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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 BEST3 |
 Gene summary |
| Gene information | Gene symbol | BEST3 | Gene ID | 144453 |
| Gene name | bestrophin 3 | |
| Synonyms | VMD2L3 | |
| Cytomap | 12q15 | |
| Type of gene | protein-coding | |
| Description | bestrophin-3vitelliform macular dystrophy 2-like 3vitelliform macular dystrophy 2-like protein 3 | |
| Modification date | 20180523 | |
| UniProtAcc | Q8N1M1 | |
| Context | PubMed: BEST3 [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 |
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Exon skipping events across known transcript of Ensembl for BEST3 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 BEST3 |
| 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 BEST3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_94615 | 12 | 70066664:70066745:70070695:70070848:70070959:70071037 | 70070695:70070848 | ENSG00000127325.14 | ENST00000331471.4,ENST00000553096.1,ENST00000330891.5 |
| exon_skip_94616 | 12 | 70066664:70066745:70070959:70071037:70072518:70072673 | 70070959:70071037 | ENSG00000127325.14 | ENST00000552295.1,ENST00000488961.1,ENST00000476098.1,ENST00000547208.1 |
| exon_skip_94623 | 12 | 70072518:70072673:70087453:70087687:70088149:70088244 | 70087453:70087687 | ENSG00000127325.14 | ENST00000331471.4,ENST00000330891.5 |
| exon_skip_94624 | 12 | 70072518:70072673:70087453:70087687:70092984:70093065 | 70087453:70087687 | ENSG00000127325.14 | ENST00000553096.1 |
| exon_skip_94628 | 12 | 70072518:70072673:70087508:70087687:70092984:70093065 | 70087508:70087687 | ENSG00000127325.14 | ENST00000476098.1 |
| exon_skip_94651 | 12 | 70087508:70087687:70088149:70088244:70091426:70091593 | 70088149:70088244 | ENSG00000127325.14 | ENST00000331471.4,ENST00000330891.5,ENST00000393365.1 |
| exon_skip_94652 | 12 | 70087508:70087687:70088149:70088244:70092984:70093065 | 70088149:70088244 | ENSG00000127325.14 | ENST00000551160.1,ENST00000533674.1 |
| exon_skip_94656 | 12 | 70088149:70088244:70091426:70091593:70092984:70093065 | 70091426:70091593 | ENSG00000127325.14 | ENST00000548658.1,ENST00000331471.4,ENST00000330891.5,ENST00000393365.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for BEST3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_94615 | 12 | 70066664:70066745:70070695:70070848:70070959:70071037 | 70070695:70070848 | ENSG00000127325.14 | ENST00000331471.4,ENST00000330891.5,ENST00000553096.1 |
| exon_skip_94616 | 12 | 70066664:70066745:70070959:70071037:70072518:70072673 | 70070959:70071037 | ENSG00000127325.14 | ENST00000547208.1,ENST00000488961.1,ENST00000476098.1,ENST00000552295.1 |
| exon_skip_94623 | 12 | 70072518:70072673:70087453:70087687:70088149:70088244 | 70087453:70087687 | ENSG00000127325.14 | ENST00000331471.4,ENST00000330891.5 |
| exon_skip_94624 | 12 | 70072518:70072673:70087453:70087687:70092984:70093065 | 70087453:70087687 | ENSG00000127325.14 | ENST00000553096.1 |
| exon_skip_94628 | 12 | 70072518:70072673:70087508:70087687:70092984:70093065 | 70087508:70087687 | ENSG00000127325.14 | ENST00000476098.1 |
| exon_skip_94651 | 12 | 70087508:70087687:70088149:70088244:70091426:70091593 | 70088149:70088244 | ENSG00000127325.14 | ENST00000331471.4,ENST00000330891.5,ENST00000393365.1 |
| exon_skip_94652 | 12 | 70087508:70087687:70088149:70088244:70092984:70093065 | 70088149:70088244 | ENSG00000127325.14 | ENST00000551160.1,ENST00000533674.1 |
| exon_skip_94656 | 12 | 70088149:70088244:70091426:70091593:70092984:70093065 | 70091426:70091593 | ENSG00000127325.14 | ENST00000331471.4,ENST00000330891.5,ENST00000548658.1,ENST00000393365.1 |
| 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 BEST3 |
| 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 |
| ENST00000331471 | 70091426 | 70091593 | 3UTR-3CDS |
| ENST00000331471 | 70088149 | 70088244 | Frame-shift |
| ENST00000331471 | 70070695 | 70070848 | In-frame |
| ENST00000331471 | 70087453 | 70087687 | 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 |
| ENST00000331471 | 70091426 | 70091593 | 3UTR-3CDS |
| ENST00000331471 | 70088149 | 70088244 | Frame-shift |
| ENST00000331471 | 70070695 | 70070848 | In-frame |
| ENST00000331471 | 70087453 | 70087687 | In-frame |
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Infer the effects of exon skipping event on protein functional features for BEST3 |
| 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 |
| ENST00000331471 | 1523 | 668 | 70087453 | 70087687 | 420 | 653 | 82 | 160 |
| ENST00000331471 | 1523 | 668 | 70070695 | 70070848 | 887 | 1039 | 238 | 289 |
| 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 |
| ENST00000331471 | 1523 | 668 | 70087453 | 70087687 | 420 | 653 | 82 | 160 |
| ENST00000331471 | 1523 | 668 | 70070695 | 70070848 | 887 | 1039 | 238 | 289 |
| 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 |
| Q8N1M1 | 82 | 160 | 1 | 162 | Alternative sequence | ID=VSP_046979;Note=In isoform 5. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8N1M1 | 82 | 160 | 1 | 106 | Alternative sequence | ID=VSP_008981;Note=In isoform 4 and isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8N1M1 | 82 | 160 | 1 | 668 | Chain | ID=PRO_0000143121;Note=Bestrophin-3 |
| Q8N1M1 | 82 | 160 | 92 | 178 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 82 | 160 | 71 | 91 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 238 | 289 | 179 | 668 | Alternative sequence | ID=VSP_008983;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8N1M1 | 238 | 289 | 239 | 289 | Alternative sequence | ID=VSP_046980;Note=In isoform 5. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8N1M1 | 238 | 289 | 1 | 668 | Chain | ID=PRO_0000143121;Note=Bestrophin-3 |
| Q8N1M1 | 238 | 289 | 229 | 249 | Intramembrane | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 238 | 289 | 250 | 270 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 238 | 289 | 271 | 291 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q8N1M1 | 82 | 160 | 1 | 162 | Alternative sequence | ID=VSP_046979;Note=In isoform 5. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8N1M1 | 82 | 160 | 1 | 106 | Alternative sequence | ID=VSP_008981;Note=In isoform 4 and isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8N1M1 | 82 | 160 | 1 | 668 | Chain | ID=PRO_0000143121;Note=Bestrophin-3 |
| Q8N1M1 | 82 | 160 | 92 | 178 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 82 | 160 | 71 | 91 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 238 | 289 | 179 | 668 | Alternative sequence | ID=VSP_008983;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8N1M1 | 238 | 289 | 239 | 289 | Alternative sequence | ID=VSP_046980;Note=In isoform 5. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8N1M1 | 238 | 289 | 1 | 668 | Chain | ID=PRO_0000143121;Note=Bestrophin-3 |
| Q8N1M1 | 238 | 289 | 229 | 249 | Intramembrane | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 238 | 289 | 250 | 270 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8N1M1 | 238 | 289 | 271 | 291 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for BEST3 |
| - 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 |
| COAD | TCGA-AD-6895-01 | exon_skip_94615 | 70070696 | 70070848 | 70070790 | 70070790 | Frame_Shift_Del | A | - | p.L258fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_94656 | 70091427 | 70091593 | 70091462 | 70091462 | Frame_Shift_Del | A | - | p.F39fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_94656 | 70091427 | 70091593 | 70091528 | 70091528 | Frame_Shift_Del | A | - | p.F17fs |
| BLCA | TCGA-G2-A2EK-01 | exon_skip_94656 | 70091427 | 70091593 | 70091534 | 70091534 | Frame_Shift_Del | A | - | p.F15fs |
| GBM | TCGA-14-1450-01 | exon_skip_94656 | 70091427 | 70091593 | 70091534 | 70091534 | Frame_Shift_Del | A | - | p.F15fs |
| STAD | TCGA-MX-A5UJ-01 | exon_skip_94656 | 70091427 | 70091593 | 70091534 | 70091534 | Frame_Shift_Del | A | - | p.F15fs |
| STAD | TCGA-MX-A5UJ-01 | exon_skip_94656 | 70091427 | 70091593 | 70091534 | 70091534 | Frame_Shift_Del | A | - | p.G16fs |
| UCEC | TCGA-AX-A06H-01 | exon_skip_94656 | 70091427 | 70091593 | 70091533 | 70091534 | Frame_Shift_Ins | - | A | p.F15fs |
| - 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 |
| TOV21G_OVARY | 70091427 | 70091593 | 70091534 | 70091534 | Frame_Shift_Del | A | - | p.F15fs |
| CW2_LARGE_INTESTINE | 70091427 | 70091593 | 70091534 | 70091534 | Frame_Shift_Del | A | - | p.F15fs |
| SNU1040_LARGE_INTESTINE | 70091427 | 70091593 | 70091534 | 70091534 | Frame_Shift_Del | A | - | p.F15fs |
| LNCAPCLONEFGC_PROSTATE | 70070696 | 70070848 | 70070731 | 70070731 | Missense_Mutation | G | T | p.L278I |
| GP2D_LARGE_INTESTINE | 70070696 | 70070848 | 70070827 | 70070827 | Missense_Mutation | T | C | p.T246A |
| SW1271_LUNG | 70070696 | 70070848 | 70070838 | 70070838 | Missense_Mutation | A | T | p.L242H |
| SNU520_STOMACH | 70070960 | 70071037 | 70070998 | 70070998 | Missense_Mutation | C | T | p.G226S |
| PA1_OVARY | 70070960 | 70071037 | 70071033 | 70071033 | Missense_Mutation | A | G | p.M214T |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70087454 | 70087687 | 70087498 | 70087498 | Missense_Mutation | G | A | p.A146V |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70087454 | 70087687 | 70087571 | 70087571 | Missense_Mutation | G | A | p.R122C |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70087509 | 70087687 | 70087571 | 70087571 | Missense_Mutation | G | A | p.R122C |
| KARPAS1106P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70087454 | 70087687 | 70087682 | 70087682 | Missense_Mutation | A | C | p.Y85D |
| KARPAS1106P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70087509 | 70087687 | 70087682 | 70087682 | Missense_Mutation | A | C | p.Y85D |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 70088150 | 70088244 | 70088227 | 70088227 | Missense_Mutation | A | G | p.V57A |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70088150 | 70088244 | 70088227 | 70088227 | Missense_Mutation | A | G | p.V57A |
| BXPC3_PANCREAS | 70091427 | 70091593 | 70091439 | 70091439 | Missense_Mutation | C | T | p.S47N |
| C33A_CERVIX | 70091427 | 70091593 | 70091461 | 70091461 | Missense_Mutation | C | G | p.A40P |
| HCC2998_LARGE_INTESTINE | 70091427 | 70091593 | 70091472 | 70091472 | Missense_Mutation | A | C | p.F36C |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BEST3 |
| 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 |
| exon_skip_94656 | 12 | 70088149:70088244:70091426:70091593:70092984:70093065 | 70091426:70091593 | ENST00000548658.1,ENST00000331471.4,ENST00000330891.5,ENST00000393365.1 | PRAD | rs1025016 | chr12:70091452 | A/G | 2.52e-05 |
| exon_skip_94656 | 12 | 70088149:70088244:70091426:70091593:70092984:70093065 | 70091426:70091593 | ENST00000548658.1,ENST00000331471.4,ENST00000330891.5,ENST00000393365.1 | PRAD | rs1025016 | chr12:70091452 | A/G | 1.87e-03 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BEST3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BEST3 |
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RelatedDrugs for BEST3 |
| 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 BEST3 |
| 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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