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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 HERC4 |
 Gene summary |
| Gene information | Gene symbol | HERC4 | Gene ID | 26091 |
| Gene name | HECT and RLD domain containing E3 ubiquitin protein ligase 4 | |
| Synonyms | - | |
| Cytomap | 10q21.3 | |
| Type of gene | protein-coding | |
| Description | probable E3 ubiquitin-protein ligase HERC4HECT domain and RCC1-like domain-containing protein 4HECT-type E3 ubiquitin transferase HERC4hect domain and RLD 4 | |
| Modification date | 20200327 | |
| 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 |
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Gene structures and expression levels for HERC4 |
| 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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ENSG00000148634
| 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 | ENST00000277817.10 | HERC4-201:protein_coding:HERC4 | 2.203045e+02 | -1.052253e+00 | 2.024701e-09 | 7.827209e-08 |
| CB | UP | ENST00000505760.5 | HERC4-212:lncRNA:HERC4 | 4.532422e+00 | 8.573187e-01 | 3.588704e-06 | 4.432729e-05 |
| CB | UP | ENST00000513996.5 | HERC4-214:protein_coding:HERC4 | 7.450600e-01 | 1.447821e+00 | 1.152738e-02 | 3.906134e-02 |
| 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 HERC4 |
| 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_10373 | chr10 | 68025546:68025676:68032778:68032869:68033965:68034186 | 68032778:68032869 |
| exon_skip_103785 | chr10 | 68044404:68044563:68072883:68073186:68073657:68073686 | 68072883:68073186 |
| exon_skip_105328 | chr10 | 67936153:67936235:67939588:67939654:67940939:67941105 | 67939588:67939654 |
| exon_skip_119666 | chr10 | 67932597:67932780:67936153:67936235:67939588:67939651 | 67936153:67936235 |
| exon_skip_14426 | chr10 | 67966683:67966802:67988043:67988144:67988663:67988835 | 67988043:67988144 |
| exon_skip_144312 | chr10 | 67966683:67966802:67988663:67988835:67990211:67990241 | 67988663:67988835 |
| exon_skip_148436 | chr10 | 68014026:68014186:68025546:68025676:68032778:68032865 | 68025546:68025676 |
| exon_skip_155223 | chr10 | 67939588:67939654:67940939:67941105:67954595:67954738 | 67940939:67941105 |
| exon_skip_161835 | chr10 | 68038093:68038169:68044404:68044563:68072883:68073186 | 68044404:68044563 |
| exon_skip_176159 | chr10 | 67988663:67988835:67990211:67990400:67990904:67991015 | 67990211:67990400 |
| exon_skip_193537 | chr10 | 68038093:68038169:68044404:68044563:68072883:68073097 | 68044404:68044563 |
| exon_skip_214919 | chr10 | 68038093:68038169:68044404:68044563:68072883:68073180 | 68044404:68044563 |
| exon_skip_2280 | chr10 | 68038093:68038169:68039417:68039488:68044404:68044563 | 68039417:68039488 |
| exon_skip_231954 | chr10 | 67988663:67988835:67990211:67990400:67990904:67990915 | 67990211:67990400 |
| exon_skip_244349 | chr10 | 67932597:67932780:67936153:67936235:67939588:67939654 | 67936153:67936235 |
| exon_skip_267418 | chr10 | 68038093:68038169:68039417:68039488:68044404:68044558 | 68039417:68039488 |
| exon_skip_269445 | chr10 | 67954963:67955130:67956878:67956976:67959113:67959136 | 67956878:67956976 |
| exon_skip_284161 | chr10 | 68014026:68014186:68025546:68025676:68032778:68032869 | 68025546:68025676 |
| exon_skip_28779 | chr10 | 67932597:67932780:67936153:67936235:67954595:67954738 | 67936153:67936235 |
| exon_skip_294228 | chr10 | 68025546:68025676:68033965:68034186:68038093:68038169 | 68033965:68034186 |
| exon_skip_42236 | chr10 | 67956878:67956976:67959113:67959136:67966683:67966802 | 67959113:67959136 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for HERC4 |
| 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 |
| ENST00000395198 | 68072883 | 68073186 | 3UTR-3CDS |
| ENST00000395198 | 67936153 | 67936235 | Frame-shift |
| ENST00000395198 | 67939588 | 67939654 | Frame-shift |
| ENST00000395198 | 67940939 | 67941105 | Frame-shift |
| ENST00000395198 | 67990211 | 67990400 | Frame-shift |
| ENST00000395198 | 68025546 | 68025676 | Frame-shift |
| ENST00000395198 | 68032778 | 68032869 | Frame-shift |
| ENST00000395198 | 68044404 | 68044563 | Frame-shift |
| ENST00000395198 | 67959113 | 67959136 | 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 |
| ENST00000395198 | 67936153 | 67936235 | Frame-shift |
| ENST00000395198 | 67939588 | 67939654 | Frame-shift |
| ENST00000395198 | 67990211 | 67990400 | Frame-shift |
| ENST00000395198 | 68025546 | 68025676 | Frame-shift |
| ENST00000395198 | 68032778 | 68032869 | Frame-shift |
| ENST00000395198 | 67959113 | 67959136 | 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 |
| ENST00000395198 | 67936153 | 67936235 | Frame-shift |
| ENST00000395198 | 67939588 | 67939654 | Frame-shift |
| ENST00000395198 | 67940939 | 67941105 | Frame-shift |
| ENST00000395198 | 67988663 | 67988835 | Frame-shift |
| ENST00000395198 | 67990211 | 67990400 | Frame-shift |
| ENST00000395198 | 68025546 | 68025676 | Frame-shift |
| ENST00000395198 | 68032778 | 68032869 | Frame-shift |
| ENST00000395198 | 68044404 | 68044563 | Frame-shift |
| ENST00000395198 | 67956878 | 67956976 | In-frame |
| ENST00000395198 | 67959113 | 67959136 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HERC4 |
p-ENSG00000148634_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 |
| 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 |
| 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 |
| ENST00000395198 | 4462 | 1057 | 67956878 | 67956976 | 2199 | 2296 | 650 | 682 |
| 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 |
| 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 |
| 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 |
| Q5GLZ8 | 650 | 682 | 111 | 1057 | Alternative sequence | ID=VSP_023175;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15676274;Dbxref=PMID:15676274 |
| Q5GLZ8 | 650 | 682 | 118 | 1057 | Alternative sequence | ID=VSP_023176;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:15676274;Dbxref=PMID:15489334,PMID:15676274 |
| Q5GLZ8 | 650 | 682 | 643 | 650 | Alternative sequence | ID=VSP_023178;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q5GLZ8 | 650 | 682 | 1 | 1057 | Chain | ID=PRO_0000278216;Note=Probable E3 ubiquitin-protein ligase HERC4 |
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3'-UTR located exon skipping events that lost miRNA binding sites in HERC4 |
| 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 HERC4 |
| - 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 HERC4 |
| 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 |
| CDR | MSBB | IFG | exon_skip_2280 | 4.298205e-01 | 2.244131e-02 | chr10 | - | 68038093 | 68038169 | 68039417 | 68039488 | 68044404 | 68044563 |
| CDR | MSBB | IFG | exon_skip_176159 | 3.887813e-01 | 4.088675e-02 | chr10 | - | 67988663 | 67988835 | 67990211 | 67990400 | 67990904 | 67991015 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HERC4 |
| 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 HERC4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_105328 | -5.187368e-01 | 2.481071e-12 |
| CB | TRA2A | exon_skip_105328 | -4.637687e-01 | 7.434799e-10 |
| CB | FUBP1 | exon_skip_279584 | -4.204405e-01 | 3.834963e-07 |
| HCC | ZNF326 | exon_skip_42236 | -4.543895e-01 | 3.677619e-15 |
| IFG | NOVA1 | exon_skip_42236 | 4.440945e-01 | 1.791150e-02 |
| IFG | MSI1 | exon_skip_176159 | 4.174599e-01 | 2.708352e-02 |
| IFG | FUBP3 | exon_skip_10373 | 4.549876e-01 | 1.498626e-02 |
| PCC | ZNF326 | exon_skip_42236 | -4.183188e-01 | 3.930600e-10 |
| PCC | ESRP2 | exon_skip_249399 | 4.588949e-01 | 1.051062e-11 |
| TC | NOVA1 | exon_skip_42236 | 6.056595e-01 | 1.381983e-16 |
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RelatedDrugs for HERC4 |
| 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 HERC4 |
| 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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