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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 RNF40 |
 Gene summary |
| Gene information | Gene symbol | RNF40 | Gene ID | 9810 |
| Gene name | ring finger protein 40 | |
| Synonyms | BRE1B|RBP95|STARING | |
| Cytomap | 16p11.2 | |
| Type of gene | protein-coding | |
| Description | E3 ubiquitin-protein ligase BRE1B95 kDa retinoblastoma protein binding protein95 kDa retinoblastoma-associated proteinBRE1 E3 ubiquitin ligase homolog BBRE1-BRING-type E3 ubiquitin transferase BRE1BRb-associated proteinring finger protein 40, E3 ub | |
| Modification date | 20180522 | |
| UniProtAcc | O75150 | |
| Context | PubMed: RNF40 [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 |
| RNF40 | GO:0010390 | histone monoubiquitination | 16307923 |
| RNF40 | GO:0033523 | histone H2B ubiquitination | 16307923 |
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Exon skipping events across known transcript of Ensembl for RNF40 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 RNF40 |
| 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 RNF40 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_135897 | 16 | 30776745:30776820:30777483:30777603:30777699:30777879 | 30777483:30777603 | ENSG00000103549.17 | ENST00000566703.1,ENST00000324685.6,ENST00000493683.1 |
| exon_skip_135898 | 16 | 30776745:30776820:30777699:30777879:30778061:30778193 | 30777699:30777879 | ENSG00000103549.17 | ENST00000563683.1 |
| exon_skip_135902 | 16 | 30780158:30780308:30780506:30780719:30780795:30780921 | 30780506:30780719 | ENSG00000103549.17 | ENST00000357890.5,ENST00000324685.6,ENST00000563683.1,ENST00000402121.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RNF40 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_135897 | 16 | 30776745:30776820:30777483:30777603:30777699:30777879 | 30777483:30777603 | ENSG00000103549.17 | ENST00000324685.6,ENST00000493683.1,ENST00000566703.1 |
| exon_skip_135898 | 16 | 30776745:30776820:30777699:30777879:30778061:30778193 | 30777699:30777879 | ENSG00000103549.17 | ENST00000563683.1 |
| exon_skip_135902 | 16 | 30780158:30780308:30780506:30780719:30780795:30780921 | 30780506:30780719 | ENSG00000103549.17 | ENST00000324685.6,ENST00000402121.3,ENST00000563683.1,ENST00000357890.5 |
| 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 RNF40 |
| 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 |
| ENST00000324685 | 30777483 | 30777603 | In-frame |
| ENST00000324685 | 30780506 | 30780719 | 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 |
| ENST00000324685 | 30777483 | 30777603 | In-frame |
| ENST00000324685 | 30780506 | 30780719 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RNF40 |
| 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 |
| ENST00000324685 | 5651 | 1001 | 30777483 | 30777603 | 1429 | 1548 | 331 | 371 |
| ENST00000324685 | 5651 | 1001 | 30780506 | 30780719 | 2683 | 2895 | 749 | 820 |
| 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 |
| ENST00000324685 | 5651 | 1001 | 30777483 | 30777603 | 1429 | 1548 | 331 | 371 |
| ENST00000324685 | 5651 | 1001 | 30780506 | 30780719 | 2683 | 2895 | 749 | 820 |
| 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 |
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SNVs in the skipped exons for RNF40 |
| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_135897 | 30777484 | 30777603 | 30777512 | 30777512 | Frame_Shift_Del | A | - | p.E341fs |
| LIHC | TCGA-DD-A3A0-01 | 30777700 | 30777879 | 30777764 | 30777764 | Frame_Shift_Del | C | - | p.A393fs | |
| SKCM | TCGA-D3-A8GM-06 | 30777700 | 30777879 | 30777817 | 30777817 | Frame_Shift_Del | G | - | p.E411fs | |
| CESC | TCGA-Q1-A73O-01 | exon_skip_135902 | 30780507 | 30780719 | 30780684 | 30780684 | Nonsense_Mutation | G | T | p.E809* |
| ESCA | TCGA-L5-A8NS-01 | exon_skip_135897 | 30777484 | 30777603 | 30777483 | 30777483 | Splice_Site | G | C | e8-1 |
| - 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 |
| CAL12T_LUNG | 30777700 | 30777879 | 30777762 | 30777762 | Frame_Shift_Del | G | - | p.Q392fs |
| SNU175_LARGE_INTESTINE | 30777484 | 30777603 | 30777562 | 30777562 | Missense_Mutation | G | A | p.A358T |
| 639V_URINARY_TRACT | 30777700 | 30777879 | 30777709 | 30777709 | Missense_Mutation | C | T | p.R375W |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30777700 | 30777879 | 30777715 | 30777715 | Missense_Mutation | C | A | p.L377I |
| NCIH2009_LUNG | 30777700 | 30777879 | 30777817 | 30777817 | Missense_Mutation | G | A | p.E411K |
| 639V_URINARY_TRACT | 30777700 | 30777879 | 30777824 | 30777824 | Missense_Mutation | G | A | p.R413Q |
| NCIH630_LARGE_INTESTINE | 30777700 | 30777879 | 30777827 | 30777827 | Missense_Mutation | G | A | p.G414D |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RNF40 |
| 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 RNF40 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RNF40 |
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RelatedDrugs for RNF40 |
| 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 RNF40 |
| 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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