|
||||||
|
 | |
| |
| |
| |
| 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 RAB6B |
 Gene summary |
| Gene information | Gene symbol | RAB6B | Gene ID | 51560 |
| Gene name | RAB6B, member RAS oncogene family | |
| Synonyms | - | |
| Cytomap | 3q22.1 | |
| Type of gene | protein-coding | |
| Description | ras-related protein Rab-6Bsmall GTP-binding proteinsmall GTPase RAB6B | |
| Modification date | 20180526 | |
| UniProtAcc | Q9NRW1 | |
| Context | PubMed: RAB6B [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 RAB6B 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 RAB6B |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for RAB6B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_388660 | 3 | 133558349:133558461:133560128:133560234:133560453:133560507 | 133560128:133560234 | ENSG00000154917.6 | ENST00000460865.3,ENST00000486858.1,ENST00000285208.4,ENST00000543906.1,ENST00000477759.1 |
| exon_skip_388661 | 3 | 133560453:133560507:133583427:133583486:133614240:133614297 | 133583427:133583486 | ENSG00000154917.6 | ENST00000543906.1 |
| exon_skip_388663 | 3 | 133583461:133583486:133604378:133604509:133614240:133614297 | 133604378:133604509 | ENSG00000154917.6 | ENST00000486858.1 |
| exon_skip_388665 | 3 | 133583461:133583486:133604414:133604509:133614240:133614297 | 133604414:133604509 | ENSG00000154917.6 | ENST00000477759.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for RAB6B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_388660 | 3 | 133558349:133558461:133560128:133560234:133560453:133560507 | 133560128:133560234 | ENSG00000154917.6 | ENST00000285208.4,ENST00000543906.1,ENST00000486858.1,ENST00000477759.1,ENST00000460865.3 |
| exon_skip_388661 | 3 | 133560453:133560507:133583427:133583486:133614240:133614297 | 133583427:133583486 | ENSG00000154917.6 | ENST00000543906.1 |
| exon_skip_388663 | 3 | 133583461:133583486:133604378:133604509:133614240:133614297 | 133604378:133604509 | ENSG00000154917.6 | ENST00000486858.1 |
| exon_skip_388665 | 3 | 133583461:133583486:133604414:133604509:133614240:133614297 | 133604414:133604509 | ENSG00000154917.6 | ENST00000477759.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for RAB6B |
| 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 |
| ENST00000285208 | 133560128 | 133560234 | Frame-shift |
| ENST00000543906 | 133560128 | 133560234 | Frame-shift |
| ENST00000543906 | 133583427 | 133583486 | Frame-shift |
| 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 |
| ENST00000285208 | 133560128 | 133560234 | Frame-shift |
| ENST00000543906 | 133560128 | 133560234 | Frame-shift |
| ENST00000543906 | 133583427 | 133583486 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for RAB6B |
| 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 |
| 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 |
| 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 RAB6B |
| - 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 |
| COAD | TCGA-AZ-6601-01 | exon_skip_388660 | 133560129 | 133560234 | 133560231 | 133560231 | Nonsense_Mutation | G | A | p.R63X |
| STAD | TCGA-RD-A8N1-01 | exon_skip_388661 | 133583428 | 133583486 | 133583487 | 133583487 | Splice_Site | C | 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 |
| BT483_BREAST | 133560129 | 133560234 | 133560132 | 133560132 | Missense_Mutation | T | A | p.T96S |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 133560129 | 133560234 | 133560150 | 133560150 | Missense_Mutation | C | T | p.V90M |
| SNU1040_LARGE_INTESTINE | 133560129 | 133560234 | 133560191 | 133560191 | Missense_Mutation | C | T | p.R76H |
| NCIH630_LARGE_INTESTINE | 133583428 | 133583486 | 133583442 | 133583442 | Missense_Mutation | C | T | p.D39N |
| RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 133560129 | 133560234 | 133560231 | 133560231 | Nonsense_Mutation | G | A | p.R63* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB6B |
| 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 RAB6B |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB6B |
Top |
RelatedDrugs for RAB6B |
| 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 RAB6B |
| 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)
|