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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 UPF3B |
 Gene summary |
| Gene information | Gene symbol | UPF3B | Gene ID | 65109 |
| Gene name | UPF3B, regulator of nonsense mediated mRNA decay | |
| Synonyms | HUPF3B|MRX62|MRXS14|RENT3B|UPF3BP1|UPF3BP2|UPF3BP3|UPF3X|Upf3p-X | |
| Cytomap | Xq24 | |
| Type of gene | protein-coding | |
| Description | regulator of nonsense transcripts 3BUPF3 regulator of nonsense transcripts homolog BUPF3B pseudogene 1UPF3B pseudogene 2UPF3B pseudogene 3mental retardation, X-linked 62nonsense mRNA reducing factor 3Bup-frameshift suppressor 3 homolog Bup-framesh | |
| Modification date | 20180523 | |
| UniProtAcc | Q9BZI7 | |
| Context | PubMed: UPF3B [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 |
| UPF3B | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 16601204 |
| UPF3B | GO:0045727 | positive regulation of translation | 16601204 |
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Exon skipping events across known transcript of Ensembl for UPF3B 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 UPF3B |
| 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 UPF3B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_516529 | X | 118967988:118968990:118971719:118972014:118972329:118972490 | 118971719:118972014 | ENSG00000125351.6 | ENST00000345865.2,ENST00000276201.2 |
| exon_skip_516534 | X | 118972329:118972490:118974556:118974647:118975038:118975219 | 118974556:118974647 | ENSG00000125351.6 | ENST00000478840.1 |
| exon_skip_516535 | X | 118972329:118972490:118974608:118974647:118975038:118975219 | 118974608:118974647 | ENSG00000125351.6 | ENST00000276201.2 |
| exon_skip_516536 | X | 118975038:118975221:118975697:118975741:118977153:118977264 | 118975697:118975741 | ENSG00000125351.6 | ENST00000345865.2,ENST00000276201.2,ENST00000478840.1 |
| exon_skip_516537 | X | 118975697:118975741:118977153:118977264:118979160:118979217 | 118977153:118977264 | ENSG00000125351.6 | ENST00000345865.2,ENST00000276201.2,ENST00000478840.1 |
| exon_skip_516538 | X | 118977153:118977264:118979160:118979259:118985457:118985564 | 118979160:118979259 | ENSG00000125351.6 | ENST00000345865.2,ENST00000276201.2 |
| exon_skip_516539 | X | 118979160:118979259:118985457:118985564:118985729:118985836 | 118985457:118985564 | ENSG00000125351.6 | ENST00000345865.2,ENST00000276201.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for UPF3B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_516529 | X | 118967988:118968990:118971719:118972014:118972329:118972490 | 118971719:118972014 | ENSG00000125351.6 | ENST00000276201.2,ENST00000345865.2 |
| exon_skip_516534 | X | 118972329:118972490:118974556:118974647:118975038:118975219 | 118974556:118974647 | ENSG00000125351.6 | ENST00000478840.1 |
| exon_skip_516535 | X | 118972329:118972490:118974608:118974647:118975038:118975219 | 118974608:118974647 | ENSG00000125351.6 | ENST00000276201.2 |
| exon_skip_516536 | X | 118975038:118975221:118975697:118975741:118977153:118977264 | 118975697:118975741 | ENSG00000125351.6 | ENST00000276201.2,ENST00000345865.2,ENST00000478840.1 |
| exon_skip_516537 | X | 118975697:118975741:118977153:118977264:118979160:118979217 | 118977153:118977264 | ENSG00000125351.6 | ENST00000276201.2,ENST00000345865.2,ENST00000478840.1 |
| exon_skip_516538 | X | 118977153:118977264:118979160:118979259:118985457:118985564 | 118979160:118979259 | ENSG00000125351.6 | ENST00000276201.2,ENST00000345865.2 |
| 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 UPF3B |
| 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 |
| ENST00000276201 | 118971719 | 118972014 | Frame-shift |
| ENST00000276201 | 118975697 | 118975741 | Frame-shift |
| ENST00000276201 | 118985457 | 118985564 | Frame-shift |
| ENST00000276201 | 118974608 | 118974647 | In-frame |
| ENST00000276201 | 118977153 | 118977264 | In-frame |
| ENST00000276201 | 118979160 | 118979259 | 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 |
| ENST00000276201 | 118971719 | 118972014 | Frame-shift |
| ENST00000276201 | 118975697 | 118975741 | Frame-shift |
| ENST00000276201 | 118974608 | 118974647 | In-frame |
| ENST00000276201 | 118977153 | 118977264 | In-frame |
| ENST00000276201 | 118979160 | 118979259 | In-frame |
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Infer the effects of exon skipping event on protein functional features for UPF3B |
| 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 |
| ENST00000276201 | 2395 | 483 | 118979160 | 118979259 | 441 | 539 | 123 | 156 |
| ENST00000276201 | 2395 | 483 | 118977153 | 118977264 | 540 | 650 | 156 | 193 |
| ENST00000276201 | 2395 | 483 | 118974608 | 118974647 | 878 | 916 | 269 | 282 |
| 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 |
| ENST00000276201 | 2395 | 483 | 118979160 | 118979259 | 441 | 539 | 123 | 156 |
| ENST00000276201 | 2395 | 483 | 118977153 | 118977264 | 540 | 650 | 156 | 193 |
| ENST00000276201 | 2395 | 483 | 118974608 | 118974647 | 878 | 916 | 269 | 282 |
| 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 |
| Q9BZI7 | 123 | 156 | 126 | 128 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1UW4 |
| Q9BZI7 | 123 | 156 | 130 | 133 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1UW4 |
| Q9BZI7 | 123 | 156 | 1 | 483 | Chain | ID=PRO_0000215297;Note=Regulator of nonsense transcripts 3B |
| Q9BZI7 | 123 | 156 | 30 | 255 | Region | Note=Necessary for interaction with UPF2 |
| Q9BZI7 | 123 | 156 | 94 | 483 | Region | Note=Sufficient for association with EJC core |
| Q9BZI7 | 156 | 193 | 1 | 483 | Chain | ID=PRO_0000215297;Note=Regulator of nonsense transcripts 3B |
| Q9BZI7 | 156 | 193 | 169 | 169 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:19690332,PMID:21406692,P |
| Q9BZI7 | 156 | 193 | 160 | 160 | Natural variant | ID=VAR_037666;Note=In MRXS14. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17704778;Dbxref=dbSNP:rs122468182,PMID:17704778 |
| Q9BZI7 | 156 | 193 | 30 | 255 | Region | Note=Necessary for interaction with UPF2 |
| Q9BZI7 | 156 | 193 | 94 | 483 | Region | Note=Sufficient for association with EJC core |
| Q9BZI7 | 269 | 282 | 270 | 282 | Alternative sequence | ID=VSP_012963;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11163187,ECO:0000303|PubMed:15489334;Dbxref=PMID:11163187,PMID:15489334 |
| Q9BZI7 | 269 | 282 | 1 | 483 | Chain | ID=PRO_0000215297;Note=Regulator of nonsense transcripts 3B |
| Q9BZI7 | 269 | 282 | 94 | 483 | Region | Note=Sufficient for association with EJC core |
| 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 |
| Q9BZI7 | 123 | 156 | 126 | 128 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1UW4 |
| Q9BZI7 | 123 | 156 | 130 | 133 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1UW4 |
| Q9BZI7 | 123 | 156 | 1 | 483 | Chain | ID=PRO_0000215297;Note=Regulator of nonsense transcripts 3B |
| Q9BZI7 | 123 | 156 | 30 | 255 | Region | Note=Necessary for interaction with UPF2 |
| Q9BZI7 | 123 | 156 | 94 | 483 | Region | Note=Sufficient for association with EJC core |
| Q9BZI7 | 156 | 193 | 1 | 483 | Chain | ID=PRO_0000215297;Note=Regulator of nonsense transcripts 3B |
| Q9BZI7 | 156 | 193 | 169 | 169 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:19690332,PMID:21406692,P |
| Q9BZI7 | 156 | 193 | 160 | 160 | Natural variant | ID=VAR_037666;Note=In MRXS14. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17704778;Dbxref=dbSNP:rs122468182,PMID:17704778 |
| Q9BZI7 | 156 | 193 | 30 | 255 | Region | Note=Necessary for interaction with UPF2 |
| Q9BZI7 | 156 | 193 | 94 | 483 | Region | Note=Sufficient for association with EJC core |
| Q9BZI7 | 269 | 282 | 270 | 282 | Alternative sequence | ID=VSP_012963;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11163187,ECO:0000303|PubMed:15489334;Dbxref=PMID:11163187,PMID:15489334 |
| Q9BZI7 | 269 | 282 | 1 | 483 | Chain | ID=PRO_0000215297;Note=Regulator of nonsense transcripts 3B |
| Q9BZI7 | 269 | 282 | 94 | 483 | Region | Note=Sufficient for association with EJC core |
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SNVs in the skipped exons for UPF3B |
| - 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. |
UPF3B_SKCM_exon_skip_516534_psi_boxplot.png |
UPF3B_SKCM_exon_skip_516535_psi_boxplot.png |
| - 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_516529 | 118971720 | 118972014 | 118971767 | 118971767 | Frame_Shift_Del | T | - | p.T419fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_516536 | 118975698 | 118975741 | 118975705 | 118975705 | Frame_Shift_Del | T | - | p.N206fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_516536 | 118975698 | 118975741 | 118975735 | 118975735 | Frame_Shift_Del | T | - | p.K196fs |
| STAD | TCGA-HU-A4G9-01 | exon_skip_516537 | 118977154 | 118977264 | 118977168 | 118977168 | Frame_Shift_Del | T | - | p.N189fs |
| HNSC | TCGA-CN-4727-01 | exon_skip_516538 | 118979161 | 118979259 | 118979179 | 118979180 | Frame_Shift_Ins | - | T | p.K150fs |
| HNSC | TCGA-CN-4727-01 | exon_skip_516538 | 118979161 | 118979259 | 118979179 | 118979180 | Frame_Shift_Ins | - | T | p.NR150fs |
| SKCM | TCGA-BF-A5EQ-01 | exon_skip_516529 | 118971720 | 118972014 | 118971734 | 118971734 | Nonsense_Mutation | G | A | p.R430* |
| SKCM | TCGA-BF-A5EQ-01 | exon_skip_516529 | 118971720 | 118972014 | 118971734 | 118971734 | Nonsense_Mutation | G | A | p.R430X |
| SKCM | TCGA-D3-A3MV-06 | exon_skip_516529 | 118971720 | 118972014 | 118971941 | 118971941 | Nonsense_Mutation | G | A | p.R361* |
| SKCM | TCGA-D3-A3MV-06 | exon_skip_516529 | 118971720 | 118972014 | 118971941 | 118971941 | Nonsense_Mutation | G | A | p.R361X |
| SKCM | TCGA-EE-A29M-06 | exon_skip_516534 | 118974557 | 118974647 | 118974617 | 118974617 | Nonsense_Mutation | G | A | p.Q280* |
| SKCM | TCGA-EE-A29M-06 | exon_skip_516534 | 118974557 | 118974647 | 118974617 | 118974617 | Nonsense_Mutation | G | A | p.Q280X |
| SKCM | TCGA-EE-A29M-06 | exon_skip_516535 | 118974609 | 118974647 | 118974617 | 118974617 | Nonsense_Mutation | G | A | p.Q280* |
| SKCM | TCGA-EE-A29M-06 | exon_skip_516535 | 118974609 | 118974647 | 118974617 | 118974617 | Nonsense_Mutation | G | A | p.Q280X |
| UCEC | TCGA-AP-A0L8-01 | exon_skip_516537 | 118977154 | 118977264 | 118977241 | 118977241 | Nonsense_Mutation | C | A | p.E165* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516535 | |
| Skipped exon start: 118974609 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280X | |
| Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516534 | |
| Skipped exon start: 118974557 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280X | |
| Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516535 | |
| Skipped exon start: 118974609 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280* | |
| Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516534 | |
| Skipped exon start: 118974557 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280* | |
exon_skip_370579_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_431783_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_516534_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_516535_SKCM_TCGA-EE-A29M-06.png | |
exon_skip_62987_SKCM_TCGA-EE-A29M-06.png | |
 | Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516535 | |
| Skipped exon start: 118974609 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280X | |
| Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516534 | |
| Skipped exon start: 118974557 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280X | |
| Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516535 | |
| Skipped exon start: 118974609 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280* | |
| Sample: TCGA-EE-A29M-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_516534 | |
| Skipped exon start: 118974557 | |
| Skipped exon end: 118974647 | |
| Mutation start: 118974617 | |
| Mutation end: 118974617 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q280* | |
| exon_skip_370579_SKCM_TCGA-EE-A29M-06.png | |
| exon_skip_431783_SKCM_TCGA-EE-A29M-06.png | |
| exon_skip_516534_SKCM_TCGA-EE-A29M-06.png | |
| exon_skip_516535_SKCM_TCGA-EE-A29M-06.png | |
| exon_skip_62987_SKCM_TCGA-EE-A29M-06.png | |
| - 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 |
| EFO27_OVARY | 118977154 | 118977264 | 118977167 | 118977168 | Frame_Shift_Ins | - | T | p.N189fs |
| MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118971720 | 118972014 | 118971729 | 118971729 | Missense_Mutation | T | C | p.I431M |
| EB3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118971720 | 118972014 | 118971791 | 118971791 | Missense_Mutation | C | T | p.E411K |
| OCUBM_BREAST | 118971720 | 118972014 | 118971807 | 118971807 | Missense_Mutation | C | G | p.K405N |
| SKRC20_KIDNEY | 118971720 | 118972014 | 118971844 | 118971844 | Missense_Mutation | A | T | p.M393K |
| JHUEM7_ENDOMETRIUM | 118971720 | 118972014 | 118971859 | 118971859 | Missense_Mutation | C | A | p.R388I |
| HEC108_ENDOMETRIUM | 118971720 | 118972014 | 118971906 | 118971906 | Missense_Mutation | C | G | p.E372D |
| MZ7MEL_SKIN | 118971720 | 118972014 | 118971998 | 118971998 | Missense_Mutation | C | T | p.G342S |
| TGBC11TKB_STOMACH | 118985458 | 118985564 | 118985464 | 118985464 | Missense_Mutation | T | G | p.N122H |
| TTC1240_SOFT_TISSUE | 118985458 | 118985564 | 118985476 | 118985476 | Missense_Mutation | C | T | p.V118I |
| NCIH196_LUNG | 118985458 | 118985564 | 118985481 | 118985481 | Missense_Mutation | C | T | p.G116D |
| HCC2998_LARGE_INTESTINE | 118971720 | 118972014 | 118971911 | 118971911 | Nonsense_Mutation | C | A | p.E371* |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 118985458 | 118985564 | 118985459 | 118985459 | Splice_Site | T | C | p.K123K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for UPF3B |
| 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 UPF3B |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for UPF3B |
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RelatedDrugs for UPF3B |
| 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 UPF3B |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| UPF3B | C1136249 | Mental Retardation, X-Linked | 1 | CTD_human |
| UPF3B | C1970822 | Mental Retardation, X-Linked, Syndromic 14 | 1 | CTD_human;UNIPROT |
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