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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 BRD3 |
 Gene summary |
| Gene information | Gene symbol | BRD3 | Gene ID | 8019 |
| Gene name | bromodomain containing 3 | |
| Synonyms | ORFX|RING3L | |
| Cytomap | 9q34.2 | |
| Type of gene | protein-coding | |
| Description | bromodomain-containing protein 3RING3-like proteinbromodomain-containing protein 3 short isoform | |
| Modification date | 20180519 | |
| UniProtAcc | Q15059 | |
| Context | PubMed: BRD3 [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 |
| BRD3 | GO:0006357 | regulation of transcription by RNA polymerase II | 18406326 |
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Exon skipping events across known transcript of Ensembl for BRD3 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 BRD3 |
| 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 BRD3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_508171 | 9 | 136899822:136899951:136901153:136901446:136906881:136906916 | 136901153:136901446 | ENSG00000169925.12 | ENST00000473349.1 |
| exon_skip_508174 | 9 | 136901153:136901446:136905155:136905391:136906881:136906916 | 136905155:136905391 | ENSG00000169925.12 | ENST00000303407.7 |
| exon_skip_508176 | 9 | 136910414:136910543:136913204:136913576:136915495:136915549 | 136913204:136913576 | ENSG00000169925.12 | ENST00000357885.2,ENST00000371834.2,ENST00000303407.7 |
| exon_skip_508178 | 9 | 136916683:136916831:136917427:136917565:136918386:136918712 | 136917427:136917565 | ENSG00000169925.12 | ENST00000357885.2,ENST00000371834.2,ENST00000303407.7 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for BRD3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_508171 | 9 | 136899822:136899951:136901153:136901446:136906881:136906916 | 136901153:136901446 | ENSG00000169925.12 | ENST00000473349.1 |
| exon_skip_508174 | 9 | 136901153:136901446:136905155:136905391:136906881:136906916 | 136905155:136905391 | ENSG00000169925.12 | ENST00000303407.7 |
| exon_skip_508176 | 9 | 136910414:136910543:136913204:136913576:136915495:136915549 | 136913204:136913576 | ENSG00000169925.12 | ENST00000303407.7,ENST00000371834.2,ENST00000357885.2 |
| exon_skip_508178 | 9 | 136916683:136916831:136917427:136917565:136918386:136918712 | 136917427:136917565 | ENSG00000169925.12 | ENST00000303407.7,ENST00000371834.2,ENST00000357885.2 |
| 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 BRD3 |
| 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 |
| ENST00000303407 | 136905155 | 136905391 | Frame-shift |
| ENST00000303407 | 136913204 | 136913576 | In-frame |
| ENST00000303407 | 136917427 | 136917565 | 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 |
| ENST00000303407 | 136905155 | 136905391 | Frame-shift |
| ENST00000303407 | 136913204 | 136913576 | In-frame |
| ENST00000303407 | 136917427 | 136917565 | In-frame |
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Infer the effects of exon skipping event on protein functional features for BRD3 |
| 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 |
| ENST00000303407 | 5669 | 726 | 136917427 | 136917565 | 400 | 537 | 71 | 117 |
| ENST00000303407 | 5669 | 726 | 136913204 | 136913576 | 901 | 1272 | 238 | 362 |
| 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 |
| ENST00000303407 | 5669 | 726 | 136917427 | 136917565 | 400 | 537 | 71 | 117 |
| ENST00000303407 | 5669 | 726 | 136913204 | 136913576 | 901 | 1272 | 238 | 362 |
| 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 |
| Q15059 | 71 | 117 | 2 | 726 | Chain | ID=PRO_0000211181;Note=Bromodomain-containing protein 3 |
| Q15059 | 71 | 117 | 51 | 123 | Domain | Note=Bromo 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00035 |
| Q15059 | 71 | 117 | 73 | 76 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2NXB |
| Q15059 | 71 | 117 | 83 | 91 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2NXB |
| Q15059 | 71 | 117 | 98 | 115 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2NXB |
| Q15059 | 71 | 117 | 78 | 80 | Region | Note=Acetylated histone H3 binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27105114;Dbxref=PMID:27105114 |
| Q15059 | 238 | 362 | 2 | 726 | Chain | ID=PRO_0000211181;Note=Bromodomain-containing protein 3 |
| Q15059 | 238 | 362 | 326 | 398 | Domain | Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00035 |
| Q15059 | 238 | 362 | 310 | 323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 325 | 327 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 328 | 331 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 332 | 334 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 348 | 351 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 358 | 366 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 263 | 263 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:20068231,PMID:21406692,PMID |
| Q15059 | 238 | 362 | 281 | 281 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| Q15059 | 238 | 362 | 340 | 344 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| 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 |
| Q15059 | 71 | 117 | 2 | 726 | Chain | ID=PRO_0000211181;Note=Bromodomain-containing protein 3 |
| Q15059 | 71 | 117 | 51 | 123 | Domain | Note=Bromo 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00035 |
| Q15059 | 71 | 117 | 73 | 76 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2NXB |
| Q15059 | 71 | 117 | 83 | 91 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2NXB |
| Q15059 | 71 | 117 | 98 | 115 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2NXB |
| Q15059 | 71 | 117 | 78 | 80 | Region | Note=Acetylated histone H3 binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27105114;Dbxref=PMID:27105114 |
| Q15059 | 238 | 362 | 2 | 726 | Chain | ID=PRO_0000211181;Note=Bromodomain-containing protein 3 |
| Q15059 | 238 | 362 | 326 | 398 | Domain | Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00035 |
| Q15059 | 238 | 362 | 310 | 323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 325 | 327 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 328 | 331 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 332 | 334 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 348 | 351 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 358 | 366 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
| Q15059 | 238 | 362 | 263 | 263 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:20068231,PMID:21406692,PMID |
| Q15059 | 238 | 362 | 281 | 281 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| Q15059 | 238 | 362 | 340 | 344 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3S92 |
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SNVs in the skipped exons for BRD3 |
| - 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-A1EG-01 | exon_skip_508171 | 136901154 | 136901446 | 136901171 | 136901171 | Frame_Shift_Del | T | - | p.K640fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_508171 | 136901154 | 136901446 | 136901171 | 136901171 | Frame_Shift_Del | T | - | p.K640fs |
| UCEC | TCGA-A5-A0GH-01 | exon_skip_508171 | 136901154 | 136901446 | 136901171 | 136901171 | Frame_Shift_Del | T | - | p.K640fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_508171 | 136901154 | 136901446 | 136901283 | 136901283 | Frame_Shift_Del | C | - | p.E603fs |
| STAD | TCGA-BR-6452-01 | exon_skip_508178 | 136917428 | 136917565 | 136917543 | 136917543 | Frame_Shift_Del | T | - | p.N79fs |
| UCEC | TCGA-AX-A0J0-01 | exon_skip_508171 | 136901154 | 136901446 | 136901247 | 136901247 | Nonsense_Mutation | C | A | p.E615* |
| LIHC | TCGA-DD-AAC8-01 | exon_skip_508174 | 136905156 | 136905391 | 136905393 | 136905393 | Splice_Site | T | A | . |
| - 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 |
| A549_LUNG | 136905156 | 136905391 | 136905272 | 136905274 | In_Frame_Del | CTC | - | p.E509del |
| HEKTE_KIDNEY | 136905156 | 136905391 | 136905272 | 136905274 | In_Frame_Del | CTC | - | p.E509del |
| NCIH513_PLEURA | 136901154 | 136901446 | 136901198 | 136901198 | Missense_Mutation | C | T | p.R631K |
| M14_SKIN | 136901154 | 136901446 | 136901264 | 136901264 | Missense_Mutation | G | A | p.S609F |
| MDAMB435S_SKIN | 136901154 | 136901446 | 136901264 | 136901264 | Missense_Mutation | G | A | p.S609F |
| NCIH1048_LUNG | 136901154 | 136901446 | 136901318 | 136901318 | Missense_Mutation | T | C | p.K591R |
| SW1783_CENTRAL_NERVOUS_SYSTEM | 136901154 | 136901446 | 136901357 | 136901357 | Missense_Mutation | C | T | p.R578H |
| CW2_LARGE_INTESTINE | 136901154 | 136901446 | 136901399 | 136901399 | Missense_Mutation | T | C | p.E564G |
| TE4_OESOPHAGUS | 136905156 | 136905391 | 136905168 | 136905168 | Missense_Mutation | G | T | p.T544N |
| KARPAS422_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 136905156 | 136905391 | 136905198 | 136905198 | Missense_Mutation | T | C | p.K534R |
| OCILY10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 136905156 | 136905391 | 136905198 | 136905198 | Missense_Mutation | T | C | p.K534R |
| MDAMB453_BREAST | 136905156 | 136905391 | 136905225 | 136905225 | Missense_Mutation | G | A | p.P525L |
| MERO95_LUNG | 136905156 | 136905391 | 136905246 | 136905246 | Missense_Mutation | T | C | p.E518G |
| KARPAS422_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 136905156 | 136905391 | 136905309 | 136905309 | Missense_Mutation | T | C | p.K497R |
| OCILY10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 136905156 | 136905391 | 136905309 | 136905309 | Missense_Mutation | T | C | p.K497R |
| KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 136905156 | 136905391 | 136905311 | 136905311 | Missense_Mutation | C | G | p.E496D |
| SNU81_LARGE_INTESTINE | 136905156 | 136905391 | 136905367 | 136905367 | Missense_Mutation | C | T | p.A478T |
| SNU175_LARGE_INTESTINE | 136905156 | 136905391 | 136905376 | 136905376 | Missense_Mutation | C | T | p.E475K |
| MEWO_SKIN | 136913205 | 136913576 | 136913227 | 136913227 | Missense_Mutation | G | A | p.P355L |
| MEWO_SKIN | 136913205 | 136913576 | 136913227 | 136913228 | Missense_Mutation | GG | AA | p.P355L |
| MEWO_SKIN | 136913205 | 136913576 | 136913228 | 136913228 | Missense_Mutation | G | A | p.P355S |
| HCT15_LARGE_INTESTINE | 136913205 | 136913576 | 136913396 | 136913396 | Missense_Mutation | G | A | p.P299S |
| HRT18_LARGE_INTESTINE | 136913205 | 136913576 | 136913396 | 136913396 | Missense_Mutation | G | A | p.P299S |
| RL952_ENDOMETRIUM | 136913205 | 136913576 | 136913440 | 136913440 | Missense_Mutation | C | T | p.R284H |
| HCT15_LARGE_INTESTINE | 136913205 | 136913576 | 136913458 | 136913458 | Missense_Mutation | C | T | p.R278Q |
| HRT18_LARGE_INTESTINE | 136913205 | 136913576 | 136913458 | 136913458 | Missense_Mutation | C | T | p.R278Q |
| HEC265_ENDOMETRIUM | 136913205 | 136913576 | 136913485 | 136913485 | Missense_Mutation | T | C | p.D269G |
| NCIH187_LUNG | 136913205 | 136913576 | 136913552 | 136913552 | Missense_Mutation | C | T | p.D247N |
| 639V_URINARY_TRACT | 136913205 | 136913576 | 136913560 | 136913560 | Missense_Mutation | C | T | p.R244Q |
| HCC2998_LARGE_INTESTINE | 136917428 | 136917565 | 136917503 | 136917503 | Missense_Mutation | A | C | p.N92K |
| HEC59_ENDOMETRIUM | 136917428 | 136917565 | 136917491 | 136917491 | Nonsense_Mutation | C | T | p.W96* |
| CW2_LARGE_INTESTINE | 136917428 | 136917565 | 136917491 | 136917491 | Nonsense_Mutation | C | T | p.W96* |
| NCIH2591_PLEURA | 136917428 | 136917565 | 136917492 | 136917492 | Nonsense_Mutation | C | T | p.W96* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BRD3 |
| 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_508176 | 9 | 136910414:136910543:136913204:136913576:136915495:136915549 | 136913204:136913576 | ENST00000357885.2,ENST00000371834.2,ENST00000303407.7 | LGG | rs464826 | chr9:136913355 | T/C | 3.96e-11 |
| exon_skip_508176 | 9 | 136910414:136910543:136913204:136913576:136915495:136915549 | 136913204:136913576 | ENST00000357885.2,ENST00000371834.2,ENST00000303407.7 | LGG | rs464826 | chr9:136913355 | T/C | 8.14e-11 |
| exon_skip_508176 | 9 | 136910414:136910543:136913204:136913576:136915495:136915549 | 136913204:136913576 | ENST00000357885.2,ENST00000371834.2,ENST00000303407.7 | LGG | rs464826 | chr9:136913355 | T/C | 3.31e-07 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BRD3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BRD3 |
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RelatedDrugs for BRD3 |
| 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 BRD3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| BRD3 | C0025149 | Medulloblastoma | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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