|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for BRDT |
 Gene summary |
| Gene information | Gene symbol | BRDT | Gene ID | 676 |
| Gene name | bromodomain testis associated | |
| Synonyms | BRD6|CT9|SPGF21 | |
| Cytomap | 1p22.1 | |
| Type of gene | protein-coding | |
| Description | bromodomain testis-specific proteinRING3-like proteinbromodomain, testis-specificcancer/testis antigen 9 | |
| Modification date | 20180519 | |
| UniProtAcc | Q58F21 | |
| Context | PubMed: BRDT [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 |
Top |
Exon skipping events across known transcript of Ensembl for BRDT 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. |
 |
Top |
Gene isoform structures and expression levels for BRDT |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for BRDT |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_7788 | 1 | 92414957:92415045:92415194:92415239:92428274:92428503 | 92415194:92415239 | ENSG00000137948.14 | ENST00000440509.1 |
| exon_skip_7790 | 1 | 92415194:92415239:92415446:92415515:92428274:92428503 | 92415446:92415515 | ENSG00000137948.14 | ENST00000548992.1 |
| exon_skip_7792 | 1 | 92415194:92415239:92415456:92416031:92428274:92428353 | 92415456:92416031 | ENSG00000137948.14 | ENST00000427104.1 |
| exon_skip_7793 | 1 | 92414990:92415239:92415861:92416031:92428274:92428353 | 92415861:92416031 | ENSG00000137948.14 | ENST00000457265.1 |
| exon_skip_7797 | 1 | 92415861:92416031:92416272:92416368:92428274:92428353 | 92416272:92416368 | ENSG00000137948.14 | ENST00000449584.1 |
| exon_skip_7798 | 1 | 92415861:92416031:92428274:92428503:92430183:92430279 | 92428274:92428503 | ENSG00000137948.14 | ENST00000427104.1 |
| exon_skip_7802 | 1 | 92415861:92416031:92430183:92430321:92433702:92433781 | 92430183:92430321 | ENSG00000137948.14 | ENST00000370389.2 |
| exon_skip_7803 | 1 | 92428363:92428503:92430183:92430321:92433702:92433781 | 92430183:92430321 | ENSG00000137948.14 | ENST00000402388.1,ENST00000426141.1,ENST00000423434.1,ENST00000399546.2,ENST00000552654.1,ENST00000427104.1,ENST00000448194.1,ENST00000440509.1,ENST00000362005.3 |
| exon_skip_7804 | 1 | 92459639:92459811:92467605:92467706:92469970:92470176 | 92467605:92467706 | ENSG00000137948.14 | ENST00000402388.1,ENST00000394530.3,ENST00000399546.2,ENST00000370389.2,ENST00000362005.3 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for BRDT |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_7788 | 1 | 92414957:92415045:92415194:92415239:92428274:92428503 | 92415194:92415239 | ENSG00000137948.14 | ENST00000440509.1 |
| exon_skip_7789 | 1 | 92414957:92415045:92415664:92416031:92428274:92428503 | 92415664:92416031 | ENSG00000137948.14 | ENST00000355011.3 |
| exon_skip_7790 | 1 | 92415194:92415239:92415446:92415515:92428274:92428503 | 92415446:92415515 | ENSG00000137948.14 | ENST00000548992.1 |
| exon_skip_7792 | 1 | 92415194:92415239:92415456:92416031:92428274:92428353 | 92415456:92416031 | ENSG00000137948.14 | ENST00000427104.1 |
| exon_skip_7797 | 1 | 92415861:92416031:92416272:92416368:92428274:92428353 | 92416272:92416368 | ENSG00000137948.14 | ENST00000449584.1 |
| exon_skip_7798 | 1 | 92415861:92416031:92428274:92428503:92430183:92430279 | 92428274:92428503 | ENSG00000137948.14 | ENST00000427104.1 |
| exon_skip_7802 | 1 | 92415861:92416031:92430183:92430321:92433702:92433781 | 92430183:92430321 | ENSG00000137948.14 | ENST00000370389.2 |
| exon_skip_7803 | 1 | 92428363:92428503:92430183:92430321:92433702:92433781 | 92430183:92430321 | ENSG00000137948.14 | ENST00000362005.3,ENST00000399546.2,ENST00000423434.1,ENST00000440509.1,ENST00000427104.1,ENST00000448194.1,ENST00000426141.1,ENST00000552654.1,ENST00000402388.1 |
| exon_skip_7804 | 1 | 92459639:92459811:92467605:92467706:92469970:92470176 | 92467605:92467706 | ENSG00000137948.14 | ENST00000362005.3,ENST00000370389.2,ENST00000399546.2,ENST00000394530.3,ENST00000402388.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for BRDT |
| 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 |
| ENST00000362005 | 92467605 | 92467706 | Frame-shift |
| ENST00000402388 | 92467605 | 92467706 | Frame-shift |
| ENST00000362005 | 92430183 | 92430321 | In-frame |
| ENST00000402388 | 92430183 | 92430321 | 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 |
| ENST00000362005 | 92467605 | 92467706 | Frame-shift |
| ENST00000402388 | 92467605 | 92467706 | Frame-shift |
| ENST00000362005 | 92430183 | 92430321 | In-frame |
| ENST00000402388 | 92430183 | 92430321 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for BRDT |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
| ENST00000362005 | 3426 | 947 | 92430183 | 92430321 | 611 | 748 | 64 | 110 |
| ENST00000402388 | 3142 | 947 | 92430183 | 92430321 | 327 | 464 | 64 | 110 |
| 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 |
| ENST00000362005 | 3426 | 947 | 92430183 | 92430321 | 611 | 748 | 64 | 110 |
| ENST00000402388 | 3142 | 947 | 92430183 | 92430321 | 327 | 464 | 64 | 110 |
| 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 |
Top |
SNVs in the skipped exons for BRDT |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - 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 |
| SKCM | TCGA-EE-A181-06 | exon_skip_7798 | 92428275 | 92428503 | 92428378 | 92428378 | Frame_Shift_Del | A | - | p.K24fs |
| SKCM | TCGA-EE-A181-06 | exon_skip_7798 | 92428275 | 92428503 | 92428378 | 92428378 | Frame_Shift_Del | A | - | p.T22fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_7798 | 92428275 | 92428503 | 92428381 | 92428381 | Frame_Shift_Del | A | - | p.K24fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_7798 | 92428275 | 92428503 | 92428381 | 92428381 | Frame_Shift_Del | A | - | p.K24fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_7798 | 92428275 | 92428503 | 92428418 | 92428418 | Frame_Shift_Del | A | - | p.Q36fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_7798 | 92428275 | 92428503 | 92428431 | 92428431 | Frame_Shift_Del | A | - | p.L40fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_7802 exon_skip_7803 | 92430184 | 92430321 | 92430201 | 92430201 | Frame_Shift_Del | A | - | p.I70fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_7802 exon_skip_7803 | 92430184 | 92430321 | 92430201 | 92430201 | Frame_Shift_Del | A | - | p.I70fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_7802 exon_skip_7803 | 92430184 | 92430321 | 92430201 | 92430201 | Frame_Shift_Del | A | - | p.I70fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_7802 exon_skip_7803 | 92430184 | 92430321 | 92430306 | 92430306 | Frame_Shift_Del | T | - | p.C32fs |
| UCEC | TCGA-AP-A059-01 | exon_skip_7798 | 92428275 | 92428503 | 92428330 | 92428330 | Nonsense_Mutation | C | T | p.Q7* |
| STAD | TCGA-BR-6452-01 | exon_skip_7798 | 92428275 | 92428503 | 92428390 | 92428390 | Nonsense_Mutation | C | T | p.R27* |
| KIRC | TCGA-AK-3427-01 | exon_skip_7802 exon_skip_7803 | 92430184 | 92430321 | 92430268 | 92430268 | Nonsense_Mutation | G | T | p.E20* |
| - 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 |
| TE125T_FIBROBLAST | 92428275 | 92428503 | 92428315 | 92428316 | Frame_Shift_Del | TC | - | p.S2fs |
| D341MED_CENTRAL_NERVOUS_SYSTEM | 92430184 | 92430321 | 92430201 | 92430201 | Frame_Shift_Del | A | - | p.I70fs |
| HS751T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 92428275 | 92428503 | 92428337 | 92428337 | Missense_Mutation | C | G | p.A9G |
| HS863T_FIBROBLAST | 92428275 | 92428503 | 92428412 | 92428412 | Missense_Mutation | A | G | p.Y34C |
| SKUT1_SOFT_TISSUE | 92428275 | 92428503 | 92428472 | 92428472 | Missense_Mutation | G | A | p.R54H |
| GP2D_LARGE_INTESTINE | 92430184 | 92430321 | 92430236 | 92430236 | Missense_Mutation | G | A | p.R82H |
| GP5D_LARGE_INTESTINE | 92430184 | 92430321 | 92430236 | 92430236 | Missense_Mutation | G | A | p.R82H |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 92430184 | 92430321 | 92430236 | 92430236 | Missense_Mutation | G | A | p.R82H |
| T173_FIBROBLAST | 92467606 | 92467706 | 92467643 | 92467643 | Missense_Mutation | G | A | p.M775I |
| BEN_LUNG | 92467606 | 92467706 | 92467624 | 92467624 | Nonsense_Mutation | C | G | p.S769* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BRDT |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BRDT |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BRDT |
Top |
RelatedDrugs for BRDT |
| 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 |
Top |
RelatedDiseases for BRDT |
| 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)
|