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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 IRF6 |
 Gene summary |
| Gene information | Gene symbol | IRF6 | Gene ID | 3664 |
| Gene name | interferon regulatory factor 6 | |
| Synonyms | LPS|OFC6|PIT|PPS|PPS1|VWS|VWS1 | |
| Cytomap | 1q32.2 | |
| Type of gene | protein-coding | |
| Description | interferon regulatory factor 6 | |
| Modification date | 20180519 | |
| UniProtAcc | O14896 | |
| Context | PubMed: IRF6 [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 |
| IRF6 | GO:0007050 | cell cycle arrest | 18212048 |
| IRF6 | GO:0008285 | negative regulation of cell proliferation | 18212048 |
| IRF6 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 21807998 |
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Exon skipping events across known transcript of Ensembl for IRF6 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 IRF6 |
| 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 IRF6 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_36741 | 1 | 209961696:209961989:209963011:209963130:209963839:209964232 | 209963011:209963130 | ENSG00000117595.6 | ENST00000542854.1,ENST00000367021.3 |
| exon_skip_36744 | 1 | 209963011:209963130:209963839:209964232:209965613:209965772 | 209963839:209964232 | ENSG00000117595.6 | ENST00000542854.1,ENST00000367021.3 |
| exon_skip_36751 | 1 | 209968634:209968763:209969692:209969897:209974584:209974761 | 209969692:209969897 | ENSG00000117595.6 | ENST00000367021.3,ENST00000456314.1 |
| exon_skip_36752 | 1 | 209968634:209968763:209969692:209969897:209979291:209979389 | 209969692:209969897 | ENSG00000117595.6 | ENST00000542854.1 |
| exon_skip_36754 | 1 | 209969692:209969897:209974584:209974761:209975316:209975388 | 209974584:209974761 | ENSG00000117595.6 | ENST00000367021.3,ENST00000456314.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for IRF6 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_36741 | 1 | 209961696:209961989:209963011:209963130:209963839:209964232 | 209963011:209963130 | ENSG00000117595.6 | ENST00000367021.3,ENST00000542854.1 |
| exon_skip_36744 | 1 | 209963011:209963130:209963839:209964232:209965613:209965772 | 209963839:209964232 | ENSG00000117595.6 | ENST00000367021.3,ENST00000542854.1 |
| exon_skip_36751 | 1 | 209968634:209968763:209969692:209969897:209974584:209974761 | 209969692:209969897 | ENSG00000117595.6 | ENST00000367021.3,ENST00000456314.1 |
| exon_skip_36754 | 1 | 209969692:209969897:209974584:209974761:209975316:209975388 | 209974584:209974761 | ENSG00000117595.6 | ENST00000367021.3,ENST00000456314.1 |
| 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 IRF6 |
| 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 |
| ENST00000367021 | 209974584 | 209974761 | 3UTR-3CDS |
| ENST00000367021 | 209963011 | 209963130 | Frame-shift |
| ENST00000367021 | 209969692 | 209969897 | Frame-shift |
| ENST00000367021 | 209963839 | 209964232 | 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 |
| ENST00000367021 | 209974584 | 209974761 | 3UTR-3CDS |
| ENST00000367021 | 209963011 | 209963130 | Frame-shift |
| ENST00000367021 | 209969692 | 209969897 | Frame-shift |
| ENST00000367021 | 209963839 | 209964232 | In-frame |
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Infer the effects of exon skipping event on protein functional features for IRF6 |
| 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 |
| ENST00000367021 | 4323 | 467 | 209963839 | 209964232 | 841 | 1233 | 222 | 353 |
| 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 |
| ENST00000367021 | 4323 | 467 | 209963839 | 209964232 | 841 | 1233 | 222 | 353 |
| 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 |
| O14896 | 222 | 353 | 1 | 467 | Chain | ID=PRO_0000154560;Note=Interferon regulatory factor 6 |
| O14896 | 222 | 353 | 250 | 250 | Natural variant | ID=VAR_014977;Note=In VWS1. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 251 | 251 | Natural variant | ID=VAR_030053;Note=In VWS1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14640121;Dbxref=PMID:14640121 |
| O14896 | 222 | 353 | 273 | 273 | Natural variant | ID=VAR_014978;Note=In VWS1. Q->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 274 | 274 | Natural variant | ID=VAR_014979;Note=Common polymorphism%3B 3%25 in European-descended and 22%25 in Asian populations%3B responsible for 12%25 of the genetic contribution to cleft lip or palate%3B tripled the risk of recurrence in families that already had 1 affected child |
| O14896 | 222 | 353 | 290 | 296 | Natural variant | ID=VAR_014980;Note=In VWS1. FTSKLLD->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 294 | 294 | Natural variant | ID=VAR_014981;Note=In VWS1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 297 | 297 | Natural variant | ID=VAR_014982;Note=In VWS1. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 320 | 320 | Natural variant | ID=VAR_014983;Note=In VWS1. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 321 | 321 | Natural variant | ID=VAR_014984;Note=In VWS1. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 325 | 325 | Natural variant | ID=VAR_014985;Note=In VWS1. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 339 | 339 | Natural variant | ID=VAR_059080;Note=In VWS1. R->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18478600;Dbxref=dbSNP:rs121434231,PMID:18478600 |
| O14896 | 222 | 353 | 345 | 345 | Natural variant | ID=VAR_014986;Note=In VWS1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 347 | 347 | Natural variant | ID=VAR_014987;Note=In VWS1. C->F;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 349 | 349 | Natural variant | ID=VAR_030054;Note=In VWS1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17122170;Dbxref=PMID:17122170 |
| 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 |
| O14896 | 222 | 353 | 1 | 467 | Chain | ID=PRO_0000154560;Note=Interferon regulatory factor 6 |
| O14896 | 222 | 353 | 250 | 250 | Natural variant | ID=VAR_014977;Note=In VWS1. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 251 | 251 | Natural variant | ID=VAR_030053;Note=In VWS1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14640121;Dbxref=PMID:14640121 |
| O14896 | 222 | 353 | 273 | 273 | Natural variant | ID=VAR_014978;Note=In VWS1. Q->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 274 | 274 | Natural variant | ID=VAR_014979;Note=Common polymorphism%3B 3%25 in European-descended and 22%25 in Asian populations%3B responsible for 12%25 of the genetic contribution to cleft lip or palate%3B tripled the risk of recurrence in families that already had 1 affected child |
| O14896 | 222 | 353 | 290 | 296 | Natural variant | ID=VAR_014980;Note=In VWS1. FTSKLLD->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 294 | 294 | Natural variant | ID=VAR_014981;Note=In VWS1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 297 | 297 | Natural variant | ID=VAR_014982;Note=In VWS1. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 320 | 320 | Natural variant | ID=VAR_014983;Note=In VWS1. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 321 | 321 | Natural variant | ID=VAR_014984;Note=In VWS1. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 325 | 325 | Natural variant | ID=VAR_014985;Note=In VWS1. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 339 | 339 | Natural variant | ID=VAR_059080;Note=In VWS1. R->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18478600;Dbxref=dbSNP:rs121434231,PMID:18478600 |
| O14896 | 222 | 353 | 345 | 345 | Natural variant | ID=VAR_014986;Note=In VWS1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 347 | 347 | Natural variant | ID=VAR_014987;Note=In VWS1. C->F;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12219090;Dbxref=PMID:12219090 |
| O14896 | 222 | 353 | 349 | 349 | Natural variant | ID=VAR_030054;Note=In VWS1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17122170;Dbxref=PMID:17122170 |
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SNVs in the skipped exons for IRF6 |
| - 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. |
IRF6_LUSC_exon_skip_36744_psi_boxplot.png |
| - 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 |
| PRAD | TCGA-ZG-A9KY-01 | exon_skip_36744 | 209963840 | 209964232 | 209963883 | 209963890 | Frame_Shift_Del | TCTCTCAA | - | p.IER337fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_36751 exon_skip_36752 | 209969693 | 209969897 | 209969861 | 209969861 | Frame_Shift_Del | C | - | p.V71fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_36754 | 209974585 | 209974761 | 209974598 | 209974598 | Frame_Shift_Del | T | - | p.N54fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_36754 | 209974585 | 209974761 | 209974602 | 209974602 | Frame_Shift_Del | C | - | p.E53fs |
| UCEC | TCGA-BS-A0TA-01 | exon_skip_36751 exon_skip_36752 | 209969693 | 209969897 | 209969860 | 209969861 | Frame_Shift_Ins | - | C | p.V71fs |
| STAD | TCGA-CG-5723-01 | exon_skip_36741 | 209963012 | 209963130 | 209963054 | 209963054 | Nonsense_Mutation | C | T | p.W379* |
| STAD | TCGA-CG-5723-01 | exon_skip_36741 | 209963012 | 209963130 | 209963054 | 209963054 | Nonsense_Mutation | C | T | p.W379X |
| ESCA | TCGA-R6-A6Y2-01 | exon_skip_36741 | 209963012 | 209963130 | 209963069 | 209963069 | Nonsense_Mutation | G | T | p.C374* |
| SKCM | TCGA-EE-A2GT-06 | exon_skip_36744 | 209963840 | 209964232 | 209964116 | 209964116 | Nonsense_Mutation | G | A | p.Q167X |
| HNSC | TCGA-CV-A45U-01 | exon_skip_36744 | 209963840 | 209964232 | 209964161 | 209964161 | Nonsense_Mutation | G | A | p.Q247* |
| LUSC | TCGA-60-2710-01 | exon_skip_36744 | 209963840 | 209964232 | 209964185 | 209964185 | Nonsense_Mutation | G | A | p.Q239* |
| LUSC | TCGA-22-1002-01 | exon_skip_36751 exon_skip_36752 | 209969693 | 209969897 | 209969720 | 209969720 | Nonsense_Mutation | G | A | p.Q118* |
| COAD | TCGA-A6-6141-01 | exon_skip_36751 exon_skip_36752 | 209969693 | 209969897 | 209969798 | 209969798 | Nonsense_Mutation | C | A | p.E92X |
| SARC | TCGA-N1-A6IA-01 | exon_skip_36751 exon_skip_36752 | 209969693 | 209969897 | 209969876 | 209969876 | Nonsense_Mutation | T | A | p.K66* |
| UCEC | TCGA-B5-A11E-01 | exon_skip_36751 exon_skip_36752 | 209969693 | 209969897 | 209969892 | 209969892 | Nonsense_Mutation | C | T | p.W60* |
| LUAD | TCGA-38-4631-01 | exon_skip_36754 | 209974585 | 209974761 | 209974728 | 209974728 | Nonsense_Mutation | T | A | p.K11* |
| HNSC | TCGA-CV-6938-01 | exon_skip_36751 exon_skip_36752 | 209969693 | 209969897 | 209969692 | 209969692 | Splice_Site | C | G | p.G127_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-60-2710-01 |
| Cancer type: LUSC | |
| ESID: exon_skip_36744 | |
| Skipped exon start: 209963840 | |
| Skipped exon end: 209964232 | |
| Mutation start: 209964185 | |
| Mutation end: 209964185 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.Q239* | |
exon_skip_36744_LUSC_TCGA-60-2710-01.png | |
| - 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 |
| HEC59_ENDOMETRIUM | 209974585 | 209974761 | 209974588 | 209974588 | Frame_Shift_Del | A | - | p.F57fs |
| LS180_LARGE_INTESTINE | 209974585 | 209974761 | 209974588 | 209974588 | Frame_Shift_Del | A | - | p.F57fs |
| HCT116_LARGE_INTESTINE | 209963012 | 209963130 | 209963080 | 209963080 | Missense_Mutation | T | C | p.I371V |
| TUHR4TKB_KIDNEY | 209963840 | 209964232 | 209963857 | 209963857 | Missense_Mutation | A | G | p.L348P |
| HCT15_LARGE_INTESTINE | 209963840 | 209964232 | 209963877 | 209963877 | Missense_Mutation | C | A | p.K341N |
| YKG1_CENTRAL_NERVOUS_SYSTEM | 209963840 | 209964232 | 209963927 | 209963927 | Missense_Mutation | C | T | p.G325R |
| EPLC272H_LUNG | 209963840 | 209964232 | 209963978 | 209963978 | Missense_Mutation | C | A | p.G308C |
| SNU349_KIDNEY | 209963840 | 209964232 | 209963996 | 209963996 | Missense_Mutation | G | T | p.L302M |
| BT483_BREAST | 209963840 | 209964232 | 209964039 | 209964039 | Missense_Mutation | C | A | p.Q287H |
| DL40_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 209969693 | 209969897 | 209969707 | 209969707 | Missense_Mutation | G | A | p.S122L |
| SF172_CENTRAL_NERVOUS_SYSTEM | 209969693 | 209969897 | 209969711 | 209969711 | Missense_Mutation | C | A | p.G121C |
| SNU520_STOMACH | 209969693 | 209969897 | 209969725 | 209969725 | Missense_Mutation | A | G | p.I116T |
| 8505C_THYROID | 209969693 | 209969897 | 209969755 | 209969755 | Missense_Mutation | T | C | p.N106S |
| HUO3N1_BONE | 209969693 | 209969897 | 209969759 | 209969759 | Missense_Mutation | T | C | p.M105V |
| SBC1_LUNG | 209969693 | 209969897 | 209969759 | 209969759 | Missense_Mutation | T | C | p.M105V |
| HEC251_ENDOMETRIUM | 209969693 | 209969897 | 209969821 | 209969821 | Missense_Mutation | C | T | p.R84H |
| CW2_LARGE_INTESTINE | 209969693 | 209969897 | 209969861 | 209969861 | Missense_Mutation | C | T | p.V71M |
| NCIH2009_LUNG | 209969693 | 209969897 | 209969869 | 209969869 | Missense_Mutation | T | A | p.Q68L |
| CW2_LARGE_INTESTINE | 209974585 | 209974761 | 209974596 | 209974596 | Missense_Mutation | T | C | p.T55A |
| SNU738_CENTRAL_NERVOUS_SYSTEM | 209974585 | 209974761 | 209974626 | 209974626 | Missense_Mutation | G | A | p.R45W |
| EN_ENDOMETRIUM | 209974585 | 209974761 | 209974673 | 209974673 | Missense_Mutation | A | G | p.L29P |
| MFE319_ENDOMETRIUM | 209963012 | 209963130 | 209963054 | 209963054 | Nonsense_Mutation | C | T | p.W379* |
| HEC265_ENDOMETRIUM | 209963840 | 209964232 | 209964204 | 209964204 | Nonsense_Mutation | G | C | p.Y232* |
| HEC251_ENDOMETRIUM | 209969693 | 209969897 | 209969798 | 209969798 | Nonsense_Mutation | C | A | p.E92* |
| OVK18_OVARY | 209969693 | 209969897 | 209969834 | 209969834 | Nonsense_Mutation | T | A | p.K80* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for IRF6 |
| 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 IRF6 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for IRF6 |
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RelatedDrugs for IRF6 |
| 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 IRF6 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| IRF6 | C0175697 | Van der Woude syndrome | 12 | CTD_human;ORPHANET;UNIPROT |
| IRF6 | C0008924 | Cleft Lip | 3 | CTD_human;HPO;ORPHANET |
| IRF6 | C0265259 | Popliteal pterygium syndrome | 3 | CTD_human;ORPHANET;UNIPROT |
| IRF6 | C0008925 | Cleft Palate | 1 | CTD_human;HPO |
| IRF6 | C0037268 | Skin Abnormalities | 1 | CTD_human |
| IRF6 | C0206762 | Limb Deformities, Congenital | 1 | CTD_human |
| IRF6 | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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