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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 OGFOD1 |
 Gene summary |
| Gene information | Gene symbol | OGFOD1 | Gene ID | 55239 |
| Gene name | 2-oxoglutarate and iron dependent oxygenase domain containing 1 | |
| Synonyms | TPA1 | |
| Cytomap | 16q13 | |
| Type of gene | protein-coding | |
| Description | prolyl 3-hydroxylase OGFOD12-oxoglutarate and iron-dependent oxygenase domain-containing protein 1TPA1, termination and polyadenylation 1, homologtermination and polyadenylation 1 homologuS12 prolyl 3-hydroxylase | |
| Modification date | 20180523 | |
| UniProtAcc | Q8N543 | |
| Context | PubMed: OGFOD1 [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 |
| OGFOD1 | GO:0018126 | protein hydroxylation | 24550447|24550462 |
| OGFOD1 | GO:0019511 | peptidyl-proline hydroxylation | 24550447 |
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Exon skipping events across known transcript of Ensembl for OGFOD1 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 OGFOD1 |
| 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 OGFOD1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_136624 | 16 | 56487174:56487320:56492459:56492506:56496445:56496540 | 56492459:56492506 | ENSG00000087263.12 | ENST00000561646.1,ENST00000568397.1,ENST00000562150.1,ENST00000566157.1 |
| exon_skip_136628 | 16 | 56492459:56492506:56496445:56496546:56500063:56500091 | 56496445:56496546 | ENSG00000087263.12 | ENST00000565209.1,ENST00000561646.1,ENST00000568397.1,ENST00000336111.5,ENST00000562150.1,ENST00000566157.1 |
| exon_skip_136629 | 16 | 56500063:56500180:56500787:56500879:56501076:56501110 | 56500787:56500879 | ENSG00000087263.12 | ENST00000561646.1,ENST00000336111.5,ENST00000566157.1 |
| exon_skip_136630 | 16 | 56500787:56500879:56501076:56501205:56501816:56501930 | 56501076:56501205 | ENSG00000087263.12 | ENST00000336111.5,ENST00000566157.1 |
| exon_skip_136632 | 16 | 56501076:56501205:56501816:56501930:56503914:56503994 | 56501816:56501930 | ENSG00000087263.12 | ENST00000336111.5,ENST00000566157.1 |
| exon_skip_136634 | 16 | 56501816:56501930:56503914:56503994:56504398:56504703 | 56503914:56503994 | ENSG00000087263.12 | ENST00000568397.1,ENST00000336111.5,ENST00000566157.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for OGFOD1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_136621 | 16 | 56487174:56487320:56488685:56488833:56496445:56496546 | 56488685:56488833 | ENSG00000087263.12 | ENST00000569802.1 |
| exon_skip_136622 | 16 | 56487174:56487320:56492424:56492506:56496445:56496540 | 56492424:56492506 | ENSG00000087263.12 | ENST00000565682.1 |
| exon_skip_136624 | 16 | 56487174:56487320:56492459:56492506:56496445:56496540 | 56492459:56492506 | ENSG00000087263.12 | ENST00000566157.1,ENST00000562150.1,ENST00000561646.1,ENST00000568397.1 |
| exon_skip_136625 | 16 | 56487174:56487320:56492459:56492506:56500063:56500091 | 56492459:56492506 | ENSG00000087263.12 | ENST00000568172.1 |
| exon_skip_136628 | 16 | 56492459:56492506:56496445:56496546:56500063:56500091 | 56496445:56496546 | ENSG00000087263.12 | ENST00000566157.1,ENST00000562150.1,ENST00000561646.1,ENST00000336111.5,ENST00000568397.1,ENST00000565209.1 |
| exon_skip_136629 | 16 | 56500063:56500180:56500787:56500879:56501076:56501110 | 56500787:56500879 | ENSG00000087263.12 | ENST00000566157.1,ENST00000561646.1,ENST00000336111.5 |
| exon_skip_136630 | 16 | 56500787:56500879:56501076:56501205:56501816:56501930 | 56501076:56501205 | ENSG00000087263.12 | ENST00000566157.1,ENST00000336111.5 |
| exon_skip_136632 | 16 | 56501076:56501205:56501816:56501930:56503914:56503994 | 56501816:56501930 | ENSG00000087263.12 | ENST00000566157.1,ENST00000336111.5 |
| exon_skip_136634 | 16 | 56501816:56501930:56503914:56503994:56504398:56504703 | 56503914:56503994 | ENSG00000087263.12 | ENST00000566157.1,ENST00000336111.5,ENST00000568397.1 |
| 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 OGFOD1 |
| 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 |
| ENST00000566157 | 56492459 | 56492506 | Frame-shift |
| ENST00000566157 | 56496445 | 56496546 | Frame-shift |
| ENST00000566157 | 56500787 | 56500879 | Frame-shift |
| ENST00000566157 | 56503914 | 56503994 | Frame-shift |
| ENST00000566157 | 56501076 | 56501205 | In-frame |
| ENST00000566157 | 56501816 | 56501930 | 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 |
| ENST00000566157 | 56492459 | 56492506 | Frame-shift |
| ENST00000566157 | 56496445 | 56496546 | Frame-shift |
| ENST00000566157 | 56500787 | 56500879 | Frame-shift |
| ENST00000566157 | 56503914 | 56503994 | Frame-shift |
| ENST00000566157 | 56501076 | 56501205 | In-frame |
| ENST00000566157 | 56501816 | 56501930 | In-frame |
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Infer the effects of exon skipping event on protein functional features for OGFOD1 |
| 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 |
| ENST00000566157 | 4664 | 542 | 56501076 | 56501205 | 781 | 909 | 219 | 262 |
| ENST00000566157 | 4664 | 542 | 56501816 | 56501930 | 910 | 1023 | 262 | 300 |
| 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 |
| ENST00000566157 | 4664 | 542 | 56501076 | 56501205 | 781 | 909 | 219 | 262 |
| ENST00000566157 | 4664 | 542 | 56501816 | 56501930 | 910 | 1023 | 262 | 300 |
| 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 |
| Q8N543 | 219 | 262 | 218 | 220 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 219 | 262 | 230 | 238 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 219 | 262 | 230 | 230 | Binding site | Note=2-oxoglutarate;Ontology_term=ECO:0000255,ECO:0000305;evidence=ECO:0000255|PROSITE-ProRule:PRU00805,ECO:0000305|PubMed:25728928;Dbxref=PMID:25728928 |
| Q8N543 | 219 | 262 | 1 | 542 | Chain | ID=PRO_0000288974;Note=Prolyl 3-hydroxylase OGFOD1 |
| Q8N543 | 219 | 262 | 134 | 239 | Domain | Note=Fe2OG dioxygenase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
| Q8N543 | 262 | 300 | 291 | 297 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 262 | 300 | 1 | 542 | Chain | ID=PRO_0000288974;Note=Prolyl 3-hydroxylase OGFOD1 |
| Q8N543 | 262 | 300 | 266 | 269 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 262 | 300 | 272 | 275 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 262 | 300 | 277 | 290 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| 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 |
| Q8N543 | 219 | 262 | 218 | 220 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 219 | 262 | 230 | 238 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 219 | 262 | 230 | 230 | Binding site | Note=2-oxoglutarate;Ontology_term=ECO:0000255,ECO:0000305;evidence=ECO:0000255|PROSITE-ProRule:PRU00805,ECO:0000305|PubMed:25728928;Dbxref=PMID:25728928 |
| Q8N543 | 219 | 262 | 1 | 542 | Chain | ID=PRO_0000288974;Note=Prolyl 3-hydroxylase OGFOD1 |
| Q8N543 | 219 | 262 | 134 | 239 | Domain | Note=Fe2OG dioxygenase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
| Q8N543 | 262 | 300 | 291 | 297 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 262 | 300 | 1 | 542 | Chain | ID=PRO_0000288974;Note=Prolyl 3-hydroxylase OGFOD1 |
| Q8N543 | 262 | 300 | 266 | 269 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 262 | 300 | 272 | 275 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
| Q8N543 | 262 | 300 | 277 | 290 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4NHX |
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SNVs in the skipped exons for OGFOD1 |
| - 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_136629 | 56500788 | 56500879 | 56500835 | 56500835 | Frame_Shift_Del | A | - | p.N205fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_136629 | 56500788 | 56500879 | 56500845 | 56500845 | Frame_Shift_Del | T | - | p.V208fs |
| STAD | TCGA-CG-4442-01 | exon_skip_136630 | 56501077 | 56501205 | 56501170 | 56501170 | Frame_Shift_Del | C | - | p.E250fs |
| THCA | TCGA-EL-A3MX-01 | exon_skip_136632 | 56501817 | 56501930 | 56501895 | 56501895 | Frame_Shift_Del | G | - | p.E289fs |
| LUSC | TCGA-18-3412-01 | exon_skip_136628 | 56496446 | 56496546 | 56496445 | 56496445 | Splice_Site | G | T | p.R116_splice |
| - 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 |
| GP2D_LARGE_INTESTINE | 56496446 | 56496546 | 56496540 | 56496540 | Missense_Mutation | T | A | p.F148I |
| GP5D_LARGE_INTESTINE | 56496446 | 56496546 | 56496540 | 56496540 | Missense_Mutation | T | A | p.F148I |
| HCC2998_LARGE_INTESTINE | 56500788 | 56500879 | 56500830 | 56500830 | Missense_Mutation | C | T | p.S203L |
| HCT15_LARGE_INTESTINE | 56501077 | 56501205 | 56501178 | 56501178 | Missense_Mutation | A | G | p.I253M |
| WM35_SKIN | 56501817 | 56501930 | 56501883 | 56501883 | Missense_Mutation | G | A | p.E285K |
| TMK1_STOMACH | 56501817 | 56501930 | 56501887 | 56501887 | Missense_Mutation | A | T | p.E286V |
| SNU324_PANCREAS | 56501817 | 56501930 | 56501918 | 56501918 | Missense_Mutation | G | T | p.K296N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for OGFOD1 |
| 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 OGFOD1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for OGFOD1 |
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RelatedDrugs for OGFOD1 |
| 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 |
| Q8N543 | DB00126 | Ascorbic acid | Prolyl 3-hydroxylase OGFOD1 | small molecule | approved|nutraceutical |
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RelatedDiseases for OGFOD1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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