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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for SMAD4 |
Gene summary |
Gene information | Gene symbol | SMAD4 | Gene ID | 4089 |
Gene name | SMAD family member 4 | |
Synonyms | DPC4|JIP|MADH4|MYHRS | |
Cytomap | 18q21.2 | |
Type of gene | protein-coding | |
Description | mothers against decapentaplegic homolog 4MAD homolog 4SMAD, mothers against DPP homolog 4deleted in pancreatic carcinoma locus 4deletion target in pancreatic carcinoma 4mothers against decapentaplegic, Drosophila, homolog of, 4 | |
Modification date | 20200329 | |
UniProtAcc | A0A024R274, A0A087WUF3, | |
Context | - 28669622(Smad4 is essential for directional progression from committed neural progenitor cells through neuronal differentiation in the postnatal mouse brain) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SMAD4 | GO:0007179 | transforming growth factor beta receptor signaling pathway | 9389648|9732876 |
SMAD4 | GO:0007183 | SMAD protein complex assembly | 10823886 |
SMAD4 | GO:0030308 | negative regulation of cell growth | 8774881 |
SMAD4 | GO:0030509 | BMP signaling pathway | 9389648 |
SMAD4 | GO:0030511 | positive regulation of transforming growth factor beta receptor signaling pathway | 19328798 |
SMAD4 | GO:0045892 | negative regulation of transcription, DNA-templated | 8774881 |
SMAD4 | GO:0045893 | positive regulation of transcription, DNA-templated | 8774881|9311995|9389648|9707553|9732876 |
SMAD4 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 9389648|18832382 |
SMAD4 | GO:0060395 | SMAD protein signal transduction | 9707553|9732876 |
SMAD4 | GO:0071559 | response to transforming growth factor beta | 9707553 |
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Gene structures and expression levels for SMAD4 |
Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
CB | UP | ENST00000611848.1 | SMAD4-217:nonsense_mediated_decay:SMAD4 | 2.369201e+02 | 9.859647e-01 | 9.419525e-05 | 7.041582e-04 |
CB | UP | ENST00000588745.5 | SMAD4-205:protein_coding:SMAD4 | 1.227010e+01 | 2.371503e+00 | 6.512240e-04 | 3.602718e-03 |
CB | UP | ENST00000589941.1 | SMAD4-209:protein_coding:SMAD4 | 7.531776e+00 | 1.760482e+00 | 8.143386e-04 | 4.345191e-03 |
CB | UP | ENST00000592186.5 | SMAD4-214:nonsense_mediated_decay:SMAD4 | 2.003226e+01 | 2.726814e+00 | 8.853284e-04 | 4.661154e-03 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SMAD4 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_151851 | chr18 | 51076638:51076776:51077307:51077419:51078256:51078467 | 51077307:51077419 |
exon_skip_186557 | chr18 | 51065423:51065606:51067019:51067187:51076638:51076776 | 51067019:51067187 |
exon_skip_210769 | chr18 | 51059866:51059916:51065423:51065606:51067019:51067187 | 51065423:51065606 |
exon_skip_93878 | chr18 | 51076638:51076776:51077307:51077419:51078256:51078301 | 51077307:51077419 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for SMAD4 |
Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000342988 | 51065423 | 51065606 | Frame-shift |
ENST00000398417 | 51065423 | 51065606 | Frame-shift |
ENST00000342988 | 51067019 | 51067187 | Frame-shift |
ENST00000398417 | 51067019 | 51067187 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SMAD4 |
p-ENSG00000141646_img4.png |
Loci of skipped exons in ROSMAP 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 |
Loci of skipped exons in MSBB 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 |
Loci of skipped exons in Mayo 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 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
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 |
Lost protein functional features of individual exon skipping events in MSBB. |
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 |
Lost protein functional features of individual exon skipping events in Mayo. |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SMAD4 |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for SMAD4 |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- 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 |
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AD stage-associated exon skippint events for SMAD4 |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMAD4 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for SMAD4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | ZNF638 | exon_skip_151851 | -4.453854e-01 | 5.678094e-09 |
CB | RBM6 | exon_skip_151851 | -5.371707e-01 | 4.850135e-13 |
CB | TRA2A | exon_skip_151851 | -4.300621e-01 | 2.106096e-08 |
CB | RBM45 | exon_skip_151851 | 6.572339e-01 | 1.184556e-20 |
IFG | DAZAP1 | exon_skip_151851 | -4.338234e-01 | 2.108565e-02 |
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RelatedDrugs for SMAD4 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for SMAD4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |