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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 SMAD9 |
 Gene summary |
| Gene information | Gene symbol | SMAD9 | Gene ID | 4093 |
| Gene name | SMAD family member 9 | |
| Synonyms | MADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B | |
| Cytomap | 13q13.3 | |
| Type of gene | protein-coding | |
| Description | mothers against decapentaplegic homolog 9MAD homolog 9Mothers against decapentaplegic, drosophila, homolog of, 9SMAD, mothers against DPP homolog 9 | |
| Modification date | 20180519 | |
| UniProtAcc | O15198 | |
| Context | PubMed: SMAD9 [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 SMAD9 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 SMAD9 |
| 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 SMAD9 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_102933 | 13 | 37427555:37427812:37439673:37439895:37446794:37447052 | 37439673:37439895 | ENSG00000120693.9 | ENST00000350148.5 |
| exon_skip_102937 | 13 | 37439673:37439895:37441409:37441520:37446794:37447052 | 37441409:37441520 | ENSG00000120693.9 | ENST00000399275.2,ENST00000379826.4 |
| exon_skip_102941 | 13 | 37439673:37439895:37446794:37447052:37453414:37453966 | 37446794:37447052 | ENSG00000120693.9 | ENST00000350148.5 |
| exon_skip_102944 | 13 | 37441409:37441520:37446794:37447052:37453414:37453966 | 37446794:37447052 | ENSG00000120693.9 | ENST00000379826.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SMAD9 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_102933 | 13 | 37427555:37427812:37439673:37439895:37446794:37447052 | 37439673:37439895 | ENSG00000120693.9 | ENST00000350148.5 |
| exon_skip_102937 | 13 | 37439673:37439895:37441409:37441520:37446794:37447052 | 37441409:37441520 | ENSG00000120693.9 | ENST00000399275.2,ENST00000379826.4 |
| exon_skip_102941 | 13 | 37439673:37439895:37446794:37447052:37453414:37453966 | 37446794:37447052 | ENSG00000120693.9 | ENST00000350148.5 |
| exon_skip_102944 | 13 | 37441409:37441520:37446794:37447052:37453414:37453966 | 37446794:37447052 | ENSG00000120693.9 | ENST00000379826.4 |
| 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 SMAD9 |
| 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 |
| ENST00000379826 | 37441409 | 37441520 | In-frame |
| ENST00000399275 | 37441409 | 37441520 | In-frame |
| ENST00000379826 | 37446794 | 37447052 | 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 |
| ENST00000379826 | 37441409 | 37441520 | In-frame |
| ENST00000399275 | 37441409 | 37441520 | In-frame |
| ENST00000379826 | 37446794 | 37447052 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMAD9 |
| 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 |
| ENST00000379826 | 5609 | 467 | 37446794 | 37447052 | 756 | 1013 | 137 | 223 |
| ENST00000379826 | 5609 | 467 | 37441409 | 37441520 | 1014 | 1124 | 223 | 260 |
| ENST00000399275 | 5406 | 467 | 37441409 | 37441520 | 811 | 921 | 223 | 260 |
| 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 |
| ENST00000379826 | 5609 | 467 | 37446794 | 37447052 | 756 | 1013 | 137 | 223 |
| ENST00000379826 | 5609 | 467 | 37441409 | 37441520 | 1014 | 1124 | 223 | 260 |
| ENST00000399275 | 5406 | 467 | 37441409 | 37441520 | 811 | 921 | 223 | 260 |
| 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 |
| O15198 | 137 | 223 | 1 | 467 | Chain | ID=PRO_0000090875;Note=Mothers against decapentaplegic homolog 9 |
| O15198 | 137 | 223 | 16 | 140 | Domain | Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00438 |
| O15198 | 223 | 260 | 224 | 260 | Alternative sequence | ID=VSP_006182;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9205116;Dbxref=PMID:15489334,PMID:9205116 |
| O15198 | 223 | 260 | 224 | 260 | Alternative sequence | ID=VSP_006182;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9205116;Dbxref=PMID:15489334,PMID:9205116 |
| O15198 | 223 | 260 | 1 | 467 | Chain | ID=PRO_0000090875;Note=Mothers against decapentaplegic homolog 9 |
| O15198 | 223 | 260 | 1 | 467 | Chain | ID=PRO_0000090875;Note=Mothers against decapentaplegic homolog 9 |
| 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 |
| O15198 | 137 | 223 | 1 | 467 | Chain | ID=PRO_0000090875;Note=Mothers against decapentaplegic homolog 9 |
| O15198 | 137 | 223 | 16 | 140 | Domain | Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00438 |
| O15198 | 223 | 260 | 224 | 260 | Alternative sequence | ID=VSP_006182;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9205116;Dbxref=PMID:15489334,PMID:9205116 |
| O15198 | 223 | 260 | 224 | 260 | Alternative sequence | ID=VSP_006182;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9205116;Dbxref=PMID:15489334,PMID:9205116 |
| O15198 | 223 | 260 | 1 | 467 | Chain | ID=PRO_0000090875;Note=Mothers against decapentaplegic homolog 9 |
| O15198 | 223 | 260 | 1 | 467 | Chain | ID=PRO_0000090875;Note=Mothers against decapentaplegic homolog 9 |
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SNVs in the skipped exons for SMAD9 |
| - 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_102933 | 37439674 | 37439895 | 37439676 | 37439676 | Frame_Shift_Del | T | - | p.K334fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_102933 | 37439674 | 37439895 | 37439797 | 37439797 | Frame_Shift_Del | G | - | p.R294fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_102944 exon_skip_102941 | 37446795 | 37447052 | 37447008 | 37447008 | Frame_Shift_Del | G | - | p.Q153fs |
| BLCA | TCGA-GC-A3YS-01 | exon_skip_102933 | 37439674 | 37439895 | 37439763 | 37439763 | Nonsense_Mutation | G | C | p.S305* |
| STAD | TCGA-CG-5723-01 | exon_skip_102933 | 37439674 | 37439895 | 37439797 | 37439797 | Nonsense_Mutation | G | A | p.R294* |
| STAD | TCGA-CG-5723-01 | exon_skip_102933 | 37439674 | 37439895 | 37439797 | 37439797 | Nonsense_Mutation | G | A | p.R294X |
| HNSC | TCGA-CR-7380-01 | exon_skip_102933 | 37439674 | 37439895 | 37439827 | 37439827 | Nonsense_Mutation | G | A | p.R284* |
| - 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 |
| EFM19_BREAST | 37439674 | 37439895 | 37439685 | 37439685 | Frame_Shift_Del | T | - | p.H331fs |
| HEC108_ENDOMETRIUM | 37439674 | 37439895 | 37439688 | 37439688 | Missense_Mutation | C | T | p.R330K |
| JHUEM7_ENDOMETRIUM | 37439674 | 37439895 | 37439695 | 37439695 | Missense_Mutation | T | C | p.T328A |
| SW684_SOFT_TISSUE | 37439674 | 37439895 | 37439782 | 37439782 | Missense_Mutation | C | T | p.D299N |
| SNU324_PANCREAS | 37446795 | 37447052 | 37446811 | 37446811 | Missense_Mutation | A | T | p.S218R |
| MCC26_SKIN | 37446795 | 37447052 | 37446974 | 37446974 | Missense_Mutation | G | A | p.S164F |
| FADU_UPPER_AERODIGESTIVE_TRACT | 37446795 | 37447052 | 37447008 | 37447008 | Nonsense_Mutation | G | A | p.Q153* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMAD9 |
| 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 SMAD9 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMAD9 |
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RelatedDrugs for SMAD9 |
| 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 SMAD9 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SMAD9 | C3888002 | PULMONARY HYPERTENSION, PRIMARY, 2 | 1 | UNIPROT |
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