase UBR4retinoblastoma-associated factor 600-like proteinretinoblastoma-associated factor of 600 kDazinc finger UBR1-type protein 1 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| UBR4 | GO:0006511 | ubiquitin-dependent protein catabolic process | 23932781 |
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Gene structures and expression levels for UBR4 |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000127481
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | DOWN | ENST00000486515.1 | UBR4-214:lncRNA:UBR4 | 2.272542e+02 | -1.257059e+00 | 2.530318e-07 | 4.652719e-06 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for UBR4 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_121246 | chr1 | 19148563:19148626:19149763:19149795:19150577:19150704 | 19149763:19149795 |
| exon_skip_128198 | chr1 | 19148563:19148626:19149763:19149795:19150577:19150793 | 19149763:19149795 |
| exon_skip_143896 | chr1 | 19110380:19110464:19110742:19110832:19112524:19112687 | 19110742:19110832 |
| exon_skip_153042 | chr1 | 19086679:19086821:19087816:19087929:19088759:19088977 | 19087816:19087929 |
| exon_skip_168862 | chr1 | 19161589:19161736:19161827:19161897:19162420:19162611 | 19161827:19161897 |
| exon_skip_169193 | chr1 | 19139083:19139220:19141347:19141524:19141647:19141777 | 19141347:19141524 |
| exon_skip_176982 | chr1 | 19124541:19124690:19125603:19125699:19126446:19126635 | 19125603:19125699 |
| exon_skip_204481 | chr1 | 19077976:19078066:19081349:19081573:19084504:19084698 | 19081349:19081573 |
| exon_skip_204564 | chr1 | 19174319:19174447:19174954:19175033:19176592:19176727 | 19174954:19175033 |
| exon_skip_205045 | chr1 | 19145793:19145933:19146023:19146106:19146826:19147000 | 19146023:19146106 |
| exon_skip_21860 | chr1 | 19117823:19117910:19118872:19118957:19119557:19119701 | 19118872:19118957 |
| exon_skip_220510 | chr1 | 19139083:19139220:19141347:19141524:19141647:19141774 | 19141347:19141524 |
| exon_skip_221188 | chr1 | 19124477:19124690:19125603:19125699:19126446:19126655 | 19125603:19125699 |
| exon_skip_226092 | chr1 | 19110380:19110464:19110742:19110832:19112524:19112547 | 19110742:19110832 |
| exon_skip_263901 | chr1 | 19139083:19139220:19140788:19140892:19141347:19141524 | 19140788:19140892 |
| exon_skip_265002 | chr1 | 19076740:19076902:19077976:19078066:19081349:19081573 | 19077976:19078066 |
| exon_skip_285123 | chr1 | 19096523:19096650:19097193:19097280:19099597:19099677 | 19097193:19097280 |
| exon_skip_31127 | chr1 | 19164799:19164997:19165249:19165349:19165656:19165757 | 19165249:19165349 |
| exon_skip_51135 | chr1 | 19124541:19124690:19125603:19125699:19126446:19126655 | 19125603:19125699 |
| exon_skip_58482 | chr1 | 19141647:19141777:19143980:19144091:19144786:19144907 | 19143980:19144091 |
| exon_skip_60713 | chr1 | 19140788:19140892:19141347:19141524:19141647:19141774 | 19141347:19141524 |
| exon_skip_6124 | chr1 | 19094095:19094139:19094906:19095025:19095545:19095652 | 19094906:19095025 |
| exon_skip_83415 | chr1 | 19199651:19199754:19201718:19201815:19210073:19210266 | 19201718:19201815 |
| exon_skip_85568 | chr1 | 19106837:19106966:19110096:19110223:19110380:19110464 | 19110096:19110223 |
| exon_skip_99673 | chr1 | 19139083:19139220:19141347:19141524:19141647:19141769 | 19141347:19141524 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_128198 | MSBB_PG | 4.631818e-01 | 5.655556e-01 | -1.023737e-01 | 4.068087e-02 |
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Open reading frame (ORF) annotation in the exon skipping event for UBR4 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000375254 | 19077976 | 19078066 | Frame-shift |
| ENST00000375254 | 19097193 | 19097280 | Frame-shift |
| ENST00000375254 | 19118872 | 19118957 | Frame-shift |
| ENST00000375254 | 19161827 | 19161897 | Frame-shift |
| ENST00000375254 | 19201718 | 19201815 | Frame-shift |
| ENST00000375254 | 19081349 | 19081573 | In-frame |
| ENST00000375254 | 19087816 | 19087929 | In-frame |
| ENST00000375254 | 19094906 | 19095025 | In-frame |
| ENST00000375254 | 19140788 | 19140892 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000375254 | 19097193 | 19097280 | Frame-shift |
| ENST00000375254 | 19161827 | 19161897 | Frame-shift |
| ENST00000375254 | 19201718 | 19201815 | Frame-shift |
| ENST00000375254 | 19087816 | 19087929 | In-frame |
| ENST00000375254 | 19140788 | 19140892 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000375254 | 19077976 | 19078066 | Frame-shift |
| ENST00000375254 | 19097193 | 19097280 | Frame-shift |
| ENST00000375254 | 19110096 | 19110223 | Frame-shift |
| ENST00000375254 | 19110742 | 19110832 | Frame-shift |
| ENST00000375254 | 19118872 | 19118957 | Frame-shift |
| ENST00000375254 | 19141347 | 19141524 | Frame-shift |
| ENST00000375254 | 19143980 | 19144091 | Frame-shift |
| ENST00000375254 | 19161827 | 19161897 | Frame-shift |
| ENST00000375254 | 19165249 | 19165349 | Frame-shift |
| ENST00000375254 | 19174954 | 19175033 | Frame-shift |
| ENST00000375254 | 19201718 | 19201815 | Frame-shift |
| ENST00000375254 | 19087816 | 19087929 | In-frame |
| ENST00000375254 | 19094906 | 19095025 | In-frame |
| ENST00000375254 | 19140788 | 19140892 | In-frame |
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Infer the effects of exon skipping event on protein functional features for UBR4 |
p-ENSG00000127481_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| ENST00000375254 | 15923 | 5183 | 19140788 | 19140892 | 8517 | 8620 | 2829 | 2864 |
| ENST00000375254 | 15923 | 5183 | 19094906 | 19095025 | 13655 | 13773 | 4542 | 4581 |
| ENST00000375254 | 15923 | 5183 | 19087816 | 19087929 | 14459 | 14571 | 4810 | 4847 |
| ENST00000375254 | 15923 | 5183 | 19081349 | 19081573 | 15037 | 15260 | 5003 | 5077 |
| Loci of skipped exons in MSBB 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 |
| ENST00000375254 | 15923 | 5183 | 19140788 | 19140892 | 8517 | 8620 | 2829 | 2864 |
| ENST00000375254 | 15923 | 5183 | 19087816 | 19087929 | 14459 | 14571 | 4810 | 4847 |
| Loci of skipped exons in Mayo 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 |
| ENST00000375254 | 15923 | 5183 | 19140788 | 19140892 | 8517 | 8620 | 2829 | 2864 |
| ENST00000375254 | 15923 | 5183 | 19094906 | 19095025 | 13655 | 13773 | 4542 | 4581 |
| ENST00000375254 | 15923 | 5183 | 19087816 | 19087929 | 14459 | 14571 | 4810 | 4847 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 |
| Q5T4S7 | 2829 | 2864 | 1 | 3585 | Alternative sequence | ID=VSP_025200;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 2829 | 2864 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 2829 | 2864 | 2830 | 2864 | Alternative sequence | ID=VSP_025206;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5T4S7 | 2829 | 2864 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Q5T4S7 | 4542 | 4581 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 4542 | 4581 | 3798 | 5183 | Alternative sequence | ID=VSP_025208;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 4542 | 4581 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Q5T4S7 | 4810 | 4847 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 4810 | 4847 | 3798 | 5183 | Alternative sequence | ID=VSP_025208;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 4810 | 4847 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Q5T4S7 | 5003 | 5077 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 5003 | 5077 | 3798 | 5183 | Alternative sequence | ID=VSP_025208;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 5003 | 5077 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 |
| Q5T4S7 | 2829 | 2864 | 1 | 3585 | Alternative sequence | ID=VSP_025200;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 2829 | 2864 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 2829 | 2864 | 2830 | 2864 | Alternative sequence | ID=VSP_025206;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5T4S7 | 2829 | 2864 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Q5T4S7 | 4810 | 4847 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 4810 | 4847 | 3798 | 5183 | Alternative sequence | ID=VSP_025208;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 4810 | 4847 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 |
| Q5T4S7 | 2829 | 2864 | 1 | 3585 | Alternative sequence | ID=VSP_025200;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 2829 | 2864 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 2829 | 2864 | 2830 | 2864 | Alternative sequence | ID=VSP_025206;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q5T4S7 | 2829 | 2864 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Q5T4S7 | 4542 | 4581 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 4542 | 4581 | 3798 | 5183 | Alternative sequence | ID=VSP_025208;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 4542 | 4581 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
| Q5T4S7 | 4810 | 4847 | 2487 | 5183 | Alternative sequence | ID=VSP_025204;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10718198;Dbxref=PMID:10718198 |
| Q5T4S7 | 4810 | 4847 | 3798 | 5183 | Alternative sequence | ID=VSP_025208;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q5T4S7 | 4810 | 4847 | 1 | 5183 | Chain | ID=PRO_0000286861;Note=E3 ubiquitin-protein ligase UBR4 |
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3'-UTR located exon skipping events that lost miRNA binding sites in UBR4 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for UBR4 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for UBR4 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for UBR4 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for UBR4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| HCC | MSI1 | exon_skip_205045 | -4.217042e-01 | 5.577902e-13 |
| HCC | RBM5 | exon_skip_205045 | -4.330115e-01 | 1.128271e-13 |
| HCC | PTBP1 | exon_skip_205045 | -4.262919e-01 | 2.937585e-13 |
| HCC | RBM6 | exon_skip_128198 | -7.392596e-01 | 6.282018e-48 |
| HCC | SAMD4A | exon_skip_128198 | -7.115319e-01 | 5.759895e-43 |
| HCC | PCBP1 | exon_skip_128198 | -4.628484e-01 | 9.682940e-16 |
| HCC | TRA2A | exon_skip_128198 | -4.451760e-01 | 1.509509e-14 |
| HCC | SF1 | exon_skip_128198 | -5.557978e-01 | 2.732499e-23 |
| IFG | HNRNPC | exon_skip_205045 | 5.373361e-01 | 3.191845e-03 |
| IFG | SAMD4A | exon_skip_128198 | -4.406366e-01 | 1.893292e-02 |
| PCC | PTBP1 | exon_skip_205045 | -4.101537e-01 | 3.147166e-09 |
| PCC | RBM6 | exon_skip_128198 | -4.698247e-01 | 2.545666e-12 |
| PCC | SAMD4A | exon_skip_128198 | -4.633893e-01 | 5.494823e-12 |
| PG | PCBP1 | exon_skip_128198 | 4.424816e-01 | 2.558140e-10 |
| PG | HNRNPK | exon_skip_128198 | 4.549637e-01 | 6.854421e-11 |
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RelatedDrugs for UBR4 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for UBR4 |
| 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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