|
||||||
|
 | |
| |
| |
| |
| 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 RAB2A |
 Gene summary |
| Gene information | Gene symbol | RAB2A | Gene ID | 5862 |
| Gene name | RAB2A, member RAS oncogene family | |
| Synonyms | LHX|RAB2 | |
| Cytomap | 8q12.1-q12.2 | |
| Type of gene | protein-coding | |
| Description | ras-related protein Rab-2ARAB2, member RAS oncogene familysmall GTP binding protein RAB2A | |
| Modification date | 20180523 | |
| UniProtAcc | P61019 | |
| Context | PubMed: RAB2A [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 RAB2A 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 RAB2A |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for RAB2A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_483717 | 8 | 61429794:61429812:61471410:61471482:61484604:61484654 | 61471410:61471482 | ENSG00000104388.10 | ENST00000466595.1,ENST00000429861.1,ENST00000529579.1 |
| exon_skip_483720 | 8 | 61429794:61429812:61484604:61484672:61496766:61496849 | 61484604:61484672 | ENSG00000104388.10 | ENST00000531289.1 |
| exon_skip_483724 | 8 | 61471410:61471482:61482513:61482616:61484604:61484654 | 61482513:61482616 | ENSG00000104388.10 | ENST00000534260.1 |
| exon_skip_483725 | 8 | 61471410:61471482:61484604:61484672:61496766:61496849 | 61484604:61484672 | ENSG00000104388.10 | ENST00000429861.1,ENST00000262646.7,ENST00000529579.1 |
| exon_skip_483732 | 8 | 61484610:61484672:61488792:61488856:61496766:61496849 | 61488792:61488856 | ENSG00000104388.10 | ENST00000466595.1 |
| exon_skip_483735 | 8 | 61497281:61497374:61504416:61504528:61531138:61531207 | 61504416:61504528 | ENSG00000104388.10 | ENST00000466595.1,ENST00000530071.1,ENST00000531289.1,ENST00000262646.7,ENST00000452437.1 |
| exon_skip_483737 | 8 | 61504416:61504528:61531138:61531207:61533232:61533454 | 61531138:61531207 | ENSG00000104388.10 | ENST00000396696.1,ENST00000466595.1,ENST00000530071.1,ENST00000531289.1,ENST00000262646.7 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for RAB2A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_483717 | 8 | 61429794:61429812:61471410:61471482:61484604:61484654 | 61471410:61471482 | ENSG00000104388.10 | ENST00000529579.1,ENST00000466595.1,ENST00000429861.1 |
| exon_skip_483720 | 8 | 61429794:61429812:61484604:61484672:61496766:61496849 | 61484604:61484672 | ENSG00000104388.10 | ENST00000531289.1 |
| exon_skip_483724 | 8 | 61471410:61471482:61482513:61482616:61484604:61484654 | 61482513:61482616 | ENSG00000104388.10 | ENST00000534260.1 |
| exon_skip_483725 | 8 | 61471410:61471482:61484604:61484672:61496766:61496849 | 61484604:61484672 | ENSG00000104388.10 | ENST00000262646.7,ENST00000529579.1,ENST00000429861.1 |
| exon_skip_483732 | 8 | 61484610:61484672:61488792:61488856:61496766:61496849 | 61488792:61488856 | ENSG00000104388.10 | ENST00000466595.1 |
| exon_skip_483735 | 8 | 61497281:61497374:61504416:61504528:61531138:61531207 | 61504416:61504528 | ENSG00000104388.10 | ENST00000262646.7,ENST00000531289.1,ENST00000466595.1,ENST00000530071.1,ENST00000452437.1 |
| exon_skip_483737 | 8 | 61504416:61504528:61531138:61531207:61533232:61533454 | 61531138:61531207 | ENSG00000104388.10 | ENST00000262646.7,ENST00000531289.1,ENST00000466595.1,ENST00000530071.1,ENST00000396696.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for RAB2A |
| 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 |
| ENST00000262646 | 61484604 | 61484672 | Frame-shift |
| ENST00000262646 | 61504416 | 61504528 | Frame-shift |
| ENST00000262646 | 61531138 | 61531207 | 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 |
| ENST00000262646 | 61484604 | 61484672 | Frame-shift |
| ENST00000262646 | 61504416 | 61504528 | Frame-shift |
| ENST00000262646 | 61531138 | 61531207 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for RAB2A |
| 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 |
| ENST00000262646 | 3865 | 212 | 61531138 | 61531207 | 826 | 894 | 158 | 181 |
| 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 |
| ENST00000262646 | 3865 | 212 | 61531138 | 61531207 | 826 | 894 | 158 | 181 |
| 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 |
| P61019 | 158 | 181 | 2 | 212 | Chain | ID=PRO_0000121066;Note=Ras-related protein Rab-2A |
| P61019 | 158 | 181 | 156 | 169 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Z0A |
| 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 |
| P61019 | 158 | 181 | 2 | 212 | Chain | ID=PRO_0000121066;Note=Ras-related protein Rab-2A |
| P61019 | 158 | 181 | 156 | 169 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Z0A |
Top |
SNVs in the skipped exons for RAB2A |
| - 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 |
| BRCA | TCGA-BH-A0DD-01 | exon_skip_483737 | 61531139 | 61531207 | 61531179 | 61531179 | Frame_Shift_Del | A | - | p.E173fs |
| STAD | TCGA-D7-A4YV-01 | exon_skip_483735 | 61504417 | 61504528 | 61504440 | 61504441 | Frame_Shift_Ins | - | A | p.V129fs |
| STAD | TCGA-D7-A4YV-01 | exon_skip_483735 | 61504417 | 61504528 | 61504441 | 61504442 | Frame_Shift_Ins | - | A | p.V129fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_483735 | 61504417 | 61504528 | 61504461 | 61504462 | Frame_Shift_Ins | - | T | p.V136fs |
| BLCA | TCGA-ZF-A9RL-01 | exon_skip_483735 | 61504417 | 61504528 | 61504457 | 61504457 | Nonsense_Mutation | G | T | p.E135* |
| ESCA | TCGA-L5-A8NW-01 | exon_skip_483735 | 61504417 | 61504528 | 61504469 | 61504469 | Nonsense_Mutation | C | T | p.R139* |
| - 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 |
| SNU1040_LARGE_INTESTINE | 61484605 | 61484672 | 61484609 | 61484610 | Frame_Shift_Del | AG | - | p.E42fs |
| EN_ENDOMETRIUM | 61504417 | 61504528 | 61504440 | 61504441 | Frame_Shift_Ins | - | A | p.VK129fs |
| HTCC3_THYROID | 61504417 | 61504528 | 61504526 | 61504526 | Missense_Mutation | G | A | p.E158K |
| DMS114_LUNG | 61531139 | 61531207 | 61531149 | 61531149 | Missense_Mutation | A | G | p.N162S |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 61531139 | 61531207 | 61531176 | 61531176 | Missense_Mutation | T | A | p.I171N |
| SKGT2_STOMACH | 61471411 | 61471482 | 61471481 | 61471481 | Splice_Site | T | A | p.I39I |
| RERFLCFM_LUNG | 61484605 | 61484672 | 61484605 | 61484605 | Splice_Site | G | C | p.G40A |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB2A |
| 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 RAB2A |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB2A |
Top |
RelatedDrugs for RAB2A |
| 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 RAB2A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RAB2A | C0032460 | Polycystic Ovary Syndrome | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|