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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 OPHN1 |
 Gene summary |
| Gene information | Gene symbol | OPHN1 | Gene ID | 4983 |
| Gene name | oligophrenin 1 | |
| Synonyms | ARHGAP41|MRX60|OPN1 | |
| Cytomap | Xq12 | |
| Type of gene | protein-coding | |
| Description | oligophrenin-1mental retardation, X-linked 60oligophrenin-1, Rho-GTPase activating protein | |
| Modification date | 20180523 | |
| UniProtAcc | O60890 | |
| Context | PubMed: OPHN1 [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 OPHN1 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 OPHN1 |
| 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 OPHN1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_515375 | X | 67266503:67267005:67268257:67268299:67272381:67272432 | 67268257:67268299 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515376 | X | 67272381:67272432:67273486:67273652:67283695:67284019 | 67273486:67273652 | ENSG00000079482.11 | ENST00000355520.5 |
| exon_skip_515378 | X | 67272381:67272432:67273486:67273652:67292993:67293141 | 67273486:67273652 | ENSG00000079482.11 | ENST00000540071.1 |
| exon_skip_515381 | X | 67273486:67273652:67283695:67284019:67292993:67293141 | 67283695:67284019 | ENSG00000079482.11 | ENST00000355520.5 |
| exon_skip_515384 | X | 67273486:67273652:67292993:67293141:67316711:67316871 | 67292993:67293141 | ENSG00000079482.11 | ENST00000540071.1 |
| exon_skip_515385 | X | 67283695:67284019:67292993:67293141:67316711:67316871 | 67292993:67293141 | ENSG00000079482.11 | ENST00000355520.5,ENST00000484842.1 |
| exon_skip_515387 | X | 67292993:67293141:67316711:67316871:67331695:67331801 | 67316711:67316871 | ENSG00000079482.11 | ENST00000355520.5,ENST00000484842.1,ENST00000540071.1 |
| exon_skip_515388 | X | 67333022:67333081:67339089:67339174:67412760:67412835 | 67339089:67339174 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515389 | X | 67413731:67413794:67414306:67414340:67417027:67417106 | 67414306:67414340 | ENSG00000079482.11 | ENST00000467444.1,ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515390 | X | 67429994:67430124:67431949:67432054:67433703:67433814 | 67431949:67432054 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515391 | X | 67454328:67454430:67494579:67494651:67502897:67502959 | 67494579:67494651 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515392 | X | 67502897:67502959:67518842:67518938:67652708:67652866 | 67518842:67518938 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for OPHN1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_515375 | X | 67266503:67267005:67268257:67268299:67272381:67272432 | 67268257:67268299 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515376 | X | 67272381:67272432:67273486:67273652:67283695:67284019 | 67273486:67273652 | ENSG00000079482.11 | ENST00000355520.5 |
| exon_skip_515378 | X | 67272381:67272432:67273486:67273652:67292993:67293141 | 67273486:67273652 | ENSG00000079482.11 | ENST00000540071.1 |
| exon_skip_515381 | X | 67273486:67273652:67283695:67284019:67292993:67293141 | 67283695:67284019 | ENSG00000079482.11 | ENST00000355520.5 |
| exon_skip_515384 | X | 67273486:67273652:67292993:67293141:67316711:67316871 | 67292993:67293141 | ENSG00000079482.11 | ENST00000540071.1 |
| exon_skip_515385 | X | 67283695:67284019:67292993:67293141:67316711:67316871 | 67292993:67293141 | ENSG00000079482.11 | ENST00000355520.5,ENST00000484842.1 |
| exon_skip_515387 | X | 67292993:67293141:67316711:67316871:67331695:67331801 | 67316711:67316871 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1,ENST00000484842.1 |
| exon_skip_515388 | X | 67333022:67333081:67339089:67339174:67412760:67412835 | 67339089:67339174 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515389 | X | 67413731:67413794:67414306:67414340:67417027:67417106 | 67414306:67414340 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1,ENST00000467444.1 |
| exon_skip_515390 | X | 67429994:67430124:67431949:67432054:67433703:67433814 | 67431949:67432054 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515391 | X | 67454328:67454430:67494579:67494651:67502897:67502959 | 67494579:67494651 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| exon_skip_515392 | X | 67502897:67502959:67518842:67518938:67652708:67652866 | 67518842:67518938 | ENSG00000079482.11 | ENST00000355520.5,ENST00000540071.1 |
| 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 OPHN1 |
| 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 |
| ENST00000355520 | 67268257 | 67268299 | 5CDS-5UTR |
| ENST00000355520 | 67273486 | 67273652 | Frame-shift |
| ENST00000355520 | 67292993 | 67293141 | Frame-shift |
| ENST00000355520 | 67316711 | 67316871 | Frame-shift |
| ENST00000355520 | 67339089 | 67339174 | Frame-shift |
| ENST00000355520 | 67414306 | 67414340 | Frame-shift |
| ENST00000355520 | 67283695 | 67284019 | In-frame |
| ENST00000355520 | 67431949 | 67432054 | In-frame |
| ENST00000355520 | 67494579 | 67494651 | In-frame |
| ENST00000355520 | 67518842 | 67518938 | 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 |
| ENST00000355520 | 67268257 | 67268299 | 5CDS-5UTR |
| ENST00000355520 | 67273486 | 67273652 | Frame-shift |
| ENST00000355520 | 67292993 | 67293141 | Frame-shift |
| ENST00000355520 | 67316711 | 67316871 | Frame-shift |
| ENST00000355520 | 67339089 | 67339174 | Frame-shift |
| ENST00000355520 | 67414306 | 67414340 | Frame-shift |
| ENST00000355520 | 67283695 | 67284019 | In-frame |
| ENST00000355520 | 67431949 | 67432054 | In-frame |
| ENST00000355520 | 67494579 | 67494651 | In-frame |
| ENST00000355520 | 67518842 | 67518938 | In-frame |
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Infer the effects of exon skipping event on protein functional features for OPHN1 |
| 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 |
| ENST00000355520 | 7896 | 802 | 67518842 | 67518938 | 797 | 892 | 51 | 83 |
| ENST00000355520 | 7896 | 802 | 67494579 | 67494651 | 955 | 1026 | 104 | 128 |
| ENST00000355520 | 7896 | 802 | 67431949 | 67432054 | 1240 | 1344 | 199 | 234 |
| ENST00000355520 | 7896 | 802 | 67283695 | 67284019 | 2477 | 2800 | 611 | 719 |
| 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 |
| ENST00000355520 | 7896 | 802 | 67518842 | 67518938 | 797 | 892 | 51 | 83 |
| ENST00000355520 | 7896 | 802 | 67494579 | 67494651 | 955 | 1026 | 104 | 128 |
| ENST00000355520 | 7896 | 802 | 67431949 | 67432054 | 1240 | 1344 | 199 | 234 |
| ENST00000355520 | 7896 | 802 | 67283695 | 67284019 | 2477 | 2800 | 611 | 719 |
| 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 |
| O60890 | 51 | 83 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 104 | 128 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 199 | 234 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 199 | 234 | 199 | 199 | Natural variant | ID=VAR_066746;Note=In MRXSO. P->PEFSLLMNGLKIFIKCL;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21796728;Dbxref=PMID:21796728 |
| O60890 | 611 | 719 | 312 | 802 | Alternative sequence | ID=VSP_055337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O60890 | 611 | 719 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 611 | 719 | 629 | 761 | Compositional bias | Note=Pro-rich |
| O60890 | 611 | 719 | 693 | 693 | Natural variant | ID=VAR_033452;Note=M->I;Dbxref=dbSNP:rs36095561 |
| 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 |
| O60890 | 51 | 83 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 104 | 128 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 199 | 234 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 199 | 234 | 199 | 199 | Natural variant | ID=VAR_066746;Note=In MRXSO. P->PEFSLLMNGLKIFIKCL;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21796728;Dbxref=PMID:21796728 |
| O60890 | 611 | 719 | 312 | 802 | Alternative sequence | ID=VSP_055337;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O60890 | 611 | 719 | 1 | 802 | Chain | ID=PRO_0000056760;Note=Oligophrenin-1 |
| O60890 | 611 | 719 | 629 | 761 | Compositional bias | Note=Pro-rich |
| O60890 | 611 | 719 | 693 | 693 | Natural variant | ID=VAR_033452;Note=M->I;Dbxref=dbSNP:rs36095561 |
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SNVs in the skipped exons for OPHN1 |
| - 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 |
| LUAD | TCGA-55-1592-01 | exon_skip_515381 | 67283696 | 67284019 | 67283757 | 67283757 | Frame_Shift_Del | G | - | p.T699fs |
| LIHC | TCGA-DD-A3A1-01 | exon_skip_515388 | 67339090 | 67339174 | 67339146 | 67339146 | Frame_Shift_Del | A | - | p.F435fs |
| SKCM | TCGA-BF-AAP2-01 | exon_skip_515390 | 67431950 | 67432054 | 67432020 | 67432020 | Frame_Shift_Del | T | - | p.N211fs |
| STAD | TCGA-MX-A5UJ-01 | exon_skip_515381 | 67283696 | 67284019 | 67283963 | 67283964 | Frame_Shift_Ins | - | G | p.A631fs |
| STAD | TCGA-MX-A5UJ-01 | exon_skip_515381 | 67283696 | 67284019 | 67283963 | 67283964 | Frame_Shift_Ins | - | G | p.K631fs |
| COAD | TCGA-AA-3516-01 | exon_skip_515384 exon_skip_515385 | 67292994 | 67293141 | 67293049 | 67293050 | Frame_Shift_Ins | - | T | p.K593fs |
| BLCA | TCGA-CF-A47X-01 | exon_skip_515375 | 67268258 | 67268299 | 67268295 | 67268295 | Nonsense_Mutation | G | A | p.Q794* |
| LUAD | TCGA-17-Z045-01 | exon_skip_515381 | 67283696 | 67284019 | 67283822 | 67283822 | Nonsense_Mutation | G | A | p.Q678* |
| STAD | TCGA-BR-4292-01 | exon_skip_515384 exon_skip_515385 | 67292994 | 67293141 | 67293039 | 67293039 | Nonsense_Mutation | G | A | p.R597* |
| COAD | TCGA-A6-2678-01 | exon_skip_515384 exon_skip_515385 | 67292994 | 67293141 | 67293120 | 67293120 | Nonsense_Mutation | C | A | p.E570X |
| SKCM | TCGA-BF-A5ES-01 | exon_skip_515387 | 67316712 | 67316871 | 67316753 | 67316753 | Nonsense_Mutation | G | A | p.Q549* |
| BRCA | TCGA-AO-A03N-01 | exon_skip_515389 | 67414307 | 67414340 | 67414316 | 67414316 | Nonsense_Mutation | G | A | p.Q377* |
| - 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 | 67273487 | 67273652 | 67273588 | 67273589 | Frame_Shift_Ins | - | G | p.P741fs |
| SNU520_STOMACH | 67283696 | 67284019 | 67283840 | 67283841 | Frame_Shift_Ins | - | C | p.K672fs |
| HCC2450_LUNG | 67316712 | 67316871 | 67316778 | 67316779 | Frame_Shift_Ins | - | A | p.V540fs |
| MCC13_SKIN | 67273487 | 67273652 | 67273503 | 67273503 | Missense_Mutation | C | T | p.E770K |
| NCIH747_LARGE_INTESTINE | 67273487 | 67273652 | 67273503 | 67273503 | Missense_Mutation | C | T | p.E770K |
| HCC1569_BREAST | 67273487 | 67273652 | 67273566 | 67273566 | Missense_Mutation | A | G | p.C749R |
| UACC62_SKIN | 67273487 | 67273652 | 67273568 | 67273568 | Missense_Mutation | G | A | p.P748L |
| NCIH1930_LUNG | 67273487 | 67273652 | 67273592 | 67273592 | Missense_Mutation | G | A | p.P740L |
| LOVO_LARGE_INTESTINE | 67273487 | 67273652 | 67273596 | 67273596 | Missense_Mutation | G | A | p.R739C |
| NCIH1836_LUNG | 67283696 | 67284019 | 67283711 | 67283711 | Missense_Mutation | C | T | p.A715T |
| KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 67292994 | 67293141 | 67293099 | 67293099 | Missense_Mutation | G | A | p.P577S |
| SNUC4_LARGE_INTESTINE | 67316712 | 67316871 | 67316776 | 67316776 | Missense_Mutation | G | A | p.A541V |
| NCIH1693_LUNG | 67316712 | 67316871 | 67316824 | 67316824 | Missense_Mutation | C | G | p.G525A |
| NCIH1819_LUNG | 67316712 | 67316871 | 67316824 | 67316824 | Missense_Mutation | C | G | p.G525A |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 67431950 | 67432054 | 67431960 | 67431960 | Missense_Mutation | C | T | p.S231N |
| SNU1040_LARGE_INTESTINE | 67431950 | 67432054 | 67432048 | 67432048 | Missense_Mutation | C | T | p.A202T |
| D502MG_CENTRAL_NERVOUS_SYSTEM | 67283696 | 67284019 | 67284019 | 67284019 | Splice_Site | T | C | p.D612G |
| MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 67339090 | 67339174 | 67339090 | 67339090 | Splice_Site | C | A | p.R454M |
| NCIH2291_LUNG | 67518843 | 67518938 | 67518844 | 67518844 | Splice_Site | G | A | p.I83I |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for OPHN1 |
| 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 OPHN1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for OPHN1 |
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RelatedDrugs for OPHN1 |
| 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 OPHN1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| OPHN1 | C1136249 | Mental Retardation, X-Linked | 1 | CTD_human |
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