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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 ARFGEF1 |
 Gene summary |
| Gene information | Gene symbol | ARFGEF1 | Gene ID | 10565 |
| Gene name | ADP ribosylation factor guanine nucleotide exchange factor 1 | |
| Synonyms | ARFGEP1|BIG1|P200 | |
| Cytomap | 8q13.2 | |
| Type of gene | protein-coding | |
| Description | brefeldin A-inhibited guanine nucleotide-exchange protein 1ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)p200 ARF guanine nucleotide exchange factor | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y6D6 | |
| Context | PubMed: ARFGEF1 [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 |
| ARFGEF1 | GO:0034260 | negative regulation of GTPase activity | 15644318 |
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Exon skipping events across known transcript of Ensembl for ARFGEF1 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 ARFGEF1 |
| 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 ARFGEF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_490160 | 8 | 68123717:68123850:68128824:68128897:68130016:68130155 | 68128824:68128897 | ENSG00000066777.4 | ENST00000520381.1,ENST00000518230.1,ENST00000262215.3 |
| exon_skip_490163 | 8 | 68140458:68140499:68145089:68145180:68150577:68150728 | 68145089:68145180 | ENSG00000066777.4 | ENST00000520381.1,ENST00000518230.1,ENST00000262215.3 |
| exon_skip_490164 | 8 | 68145089:68145180:68150577:68150728:68150969:68151128 | 68150577:68150728 | ENSG00000066777.4 | ENST00000520381.1,ENST00000262215.3 |
| exon_skip_490166 | 8 | 68170319:68170525:68172049:68172161:68178240:68178442 | 68172049:68172161 | ENSG00000066777.4 | ENST00000520381.1,ENST00000262215.3 |
| exon_skip_490168 | 8 | 68188210:68188344:68189516:68189692:68200189:68200300 | 68189516:68189692 | ENSG00000066777.4 | ENST00000262215.3 |
| exon_skip_490169 | 8 | 68208665:68208845:68211443:68211590:68213458:68213615 | 68211443:68211590 | ENSG00000066777.4 | ENST00000262215.3 |
| exon_skip_490170 | 8 | 68213458:68213615:68214670:68214701:68255398:68255571 | 68214670:68214701 | ENSG00000066777.4 | ENST00000262215.3,ENST00000519436.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for ARFGEF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_490160 | 8 | 68123717:68123850:68128824:68128897:68130016:68130155 | 68128824:68128897 | ENSG00000066777.4 | ENST00000520381.1,ENST00000262215.3,ENST00000518230.1 |
| exon_skip_490163 | 8 | 68140458:68140499:68145089:68145180:68150577:68150728 | 68145089:68145180 | ENSG00000066777.4 | ENST00000520381.1,ENST00000262215.3,ENST00000518230.1 |
| exon_skip_490164 | 8 | 68145089:68145180:68150577:68150728:68150969:68151128 | 68150577:68150728 | ENSG00000066777.4 | ENST00000520381.1,ENST00000262215.3 |
| exon_skip_490166 | 8 | 68170319:68170525:68172049:68172161:68178240:68178442 | 68172049:68172161 | ENSG00000066777.4 | ENST00000520381.1,ENST00000262215.3 |
| exon_skip_490168 | 8 | 68188210:68188344:68189516:68189692:68200189:68200300 | 68189516:68189692 | ENSG00000066777.4 | ENST00000262215.3 |
| exon_skip_490169 | 8 | 68208665:68208845:68211443:68211590:68213458:68213615 | 68211443:68211590 | ENSG00000066777.4 | ENST00000262215.3 |
| exon_skip_490170 | 8 | 68213458:68213615:68214670:68214701:68255398:68255571 | 68214670:68214701 | ENSG00000066777.4 | ENST00000262215.3,ENST00000519436.1 |
| 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 ARFGEF1 |
| 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 |
| ENST00000262215 | 68128824 | 68128897 | Frame-shift |
| ENST00000262215 | 68145089 | 68145180 | Frame-shift |
| ENST00000262215 | 68150577 | 68150728 | Frame-shift |
| ENST00000262215 | 68172049 | 68172161 | Frame-shift |
| ENST00000262215 | 68189516 | 68189692 | Frame-shift |
| ENST00000262215 | 68214670 | 68214701 | Frame-shift |
| ENST00000262215 | 68211443 | 68211590 | 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 |
| ENST00000262215 | 68128824 | 68128897 | Frame-shift |
| ENST00000262215 | 68145089 | 68145180 | Frame-shift |
| ENST00000262215 | 68150577 | 68150728 | Frame-shift |
| ENST00000262215 | 68172049 | 68172161 | Frame-shift |
| ENST00000262215 | 68189516 | 68189692 | Frame-shift |
| ENST00000262215 | 68214670 | 68214701 | Frame-shift |
| ENST00000262215 | 68211443 | 68211590 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ARFGEF1 |
| 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 |
| ENST00000262215 | 7242 | 1849 | 68211443 | 68211590 | 703 | 849 | 104 | 153 |
| 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 |
| ENST00000262215 | 7242 | 1849 | 68211443 | 68211590 | 703 | 849 | 104 | 153 |
| 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 |
| Q9Y6D6 | 104 | 153 | 122 | 124 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5J5C |
| Q9Y6D6 | 104 | 153 | 1 | 1849 | Chain | ID=PRO_0000120207;Note=Brefeldin A-inhibited guanine nucleotide-exchange protein 1 |
| Q9Y6D6 | 104 | 153 | 93 | 108 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5EE5 |
| Q9Y6D6 | 104 | 153 | 126 | 135 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5EE5 |
| Q9Y6D6 | 104 | 153 | 145 | 160 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5EE5 |
| Q9Y6D6 | 104 | 153 | 2 | 224 | Region | Note=DCB%3B DCB:DCB domain and DCB:HUS domain interaction |
| 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 |
| Q9Y6D6 | 104 | 153 | 122 | 124 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5J5C |
| Q9Y6D6 | 104 | 153 | 1 | 1849 | Chain | ID=PRO_0000120207;Note=Brefeldin A-inhibited guanine nucleotide-exchange protein 1 |
| Q9Y6D6 | 104 | 153 | 93 | 108 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5EE5 |
| Q9Y6D6 | 104 | 153 | 126 | 135 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5EE5 |
| Q9Y6D6 | 104 | 153 | 145 | 160 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5EE5 |
| Q9Y6D6 | 104 | 153 | 2 | 224 | Region | Note=DCB%3B DCB:DCB domain and DCB:HUS domain interaction |
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SNVs in the skipped exons for ARFGEF1 |
| - 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 |
| COAD | TCGA-AZ-6598-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128856 | Frame_Shift_Del | G | - | p.P1552fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128856 | Frame_Shift_Del | G | - | p.P1554fs |
| STAD | TCGA-BR-8487-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128856 | Frame_Shift_Del | G | - | p.P1552fs |
| BLCA | TCGA-DK-A3WW-01 | exon_skip_490164 | 68150578 | 68150728 | 68150658 | 68150658 | Frame_Shift_Del | G | - | p.S1070fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_490166 | 68172050 | 68172161 | 68172101 | 68172101 | Frame_Shift_Del | G | - | p.T729fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_490168 | 68189517 | 68189692 | 68189668 | 68189668 | Frame_Shift_Del | T | - | p.N351fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_490169 | 68211444 | 68211590 | 68211528 | 68211528 | Frame_Shift_Del | T | - | p.K125fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_490170 | 68214671 | 68214701 | 68214691 | 68214691 | Frame_Shift_Del | T | - | p.K45fs |
| BRCA | TCGA-E9-A1NC-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1553fs |
| COAD | TCGA-CM-6674-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3308-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3346-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3363-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3365-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3372-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3374-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3378-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3380-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-A3-3382-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-AK-3465-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| KIRC | TCGA-AS-3778-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-35-3615-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-44-2655-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-44-2656-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-44-2659-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-44-2662-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-44-2665-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-44-2666-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-44-2668-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-64-1676-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-64-1678-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| LUAD | TCGA-67-3770-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-BR-7707-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-BR-8368-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-BR-8372-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-HU-A4G8-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-VQ-AA68-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| UCEC | TCGA-BG-A0M3-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| UCEC | TCGA-BG-A0M9-01 | exon_skip_490160 | 68128825 | 68128897 | 68128855 | 68128856 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-BR-7707-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128857 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-BR-8368-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128857 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-BR-8372-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128857 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-HU-A4G8-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128857 | Frame_Shift_Ins | - | G | p.P1552fs |
| STAD | TCGA-HU-A4GT-01 | exon_skip_490160 | 68128825 | 68128897 | 68128856 | 68128857 | Frame_Shift_Ins | - | G | p.P1552fs |
| SARC | TCGA-DX-A6B7-01 | exon_skip_490166 | 68172050 | 68172161 | 68172143 | 68172144 | Frame_Shift_Ins | - | TT | p.G716fs |
| SARC | TCGA-DX-A6B7-01 | exon_skip_490166 | 68172050 | 68172161 | 68172143 | 68172144 | Frame_Shift_Ins | - | TT | p.K714fs |
| BLCA | TCGA-XF-A9T5-01 | exon_skip_490163 | 68145090 | 68145180 | 68145142 | 68145142 | Nonsense_Mutation | G | A | p.Q1110* |
| - 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 |
| SNU175_LARGE_INTESTINE | 68128825 | 68128897 | 68128856 | 68128856 | Frame_Shift_Del | G | - | p.P1554fs |
| RKO_LARGE_INTESTINE | 68145090 | 68145180 | 68145151 | 68145154 | Frame_Shift_Del | CTAT | - | p.IA1106fs |
| EN_ENDOMETRIUM | 68211444 | 68211590 | 68211527 | 68211528 | Frame_Shift_Ins | - | T | p.L126fs |
| TGBC1TKB_BILIARY_TRACT | 68128825 | 68128897 | 68128869 | 68128869 | Missense_Mutation | C | T | p.E1548K |
| MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 68128825 | 68128897 | 68128883 | 68128883 | Missense_Mutation | C | T | p.R1543Q |
| GP2D_LARGE_INTESTINE | 68145090 | 68145180 | 68145121 | 68145121 | Missense_Mutation | T | C | p.S1117G |
| EMCBAC2_LUNG | 68150578 | 68150728 | 68150611 | 68150611 | Missense_Mutation | G | T | p.Q1086K |
| SNU719_STOMACH | 68172050 | 68172161 | 68172066 | 68172066 | Missense_Mutation | T | C | p.E740G |
| HEC108_ENDOMETRIUM | 68172050 | 68172161 | 68172134 | 68172134 | Missense_Mutation | T | C | p.I717M |
| CW2_LARGE_INTESTINE | 68189517 | 68189692 | 68189537 | 68189537 | Missense_Mutation | C | T | p.V395I |
| P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 68189517 | 68189692 | 68189647 | 68189647 | Missense_Mutation | A | C | p.I358S |
| ROS50_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 68189517 | 68189692 | 68189690 | 68189690 | Missense_Mutation | T | C | p.M344V |
| SNU81_LARGE_INTESTINE | 68211444 | 68211590 | 68211532 | 68211532 | Missense_Mutation | T | G | p.K124T |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 68211444 | 68211590 | 68211558 | 68211559 | Missense_Mutation | AT | CC | p.N115R |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 68211444 | 68211590 | 68211558 | 68211558 | Missense_Mutation | A | C | p.N115K |
| S117_SOFT_TISSUE | 68211444 | 68211590 | 68211558 | 68211558 | Missense_Mutation | A | C | p.N115K |
| S117_SOFT_TISSUE | 68211444 | 68211590 | 68211558 | 68211559 | Missense_Mutation | AT | CC | p.N115R |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 68211444 | 68211590 | 68211559 | 68211559 | Missense_Mutation | T | C | p.N115S |
| S117_SOFT_TISSUE | 68211444 | 68211590 | 68211559 | 68211559 | Missense_Mutation | T | C | p.N115S |
| DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 68128825 | 68128897 | 68128825 | 68128825 | Splice_Site | C | T | p.L1562L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARFGEF1 |
| 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 ARFGEF1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARFGEF1 |
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RelatedDrugs for ARFGEF1 |
| 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 ARFGEF1 |
| 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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