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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 RAPGEF1 |
 Gene summary |
| Gene information | Gene symbol | RAPGEF1 | Gene ID | 2889 |
| Gene name | Rap guanine nucleotide exchange factor 1 | |
| Synonyms | C3G|GRF2 | |
| Cytomap | 9q34.13 | |
| Type of gene | protein-coding | |
| Description | rap guanine nucleotide exchange factor 1CRK SH3-binding GNRPRap guanine nucleotide exchange factor (GEF) 1guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene) | |
| Modification date | 20180522 | |
| UniProtAcc | Q13905 | |
| Context | PubMed: RAPGEF1 [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 |
| RAPGEF1 | GO:0038180 | nerve growth factor signaling pathway | 17724123 |
| RAPGEF1 | GO:0043547 | positive regulation of GTPase activity | 10548487 |
| RAPGEF1 | GO:0071320 | cellular response to cAMP | 21840392 |
| RAPGEF1 | GO:1990090 | cellular response to nerve growth factor stimulus | 17724123 |
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Exon skipping events across known transcript of Ensembl for RAPGEF1 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 RAPGEF1 |
| 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 RAPGEF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_507783 | 9 | 134473585:134473697:134477447:134477536:134497182:134497225 | 134477447:134477536 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3 |
| exon_skip_507787 | 9 | 134477500:134477536:134479347:134479440:134497182:134497225 | 134479347:134479440 | ENSG00000107263.14 | ENST00000414781.1 |
| exon_skip_507788 | 9 | 134477500:134477536:134480317:134480575:134494437:134494593 | 134480317:134480575 | ENSG00000107263.14 | ENST00000419442.1 |
| exon_skip_507800 | 9 | 134480317:134480575:134494437:134494596:134497182:134497225 | 134494437:134494596 | ENSG00000107263.14 | ENST00000419442.1 |
| exon_skip_507805 | 9 | 134504488:134504641:134505622:134505711:134514021:134514173 | 134505622:134505711 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3 |
| exon_skip_507809 | 9 | 134504488:134504641:134514021:134514178:134518625:134518778 | 134514021:134514178 | ENSG00000107263.14 | ENST00000481260.1 |
| exon_skip_507812 | 9 | 134505622:134505711:134514021:134514178:134518625:134518778 | 134514021:134514178 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3 |
| exon_skip_507814 | 9 | 134514095:134514178:134518625:134518804:134525515:134525629 | 134518625:134518804 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3,ENST00000427994.1 |
| exon_skip_507815 | 9 | 134514095:134514178:134518625:134518804:134526196:134526336 | 134518625:134518804 | ENSG00000107263.14 | ENST00000438647.1 |
| exon_skip_507819 | 9 | 134518625:134518804:134525515:134525629:134526196:134526336 | 134525515:134525629 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3,ENST00000427994.1 |
| exon_skip_507825 | 9 | 134518625:134518804:134526196:134526336:134615156:134615331 | 134526196:134526336 | ENSG00000107263.14 | ENST00000438647.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RAPGEF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_507783 | 9 | 134473585:134473697:134477447:134477536:134497182:134497225 | 134477447:134477536 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3 |
| exon_skip_507787 | 9 | 134477500:134477536:134479347:134479440:134497182:134497225 | 134479347:134479440 | ENSG00000107263.14 | ENST00000414781.1 |
| exon_skip_507788 | 9 | 134477500:134477536:134480317:134480575:134494437:134494593 | 134480317:134480575 | ENSG00000107263.14 | ENST00000419442.1 |
| exon_skip_507800 | 9 | 134480317:134480575:134494437:134494596:134497182:134497225 | 134494437:134494596 | ENSG00000107263.14 | ENST00000419442.1 |
| exon_skip_507805 | 9 | 134504488:134504641:134505622:134505711:134514021:134514173 | 134505622:134505711 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3 |
| exon_skip_507809 | 9 | 134504488:134504641:134514021:134514178:134518625:134518778 | 134514021:134514178 | ENSG00000107263.14 | ENST00000481260.1 |
| exon_skip_507812 | 9 | 134505622:134505711:134514021:134514178:134518625:134518778 | 134514021:134514178 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3 |
| exon_skip_507814 | 9 | 134514095:134514178:134518625:134518804:134525515:134525629 | 134518625:134518804 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3,ENST00000427994.1 |
| exon_skip_507815 | 9 | 134514095:134514178:134518625:134518804:134526196:134526336 | 134518625:134518804 | ENSG00000107263.14 | ENST00000438647.1 |
| exon_skip_507819 | 9 | 134518625:134518804:134525515:134525629:134526196:134526336 | 134525515:134525629 | ENSG00000107263.14 | ENST00000372189.3,ENST00000372195.1,ENST00000372190.3,ENST00000427994.1 |
| exon_skip_507825 | 9 | 134518625:134518804:134526196:134526336:134615156:134615331 | 134526196:134526336 | ENSG00000107263.14 | ENST00000438647.1 |
| 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 RAPGEF1 |
| 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 |
| ENST00000372189 | 134477447 | 134477536 | Frame-shift |
| ENST00000372189 | 134505622 | 134505711 | Frame-shift |
| ENST00000372189 | 134514021 | 134514178 | Frame-shift |
| ENST00000372189 | 134518625 | 134518804 | Frame-shift |
| ENST00000372189 | 134525515 | 134525629 | 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 |
| ENST00000372189 | 134477447 | 134477536 | Frame-shift |
| ENST00000372189 | 134505622 | 134505711 | Frame-shift |
| ENST00000372189 | 134514021 | 134514178 | Frame-shift |
| ENST00000372189 | 134518625 | 134518804 | Frame-shift |
| ENST00000372189 | 134525515 | 134525629 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RAPGEF1 |
| 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 |
| ENST00000372189 | 6102 | 1077 | 134525515 | 134525629 | 275 | 388 | 50 | 88 |
| 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 |
| ENST00000372189 | 6102 | 1077 | 134525515 | 134525629 | 275 | 388 | 50 | 88 |
| 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 |
| Q13905 | 50 | 88 | 50 | 88 | Alternative sequence | ID=VSP_001822;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q13905 | 50 | 88 | 1 | 1077 | Chain | ID=PRO_0000068864;Note=Rap guanine nucleotide exchange factor 1 |
| 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 |
| Q13905 | 50 | 88 | 50 | 88 | Alternative sequence | ID=VSP_001822;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q13905 | 50 | 88 | 1 | 1077 | Chain | ID=PRO_0000068864;Note=Rap guanine nucleotide exchange factor 1 |
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SNVs in the skipped exons for RAPGEF1 |
| - 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-G3-A3CJ-01 | exon_skip_507815 exon_skip_507814 | 134518626 | 134518804 | 134518711 | 134518711 | Frame_Shift_Del | C | - | p.V137fs |
| UCEC | TCGA-BG-A0VZ-01 | exon_skip_507809 exon_skip_507812 | 134514022 | 134514178 | 134514084 | 134514084 | Nonsense_Mutation | C | A | p.E198* |
| KIRP | TCGA-GL-A59T-01 | exon_skip_507805 | 134505623 | 134505711 | 134505712 | 134505712 | Splice_Site | C | T | . |
| KIRP | TCGA-GL-A59T-01 | exon_skip_507805 | 134505623 | 134505711 | 134505712 | 134505712 | Splice_Site | C | T | p.E219_splice |
| UCEC | TCGA-D1-A103-01 | exon_skip_507809 exon_skip_507812 | 134514022 | 134514178 | 134514179 | 134514179 | Splice_Site | C | A | e5-1 |
| - 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 |
| OC316_OVARY | 134477448 | 134477536 | 134477458 | 134477458 | Missense_Mutation | C | T | p.G645S |
| OC314_OVARY | 134477448 | 134477536 | 134477458 | 134477458 | Missense_Mutation | C | T | p.G645S |
| HUG1N_STOMACH | 134477448 | 134477536 | 134477503 | 134477503 | Missense_Mutation | C | T | p.D630N |
| PK59_PANCREAS | 134477448 | 134477536 | 134477503 | 134477503 | Missense_Mutation | C | T | p.D630N |
| RERFLCMS_LUNG | 134477448 | 134477536 | 134477503 | 134477503 | Missense_Mutation | C | T | p.D630N |
| LC41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 134477448 | 134477536 | 134477503 | 134477503 | Missense_Mutation | C | T | p.D630N |
| LK2_LUNG | 134477448 | 134477536 | 134477503 | 134477503 | Missense_Mutation | C | T | p.D630N |
| CHLA06ATRT_SOFT_TISSUE | 134477448 | 134477536 | 134477529 | 134477529 | Missense_Mutation | G | A | p.P621L |
| HEC1A_ENDOMETRIUM | 134477448 | 134477536 | 134477529 | 134477529 | Missense_Mutation | G | A | p.P621L |
| HEC1_ENDOMETRIUM | 134477448 | 134477536 | 134477529 | 134477529 | Missense_Mutation | G | A | p.P621L |
| HEC1B_ENDOMETRIUM | 134477448 | 134477536 | 134477529 | 134477529 | Missense_Mutation | G | A | p.P621L |
| SNU349_KIDNEY | 134505623 | 134505711 | 134505630 | 134505630 | Missense_Mutation | G | A | p.P228S |
| HCC2998_LARGE_INTESTINE | 134518626 | 134518804 | 134518638 | 134518638 | Missense_Mutation | C | T | p.R144Q |
| HARA_LUNG | 134518626 | 134518804 | 134518725 | 134518725 | Missense_Mutation | G | T | p.A115E |
| MDAMB435S_SKIN | 134518626 | 134518804 | 134518773 | 134518773 | Missense_Mutation | T | G | p.E99A |
| LS411N_LARGE_INTESTINE | 134518626 | 134518804 | 134518788 | 134518788 | Missense_Mutation | T | C | p.E94G |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 134518626 | 134518804 | 134518798 | 134518798 | Missense_Mutation | T | A | p.S91C |
| AU565_BREAST | 134525516 | 134525629 | 134525590 | 134525590 | Missense_Mutation | G | A | p.P64S |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 134525516 | 134525629 | 134525593 | 134525593 | Missense_Mutation | G | T | p.L63I |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 134525516 | 134525629 | 134525593 | 134525593 | Missense_Mutation | G | T | p.L63I |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 134525516 | 134525629 | 134525593 | 134525593 | Missense_Mutation | G | T | p.L63I |
| OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 134525516 | 134525629 | 134525593 | 134525593 | Missense_Mutation | G | T | p.L63I |
| S117_SOFT_TISSUE | 134525516 | 134525629 | 134525593 | 134525593 | Missense_Mutation | G | T | p.L63I |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 134525516 | 134525629 | 134525622 | 134525622 | Missense_Mutation | G | C | p.T53R |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 134525516 | 134525629 | 134525622 | 134525622 | Missense_Mutation | G | C | p.T53R |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 134525516 | 134525629 | 134525622 | 134525622 | Missense_Mutation | G | C | p.T53R |
| TM87_SOFT_TISSUE | 134526197 | 134526336 | 134526199 | 134526199 | Missense_Mutation | T | C | p.K50E |
| NCIH660_PROSTATE | 134526197 | 134526336 | 134526328 | 134526328 | Missense_Mutation | G | A | p.R7C |
| SW837_LARGE_INTESTINE | 134526197 | 134526336 | 134526333 | 134526333 | Missense_Mutation | G | A | p.S5F |
| KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 134525516 | 134525629 | 134525516 | 134525516 | Splice_Site | C | T | p.K88K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAPGEF1 |
| 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 RAPGEF1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAPGEF1 |
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RelatedDrugs for RAPGEF1 |
| 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 RAPGEF1 |
| 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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