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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 SGMS1 |
Gene summary |
Gene information | Gene symbol | SGMS1 | Gene ID | 259230 |
Gene name | sphingomyelin synthase 1 | |
Synonyms | MOB|MOB1|SMS1|TMEM23|hmob33 | |
Cytomap | 10q11.23 | |
Type of gene | protein-coding | |
Description | phosphatidylcholine:ceramide cholinephosphotransferase 1medulla oblongata-derived proteinprotein Mobtransmembrane protein 23 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SGMS1 | GO:0006686 | sphingomyelin biosynthetic process | 14685263|14976195 |
SGMS1 | GO:0046513 | ceramide biosynthetic process | 25605874 |
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Gene structures and expression levels for SGMS1 |
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 |
TC | DOWN | ENST00000429490.5 | SGMS1-203:protein_coding:SGMS1 | 1.028103e+02 | -9.220474e-01 | 1.785984e-03 | 1.539124e-02 |
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 SGMS1 |
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_124051 | chr10 | 50327278:50327322:50343492:50344345:50433476:50433556 | 50343492:50344345 |
exon_skip_142609 | chr10 | 50305600:50307321:50307982:50308148:50311262:50311415 | 50307982:50308148 |
exon_skip_243983 | chr10 | 50311363:50311415:50327205:50327322:50340387:50340464 | 50327205:50327322 |
exon_skip_272683 | chr10 | 50466890:50466932:50519831:50519921:50590153:50590247 | 50519831:50519921 |
exon_skip_292033 | chr10 | 50311363:50311415:50327205:50327322:50343492:50344246 | 50327205:50327322 |
exon_skip_41201 | chr10 | 50344271:50344345:50433476:50433556:50460673:50460814 | 50433476:50433556 |
exon_skip_80443 | chr10 | 50311363:50311415:50327205:50327322:50343492:50343967 | 50327205:50327322 |
exon_skip_8327 | chr10 | 50311262:50311415:50327205:50327322:50343492:50344345 | 50327205:50327322 |
exon_skip_89709 | chr10 | 50460673:50460814:50466890:50466932:50519831:50519921 | 50466890:50466932 |
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 SGMS1 |
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 |
ENST00000361781 | 50433476 | 50433556 | 3UTR-3UTR |
ENST00000361781 | 50466890 | 50466932 | 3UTR-3UTR |
ENST00000361781 | 50327205 | 50327322 | Frame-shift |
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 |
ENST00000361781 | 50343492 | 50344345 | 3UTR-3CDS |
ENST00000361781 | 50466890 | 50466932 | 3UTR-3UTR |
ENST00000361781 | 50519831 | 50519921 | 3UTR-3UTR |
ENST00000361781 | 50327205 | 50327322 | Frame-shift |
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 |
ENST00000361781 | 50343492 | 50344345 | 3UTR-3CDS |
ENST00000361781 | 50433476 | 50433556 | 3UTR-3UTR |
ENST00000361781 | 50466890 | 50466932 | 3UTR-3UTR |
ENST00000361781 | 50307982 | 50308148 | Frame-shift |
ENST00000361781 | 50327205 | 50327322 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SGMS1 |
p-ENSG00000198964_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 SGMS1 |
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 |
Mayo | ENST00000361781 | 50433476 | 50433556 | hsa-miR-6878-5p | chr10:50433526-50433533 | 8mer-1a | chr10:50433512-50433533 | 167.00 | -20.57 |
Mayo | ENST00000361781 | 50433476 | 50433556 | hsa-miR-21-5p | chr10:50433513-50433520 | 8mer-1a | chr10:50433512-50433533 | 167.00 | -20.57 |
Mayo | ENST00000361781 | 50433476 | 50433556 | hsa-miR-590-5p | chr10:50433513-50433520 | 8mer-1a | chr10:50433512-50433533 | 167.00 | -20.57 |
Mayo | ENST00000361781 | 50466890 | 50466932 | hsa-miR-3978 | chr10:50466924-50466931 | 8mer-1a | chr10:50466906-50466931 | 148.00 | -12.56 |
MSBB | ENST00000361781 | 50466890 | 50466932 | hsa-miR-3978 | chr10:50466924-50466931 | 8mer-1a | chr10:50466906-50466931 | 148.00 | -12.56 |
ROSMAP | ENST00000361781 | 50433476 | 50433556 | hsa-miR-6878-5p | chr10:50433526-50433533 | 8mer-1a | chr10:50433512-50433533 | 167.00 | -20.57 |
ROSMAP | ENST00000361781 | 50433476 | 50433556 | hsa-miR-21-5p | chr10:50433513-50433520 | 8mer-1a | chr10:50433512-50433533 | 167.00 | -20.57 |
ROSMAP | ENST00000361781 | 50433476 | 50433556 | hsa-miR-590-5p | chr10:50433513-50433520 | 8mer-1a | chr10:50433512-50433533 | 167.00 | -20.57 |
ROSMAP | ENST00000361781 | 50466890 | 50466932 | hsa-miR-3978 | chr10:50466924-50466931 | 8mer-1a | chr10:50466906-50466931 | 148.00 | -12.56 |
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SNVs in the skipped exons for SGMS1 |
- 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 SGMS1 |
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 SGMS1 |
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 SGMS1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SGMS1 |
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 SGMS1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |