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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 RAB4A |
 Gene summary |
| Gene information | Gene symbol | RAB4A | Gene ID | 5867 |
| Gene name | RAB4A, member RAS oncogene family | |
| Synonyms | HRES-1|HRES-1/RAB4|HRES1|RAB4 | |
| Cytomap | 1q42.13 | |
| Type of gene | protein-coding | |
| Description | ras-related protein Rab-4AHTLV-1 related endogenous sequence | |
| Modification date | 20180523 | |
| UniProtAcc | P20338 | |
| Context | PubMed: RAB4A [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 RAB4A 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 RAB4A |
| 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 RAB4A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_19175 | 1 | 229406940:229407117:229422232:229422313:229424475:229424590 | 229422232:229422313 | ENSG00000168118.7 | ENST00000366690.4 |
| exon_skip_19182 | 1 | 229406940:229407117:229431594:229431657:229433228:229433383 | 229431594:229431657 | ENSG00000168118.7 | ENST00000473894.1 |
| exon_skip_19184 | 1 | 229422232:229422313:229424475:229424590:229431594:229431657 | 229424475:229424590 | ENSG00000168118.7 | ENST00000366690.4 |
| exon_skip_19187 | 1 | 229424475:229424590:229431594:229431657:229433228:229433383 | 229431594:229431657 | ENSG00000168118.7 | ENST00000366690.4 |
| exon_skip_19191 | 1 | 229434723:229434819:229438608:229438736:229439552:229439641 | 229438608:229438736 | ENSG00000168118.7 | ENST00000473894.1,ENST00000366690.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RAB4A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_19175 | 1 | 229406940:229407117:229422232:229422313:229424475:229424590 | 229422232:229422313 | ENSG00000168118.7 | ENST00000366690.4 |
| exon_skip_19182 | 1 | 229406940:229407117:229431594:229431657:229433228:229433383 | 229431594:229431657 | ENSG00000168118.7 | ENST00000473894.1 |
| exon_skip_19184 | 1 | 229422232:229422313:229424475:229424590:229431594:229431657 | 229424475:229424590 | ENSG00000168118.7 | ENST00000366690.4 |
| exon_skip_19187 | 1 | 229424475:229424590:229431594:229431657:229433228:229433383 | 229431594:229431657 | ENSG00000168118.7 | ENST00000366690.4 |
| exon_skip_19191 | 1 | 229434723:229434819:229438608:229438736:229439552:229439641 | 229438608:229438736 | ENSG00000168118.7 | ENST00000366690.4,ENST00000473894.1 |
| 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 RAB4A |
| 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 |
| ENST00000366690 | 229438608 | 229438736 | 3UTR-3CDS |
| ENST00000366690 | 229424475 | 229424590 | Frame-shift |
| ENST00000366690 | 229422232 | 229422313 | In-frame |
| ENST00000366690 | 229431594 | 229431657 | 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 |
| ENST00000366690 | 229438608 | 229438736 | 3UTR-3CDS |
| ENST00000366690 | 229424475 | 229424590 | Frame-shift |
| ENST00000366690 | 229422232 | 229422313 | In-frame |
| ENST00000366690 | 229431594 | 229431657 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RAB4A |
| 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 |
| ENST00000366690 | 2983 | 218 | 229422232 | 229422313 | 240 | 320 | 10 | 37 |
| ENST00000366690 | 2983 | 218 | 229431594 | 229431657 | 436 | 498 | 76 | 96 |
| 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 |
| ENST00000366690 | 2983 | 218 | 229422232 | 229422313 | 240 | 320 | 10 | 37 |
| ENST00000366690 | 2983 | 218 | 229431594 | 229431657 | 436 | 498 | 76 | 96 |
| 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 |
| P20338 | 10 | 37 | 11 | 21 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
| P20338 | 10 | 37 | 1 | 218 | Chain | ID=PRO_0000121093;Note=Ras-related protein Rab-4A |
| P20338 | 10 | 37 | 26 | 35 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
| P20338 | 10 | 37 | 20 | 28 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16034420;Dbxref=PMID:16034420 |
| P20338 | 76 | 96 | 87 | 94 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
| P20338 | 76 | 96 | 1 | 218 | Chain | ID=PRO_0000121093;Note=Ras-related protein Rab-4A |
| P20338 | 76 | 96 | 76 | 80 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
| 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 |
| P20338 | 10 | 37 | 11 | 21 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
| P20338 | 10 | 37 | 1 | 218 | Chain | ID=PRO_0000121093;Note=Ras-related protein Rab-4A |
| P20338 | 10 | 37 | 26 | 35 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
| P20338 | 10 | 37 | 20 | 28 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16034420;Dbxref=PMID:16034420 |
| P20338 | 76 | 96 | 87 | 94 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
| P20338 | 76 | 96 | 1 | 218 | Chain | ID=PRO_0000121093;Note=Ras-related protein Rab-4A |
| P20338 | 76 | 96 | 76 | 80 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2BME |
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SNVs in the skipped exons for RAB4A |
| - 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 |
| CESC | TCGA-EA-A3HU-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.K37fs |
| KIRC | TCGA-B2-3924-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.E35fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.E35fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.E35fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.E35fs |
| UCEC | TCGA-AP-A0LF-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.E35fs |
| UCEC | TCGA-B5-A11O-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.E35fs |
| UCEC | TCGA-D1-A17L-01 | exon_skip_19175 | 229422233 | 229422313 | 229422305 | 229422305 | Frame_Shift_Del | A | - | p.E35fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_19184 | 229424476 | 229424590 | 229424489 | 229424489 | Frame_Shift_Del | A | - | p.S42fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_19184 | 229424476 | 229424590 | 229424557 | 229424557 | Frame_Shift_Del | A | - | p.Q65fs |
| COAD | TCGA-G4-6628-01 | exon_skip_19175 | 229422233 | 229422313 | 229422304 | 229422305 | Frame_Shift_Ins | - | A | p.E35fs |
| - 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 |
| MFE296_ENDOMETRIUM | 229422233 | 229422313 | 229422304 | 229422305 | Frame_Shift_Ins | - | A | p.E35fs |
| CW2_LARGE_INTESTINE | 229422233 | 229422313 | 229422304 | 229422305 | Frame_Shift_Ins | - | A | p.E35fs |
| HEC251_ENDOMETRIUM | 229422233 | 229422313 | 229422299 | 229422299 | Missense_Mutation | T | G | p.F33C |
| HCC2998_LARGE_INTESTINE | 229424476 | 229424590 | 229424558 | 229424558 | Missense_Mutation | A | C | p.Q65H |
| 22RV1_PROSTATE | 229431595 | 229431657 | 229431629 | 229431629 | Missense_Mutation | G | A | p.G88R |
| SKUT1_SOFT_TISSUE | 229431595 | 229431657 | 229431641 | 229431641 | Missense_Mutation | G | A | p.V92I |
| JHH5_LIVER | 229438609 | 229438736 | 229438619 | 229438619 | Missense_Mutation | C | G | p.D184E |
| TOV21G_OVARY | 229438609 | 229438736 | 229438686 | 229438686 | Missense_Mutation | C | T | p.R207C |
| SNU245_BILIARY_TRACT | 229438609 | 229438736 | 229438704 | 229438704 | Missense_Mutation | G | A | p.A213T |
| SNU475_LIVER | 229438609 | 229438736 | 229438704 | 229438704 | Missense_Mutation | G | A | p.A213T |
| LC41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 229438609 | 229438736 | 229438704 | 229438704 | Missense_Mutation | G | A | p.A213T |
| LU65_LUNG | 229438609 | 229438736 | 229438704 | 229438704 | Missense_Mutation | G | A | p.A213T |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB4A |
| 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 RAB4A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB4A |
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RelatedDrugs for RAB4A |
| 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 RAB4A |
| 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)
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