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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 ARFGAP3 |
 Gene summary |
| Gene information | Gene symbol | ARFGAP3 | Gene ID | 26286 |
| Gene name | ADP ribosylation factor GTPase activating protein 3 | |
| Synonyms | ARFGAP1 | |
| Cytomap | 22q13.2 | |
| Type of gene | protein-coding | |
| Description | ADP-ribosylation factor GTPase-activating protein 3ADP-ribosylation factor GTPase activating protein 1ARF GAP 3 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9NP61 | |
| Context | PubMed: ARFGAP3 [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 ARFGAP3 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 ARFGAP3 |
| 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 ARFGAP3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_370144 | 22 | 43195044:43195166:43203078:43203169:43204772:43204896 | 43203078:43203169 | ENSG00000242247.6 | ENST00000437119.2,ENST00000263245.5,ENST00000429508.2 |
| exon_skip_370145 | 22 | 43203079:43203169:43204772:43204896:43206818:43206950 | 43204772:43204896 | ENSG00000242247.6 | ENST00000437119.2,ENST00000263245.5,ENST00000429508.2 |
| exon_skip_370147 | 22 | 43204772:43204896:43206818:43206950:43213147:43213270 | 43206818:43206950 | ENSG00000242247.6 | ENST00000437119.2,ENST00000263245.5,ENST00000429508.2 |
| exon_skip_370148 | 22 | 43213734:43213863:43218275:43218415:43219661:43219708 | 43218275:43218415 | ENSG00000242247.6 | ENST00000437119.2,ENST00000263245.5,ENST00000429508.2,ENST00000453516.1 |
| exon_skip_370149 | 22 | 43218275:43218415:43219661:43219708:43222945:43223005 | 43219661:43219708 | ENSG00000242247.6 | ENST00000437119.2,ENST00000263245.5,ENST00000429508.2,ENST00000453516.1 |
| exon_skip_370151 | 22 | 43219661:43219708:43222945:43223005:43227554:43227642 | 43222945:43223005 | ENSG00000242247.6 | ENST00000437119.2,ENST00000454099.1,ENST00000263245.5,ENST00000429508.2,ENST00000453516.1 |
| exon_skip_370156 | 22 | 43222945:43223005:43227554:43227642:43230247:43230331 | 43227554:43227642 | ENSG00000242247.6 | ENST00000437119.2,ENST00000263245.5 |
| exon_skip_370158 | 22 | 43227554:43227642:43230247:43230331:43236949:43237022 | 43230247:43230331 | ENSG00000242247.6 | ENST00000437119.2 |
| exon_skip_370159 | 22 | 43230247:43230331:43231367:43231499:43236949:43237022 | 43231367:43231499 | ENSG00000242247.6 | ENST00000263245.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for ARFGAP3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_370144 | 22 | 43195044:43195166:43203078:43203169:43204772:43204896 | 43203078:43203169 | ENSG00000242247.6 | ENST00000263245.5,ENST00000429508.2,ENST00000437119.2 |
| exon_skip_370145 | 22 | 43203079:43203169:43204772:43204896:43206818:43206950 | 43204772:43204896 | ENSG00000242247.6 | ENST00000263245.5,ENST00000429508.2,ENST00000437119.2 |
| exon_skip_370147 | 22 | 43204772:43204896:43206818:43206950:43213147:43213270 | 43206818:43206950 | ENSG00000242247.6 | ENST00000263245.5,ENST00000429508.2,ENST00000437119.2 |
| exon_skip_370148 | 22 | 43213734:43213863:43218275:43218415:43219661:43219708 | 43218275:43218415 | ENSG00000242247.6 | ENST00000263245.5,ENST00000429508.2,ENST00000437119.2,ENST00000453516.1 |
| exon_skip_370149 | 22 | 43218275:43218415:43219661:43219708:43222945:43223005 | 43219661:43219708 | ENSG00000242247.6 | ENST00000263245.5,ENST00000429508.2,ENST00000437119.2,ENST00000453516.1 |
| exon_skip_370151 | 22 | 43219661:43219708:43222945:43223005:43227554:43227642 | 43222945:43223005 | ENSG00000242247.6 | ENST00000263245.5,ENST00000429508.2,ENST00000437119.2,ENST00000453516.1,ENST00000454099.1 |
| exon_skip_370156 | 22 | 43222945:43223005:43227554:43227642:43230247:43230331 | 43227554:43227642 | ENSG00000242247.6 | ENST00000263245.5,ENST00000437119.2 |
| exon_skip_370158 | 22 | 43227554:43227642:43230247:43230331:43236949:43237022 | 43230247:43230331 | ENSG00000242247.6 | ENST00000437119.2 |
| exon_skip_370159 | 22 | 43230247:43230331:43231367:43231499:43236949:43237022 | 43231367:43231499 | ENSG00000242247.6 | ENST00000263245.5 |
| 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 ARFGAP3 |
| 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 |
| ENST00000263245 | 43203078 | 43203169 | Frame-shift |
| ENST00000263245 | 43204772 | 43204896 | Frame-shift |
| ENST00000263245 | 43218275 | 43218415 | Frame-shift |
| ENST00000263245 | 43219661 | 43219708 | Frame-shift |
| ENST00000263245 | 43227554 | 43227642 | Frame-shift |
| ENST00000263245 | 43206818 | 43206950 | In-frame |
| ENST00000263245 | 43222945 | 43223005 | In-frame |
| ENST00000263245 | 43231367 | 43231499 | 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 |
| ENST00000263245 | 43203078 | 43203169 | Frame-shift |
| ENST00000263245 | 43204772 | 43204896 | Frame-shift |
| ENST00000263245 | 43218275 | 43218415 | Frame-shift |
| ENST00000263245 | 43219661 | 43219708 | Frame-shift |
| ENST00000263245 | 43227554 | 43227642 | Frame-shift |
| ENST00000263245 | 43206818 | 43206950 | In-frame |
| ENST00000263245 | 43222945 | 43223005 | In-frame |
| ENST00000263245 | 43231367 | 43231499 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ARFGAP3 |
| 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 |
| ENST00000263245 | 2874 | 516 | 43231367 | 43231499 | 482 | 613 | 87 | 131 |
| ENST00000263245 | 2874 | 516 | 43222945 | 43223005 | 786 | 845 | 188 | 208 |
| ENST00000263245 | 2874 | 516 | 43206818 | 43206950 | 1285 | 1416 | 355 | 398 |
| 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 |
| ENST00000263245 | 2874 | 516 | 43231367 | 43231499 | 482 | 613 | 87 | 131 |
| ENST00000263245 | 2874 | 516 | 43222945 | 43223005 | 786 | 845 | 188 | 208 |
| ENST00000263245 | 2874 | 516 | 43206818 | 43206950 | 1285 | 1416 | 355 | 398 |
| 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 |
| Q9NP61 | 87 | 131 | 88 | 131 | Alternative sequence | ID=VSP_046888;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NP61 | 87 | 131 | 129 | 131 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 87 | 131 | 1 | 516 | Chain | ID=PRO_0000074193;Note=ADP-ribosylation factor GTPase-activating protein 3 |
| Q9NP61 | 87 | 131 | 10 | 126 | Domain | Note=Arf-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00288 |
| Q9NP61 | 87 | 131 | 84 | 94 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 87 | 131 | 101 | 104 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 87 | 131 | 108 | 126 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 188 | 208 | 1 | 516 | Chain | ID=PRO_0000074193;Note=ADP-ribosylation factor GTPase-activating protein 3 |
| Q9NP61 | 355 | 398 | 1 | 516 | Chain | ID=PRO_0000074193;Note=ADP-ribosylation factor GTPase-activating protein 3 |
| Q9NP61 | 355 | 398 | 348 | 377 | Compositional bias | Note=Ser-rich |
| Q9NP61 | 355 | 398 | 370 | 370 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19690332;Dbxref=PMID:19690332 |
| Q9NP61 | 355 | 398 | 355 | 355 | Natural variant | ID=VAR_013447;Note=S->R;Ontology_term=ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PubMed:15592455,ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:15461802,ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs1018448,PMID:15592455,PMID:147020 |
| Q9NP61 | 355 | 398 | 370 | 370 | Natural variant | ID=VAR_055524;Note=S->G;Dbxref=dbSNP:rs16986123 |
| 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 |
| Q9NP61 | 87 | 131 | 88 | 131 | Alternative sequence | ID=VSP_046888;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NP61 | 87 | 131 | 129 | 131 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 87 | 131 | 1 | 516 | Chain | ID=PRO_0000074193;Note=ADP-ribosylation factor GTPase-activating protein 3 |
| Q9NP61 | 87 | 131 | 10 | 126 | Domain | Note=Arf-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00288 |
| Q9NP61 | 87 | 131 | 84 | 94 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 87 | 131 | 101 | 104 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 87 | 131 | 108 | 126 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRW |
| Q9NP61 | 188 | 208 | 1 | 516 | Chain | ID=PRO_0000074193;Note=ADP-ribosylation factor GTPase-activating protein 3 |
| Q9NP61 | 355 | 398 | 1 | 516 | Chain | ID=PRO_0000074193;Note=ADP-ribosylation factor GTPase-activating protein 3 |
| Q9NP61 | 355 | 398 | 348 | 377 | Compositional bias | Note=Ser-rich |
| Q9NP61 | 355 | 398 | 370 | 370 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19690332;Dbxref=PMID:19690332 |
| Q9NP61 | 355 | 398 | 355 | 355 | Natural variant | ID=VAR_013447;Note=S->R;Ontology_term=ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PubMed:15592455,ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:15461802,ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs1018448,PMID:15592455,PMID:147020 |
| Q9NP61 | 355 | 398 | 370 | 370 | Natural variant | ID=VAR_055524;Note=S->G;Dbxref=dbSNP:rs16986123 |
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SNVs in the skipped exons for ARFGAP3 |
| - 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_370145 | 43204773 | 43204896 | 43204794 | 43204794 | Frame_Shift_Del | A | - | p.F433fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_370148 | 43218276 | 43218415 | 43218401 | 43218401 | Frame_Shift_Del | T | - | p.K229fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_370149 | 43219662 | 43219708 | 43219687 | 43219687 | Frame_Shift_Del | T | - | p.K217fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_370156 | 43227555 | 43227642 | 43227563 | 43227563 | Frame_Shift_Del | T | - | p.N187fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_370159 | 43231368 | 43231499 | 43231488 | 43231488 | Frame_Shift_Del | A | - | p.F91fs |
| UCEC | TCGA-BS-A0U8-01 | exon_skip_370148 | 43218276 | 43218415 | 43218346 | 43218347 | Frame_Shift_Ins | - | T | p.K247fs |
| BLCA | TCGA-DK-A3X1-01 | exon_skip_370158 | 43230248 | 43230331 | 43230283 | 43230283 | Nonsense_Mutation | C | A | p.E148* |
| STAD | TCGA-CG-5726-01 | exon_skip_370149 | 43219662 | 43219708 | 43219661 | 43219661 | Splice_Site | C | T | . |
| STAD | TCGA-CG-5726-01 | exon_skip_370149 | 43219662 | 43219708 | 43219661 | 43219661 | Splice_Site | C | T | p.G224_splice |
| BRCA | TCGA-BH-A0AZ-01 | exon_skip_370156 | 43227555 | 43227642 | 43227644 | 43227644 | Splice_Site | T | G | e6-2 |
| - 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 |
| HEC151_ENDOMETRIUM | 43206819 | 43206950 | 43206872 | 43206872 | Frame_Shift_Del | T | - | p.K381fs |
| CW2_LARGE_INTESTINE | 43219662 | 43219708 | 43219665 | 43219665 | Frame_Shift_Del | T | - | p.K223fs |
| T3M10_LUNG | 43218276 | 43218415 | 43218400 | 43218401 | Frame_Shift_Ins | - | T | p.G230fs |
| SNU1040_LARGE_INTESTINE | 43203079 | 43203169 | 43203135 | 43203135 | Missense_Mutation | G | A | p.A452V |
| SNU407_LARGE_INTESTINE | 43203079 | 43203169 | 43203138 | 43203138 | Missense_Mutation | G | A | p.S451L |
| KHYG_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43203079 | 43203169 | 43203150 | 43203150 | Missense_Mutation | A | G | p.L447P |
| SNU1040_LARGE_INTESTINE | 43203079 | 43203169 | 43203153 | 43203153 | Missense_Mutation | C | T | p.R446H |
| SNU81_LARGE_INTESTINE | 43204773 | 43204896 | 43204831 | 43204831 | Missense_Mutation | A | G | p.F421S |
| IGR39_SKIN | 43206819 | 43206950 | 43206828 | 43206828 | Missense_Mutation | T | C | p.Y396C |
| IGR37_SKIN | 43206819 | 43206950 | 43206828 | 43206828 | Missense_Mutation | T | C | p.Y396C |
| SNU308_BILIARY_TRACT | 43206819 | 43206950 | 43206858 | 43206858 | Missense_Mutation | T | C | p.D386G |
| VMCUB1_URINARY_TRACT | 43222946 | 43223005 | 43223002 | 43223002 | Missense_Mutation | C | T | p.G190E |
| KM12_LARGE_INTESTINE | 43231368 | 43231499 | 43231403 | 43231403 | Missense_Mutation | G | T | p.L120I |
| LU135_LUNG | 43231368 | 43231499 | 43231474 | 43231474 | Missense_Mutation | C | T | p.C96Y |
| NKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43231368 | 43231499 | 43231474 | 43231474 | Missense_Mutation | C | T | p.C96Y |
| BICR22_UPPER_AERODIGESTIVE_TRACT | 43206819 | 43206950 | 43206903 | 43206903 | Nonsense_Mutation | C | T | p.W371* |
| JHUEM7_ENDOMETRIUM | 43218276 | 43218415 | 43218283 | 43218283 | Nonsense_Mutation | C | A | p.E269* |
| LOVO_LARGE_INTESTINE | 43230248 | 43230331 | 43230330 | 43230330 | Splice_Site | A | C | p.L132R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARFGAP3 |
| 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 ARFGAP3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARFGAP3 |
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RelatedDrugs for ARFGAP3 |
| 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 ARFGAP3 |
| 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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