|
||||||
|
 | |
| |
| |
| |
| 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 RAB4B |
 Gene summary |
| Gene information | Gene symbol | RAB4B | Gene ID | 53916 |
| Gene name | RAB4B, member RAS oncogene family | |
| Synonyms | - | |
| Cytomap | 19q13.2 | |
| Type of gene | protein-coding | |
| Description | ras-related protein Rab-4Bras-related GTP-binding protein 4bsmall GTP binding protein RAB4B | |
| Modification date | 20180526 | |
| UniProtAcc | P61018 | |
| Context | PubMed: RAB4B [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 RAB4B 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 RAB4B |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for RAB4B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_307385 | 19 | 41286289:41286404:41289682:41289745:41289825:41289980 | 41289682:41289745 | ENSG00000167578.12 | ENST00000600078.1,ENST00000597476.1,ENST00000357052.2,ENST00000595728.1,ENST00000594800.1 |
| exon_skip_307386 | 19 | 41289682:41289745:41289825:41289980:41292569:41292665 | 41289825:41289980 | ENSG00000167578.12 | ENST00000597476.1,ENST00000357052.2,ENST00000595728.1,ENST00000594800.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for RAB4B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_307385 | 19 | 41286289:41286404:41289682:41289745:41289825:41289980 | 41289682:41289745 | ENSG00000167578.12 | ENST00000594800.1,ENST00000357052.2,ENST00000600078.1,ENST00000597476.1,ENST00000595728.1 |
| exon_skip_307386 | 19 | 41289682:41289745:41289825:41289980:41292569:41292665 | 41289825:41289980 | ENSG00000167578.12 | ENST00000594800.1,ENST00000357052.2,ENST00000597476.1,ENST00000595728.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for RAB4B |
| 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 |
| ENST00000357052 | 41289825 | 41289980 | Frame-shift |
| ENST00000594800 | 41289825 | 41289980 | Frame-shift |
| ENST00000357052 | 41289682 | 41289745 | In-frame |
| ENST00000594800 | 41289682 | 41289745 | 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 |
| ENST00000357052 | 41289825 | 41289980 | Frame-shift |
| ENST00000594800 | 41289825 | 41289980 | Frame-shift |
| ENST00000357052 | 41289682 | 41289745 | In-frame |
| ENST00000594800 | 41289682 | 41289745 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for RAB4B |
| 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 |
| ENST00000357052 | 1157 | 213 | 41289682 | 41289745 | 323 | 385 | 71 | 91 |
| ENST00000594800 | 1190 | 213 | 41289682 | 41289745 | 373 | 435 | 71 | 91 |
| 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 |
| ENST00000357052 | 1157 | 213 | 41289682 | 41289745 | 323 | 385 | 71 | 91 |
| ENST00000594800 | 1190 | 213 | 41289682 | 41289745 | 373 | 435 | 71 | 91 |
| 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 |
| P61018 | 71 | 91 | 82 | 89 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
| P61018 | 71 | 91 | 82 | 89 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
| P61018 | 71 | 91 | 2 | 213 | Chain | ID=PRO_0000121099;Note=Ras-related protein Rab-4B |
| P61018 | 71 | 91 | 2 | 213 | Chain | ID=PRO_0000121099;Note=Ras-related protein Rab-4B |
| P61018 | 71 | 91 | 75 | 78 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
| P61018 | 71 | 91 | 75 | 78 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
| 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 |
| P61018 | 71 | 91 | 82 | 89 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
| P61018 | 71 | 91 | 82 | 89 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
| P61018 | 71 | 91 | 2 | 213 | Chain | ID=PRO_0000121099;Note=Ras-related protein Rab-4B |
| P61018 | 71 | 91 | 2 | 213 | Chain | ID=PRO_0000121099;Note=Ras-related protein Rab-4B |
| P61018 | 71 | 91 | 75 | 78 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
| P61018 | 71 | 91 | 75 | 78 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2O52 |
Top |
SNVs in the skipped exons for RAB4B |
| - 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 |
| - 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 |
| SNGM_ENDOMETRIUM | 41289683 | 41289745 | 41289714 | 41289714 | Missense_Mutation | G | A | p.A82T |
| SNU1040_LARGE_INTESTINE | 41289826 | 41289980 | 41289840 | 41289840 | Missense_Mutation | A | C | p.N97T |
| PACADD137_PANCREAS | 41289683 | 41289745 | 41289705 | 41289705 | Nonsense_Mutation | C | T | p.R79* |
| MFE319_ENDOMETRIUM | 41289683 | 41289745 | 41289684 | 41289684 | Splice_Site | T | A | p.S72T |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB4B |
| 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 RAB4B |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB4B |
Top |
RelatedDrugs for RAB4B |
| 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 RAB4B |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RAB4B | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|