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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 RAB40B |
 Gene summary |
| Gene information | Gene symbol | RAB40B | Gene ID | 10966 |
| Gene name | RAB40B, member RAS oncogene family | |
| Synonyms | RAR|SEC4L | |
| Cytomap | 17q25.3 | |
| Type of gene | protein-coding | |
| Description | ras-related protein Rab-40BGTP-binding protein homologous to Saccharomyces cerevisiae SEC4SOCS box-containing protein RARprotein Rar | |
| Modification date | 20180523 | |
| UniProtAcc | Q12829 | |
| Context | PubMed: RAB40B [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 RAB40B 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 RAB40B |
| 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 RAB40B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_295195 | 17 | 80615852:80616010:80616366:80616438:80617455:80617533 | 80616366:80616438 | ENSG00000141542.6 | ENST00000538809.2 |
| exon_skip_295196 | 17 | 80615852:80616010:80616366:80616589:80617455:80617533 | 80616366:80616589 | ENSG00000141542.6 | ENST00000571995.1,ENST00000574132.1,ENST00000570676.1,ENST00000269347.6 |
| exon_skip_295201 | 17 | 80617455:80617533:80618862:80618923:80622371:80622432 | 80618862:80618923 | ENSG00000141542.6 | ENST00000571995.1,ENST00000570676.1,ENST00000269347.6,ENST00000538809.2 |
| exon_skip_295224 | 17 | 80622371:80622432:80654264:80654729:80656330:80656530 | 80654264:80654729 | ENSG00000141542.6 | ENST00000269347.6 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RAB40B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_295195 | 17 | 80615852:80616010:80616366:80616438:80617455:80617533 | 80616366:80616438 | ENSG00000141542.6 | ENST00000538809.2 |
| exon_skip_295196 | 17 | 80615852:80616010:80616366:80616589:80617455:80617533 | 80616366:80616589 | ENSG00000141542.6 | ENST00000571995.1,ENST00000269347.6,ENST00000574132.1,ENST00000570676.1 |
| exon_skip_295201 | 17 | 80617455:80617533:80618862:80618923:80622371:80622432 | 80618862:80618923 | ENSG00000141542.6 | ENST00000571995.1,ENST00000269347.6,ENST00000570676.1,ENST00000538809.2 |
| exon_skip_295224 | 17 | 80622371:80622432:80654264:80654729:80656330:80656530 | 80654264:80654729 | ENSG00000141542.6 | ENST00000269347.6 |
| 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 RAB40B |
| 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 |
| ENST00000571995 | 80616366 | 80616589 | Frame-shift |
| ENST00000571995 | 80618862 | 80618923 | 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 |
| ENST00000571995 | 80616366 | 80616589 | Frame-shift |
| ENST00000571995 | 80618862 | 80618923 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for RAB40B |
| 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 |
| 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 |
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SNVs in the skipped exons for RAB40B |
| - 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_295201 | 80618863 | 80618923 | 80618870 | 80618870 | Frame_Shift_Del | C | - | p.G86fs |
| - 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 |
| MFE319_ENDOMETRIUM | 80616367 | 80616589 | 80616399 | 80616399 | Missense_Mutation | T | C | p.H178R |
| MFE319_ENDOMETRIUM | 80616367 | 80616438 | 80616399 | 80616399 | Missense_Mutation | T | C | p.H178R |
| CCFSTTG1_CENTRAL_NERVOUS_SYSTEM | 80616367 | 80616589 | 80616454 | 80616454 | Missense_Mutation | T | C | p.N160D |
| LAMA84_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 80616367 | 80616589 | 80616492 | 80616492 | Missense_Mutation | C | T | p.R147H |
| CALU3_LUNG | 80616367 | 80616589 | 80616494 | 80616494 | Missense_Mutation | C | G | p.E146D |
| SW684_SOFT_TISSUE | 80616367 | 80616589 | 80616498 | 80616498 | Missense_Mutation | G | A | p.A145V |
| NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 80616367 | 80616589 | 80616531 | 80616531 | Missense_Mutation | C | T | p.R134Q |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 80618863 | 80618923 | 80618885 | 80618885 | Missense_Mutation | C | T | p.R81H |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB40B |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB40B |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB40B |
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RelatedDrugs for RAB40B |
| 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 RAB40B |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RAB40B | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
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