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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for SF3B1 |
 Gene summary |
| Gene information | Gene symbol | SF3B1 | Gene ID | 23451 |
| Gene name | splicing factor 3b subunit 1 | |
| Synonyms | Hsh155|MDS|PRP10|PRPF10|SAP155|SF3b155 | |
| Cytomap | 2q33.1 | |
| Type of gene | protein-coding | |
| Description | splicing factor 3B subunit 1pre-mRNA processing 10pre-mRNA splicing factor SF3b, 155 kDa subunitspliceosome-associated protein 155splicing factor 3b, subunit 1, 155kDa | |
| Modification date | 20200329 | |
| UniProtAcc | A0A494C1M2, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SF3B1 | GO:0000398 | mRNA splicing, via spliceosome | 11252167|28781166|29360106 |
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Gene structures and expression levels for SF3B1 |
| 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. |
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ENSG00000115524
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000409915.8 | SF3B1-202:nonsense_mediated_decay:SF3B1 | 1.933295e+01 | 1.004027e+00 | 1.790240e-05 | 1.725548e-04 |
| CB | DOWN | ENST00000652738.1 | SF3B1-214:nonsense_mediated_decay:SF3B1 | 1.666149e+02 | -1.428788e+00 | 6.935709e-03 | 2.574838e-02 |
| CB | UP | ENST00000414963.2 | SF3B1-204:protein_coding:SF3B1 | 1.799738e+00 | 9.466854e-01 | 1.240378e-02 | 4.141192e-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 SF3B1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_120631 | chr2 | 197397985:197398116:197398461:197398581:197400055:197400166 | 197398461:197398581 |
| exon_skip_139826 | chr2 | 197392255:197392461:197392972:197393188:197396056:197396328 | 197392972:197393188 |
| exon_skip_178638 | chr2 | 197392255:197392461:197392972:197393186:197396056:197396328 | 197392972:197393186 |
| exon_skip_187375 | chr2 | 197396056:197396328:197397985:197398116:197398461:197398581 | 197397985:197398116 |
| exon_skip_206351 | chr2 | 197418509:197418588:197418896:197419640:197420428:197420542 | 197418896:197419640 |
| exon_skip_214756 | chr2 | 197405275:197405472:197407998:197408119:197408369:197408581 | 197407998:197408119 |
| exon_skip_230235 | chr2 | 197418509:197418588:197418896:197418951:197420428:197420542 | 197418896:197418951 |
| exon_skip_233506 | chr2 | 197408369:197408581:197409770:197410007:197416741:197416911 | 197409770:197410007 |
| exon_skip_244406 | chr2 | 197421029:197421133:197423894:197423974:197434972:197435016 | 197423894:197423974 |
| exon_skip_264584 | chr2 | 197421029:197421133:197423808:197423974:197434972:197435016 | 197423808:197423974 |
| 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 SF3B1 |
| 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 |
| ENST00000335508 | 197392972 | 197393188 | Frame-shift |
| ENST00000335508 | 197409770 | 197410007 | Frame-shift |
| ENST00000335508 | 197423808 | 197423974 | Frame-shift |
| ENST00000335508 | 197397985 | 197398116 | In-frame |
| 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 |
| ENST00000335508 | 197409770 | 197410007 | Frame-shift |
| ENST00000335508 | 197423808 | 197423974 | 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 |
| ENST00000335508 | 197392972 | 197393188 | Frame-shift |
| ENST00000335508 | 197398461 | 197398581 | Frame-shift |
| ENST00000335508 | 197407998 | 197408119 | Frame-shift |
| ENST00000335508 | 197409770 | 197410007 | Frame-shift |
| ENST00000335508 | 197423808 | 197423974 | Frame-shift |
| ENST00000335508 | 197397985 | 197398116 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SF3B1 |
p-ENSG00000115524_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 |
| ENST00000335508 | 6543 | 1304 | 197397985 | 197398116 | 3227 | 3357 | 1045 | 1088 |
| 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 |
| ENST00000335508 | 6543 | 1304 | 197397985 | 197398116 | 3227 | 3357 | 1045 | 1088 |
| 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 |
| O75533 | 1045 | 1088 | 145 | 1304 | Alternative sequence | ID=VSP_046183;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| O75533 | 1045 | 1088 | 1 | 1304 | Chain | ID=PRO_0000174323;Note=Splicing factor 3B subunit 1 |
| O75533 | 1045 | 1088 | 1029 | 1045 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1047 | 1049 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1052 | 1062 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1063 | 1067 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1071 | 1088 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1010 | 1048 | Repeat | Note=HEAT 8 |
| O75533 | 1045 | 1088 | 1052 | 1090 | Repeat | Note=HEAT 9 |
| O75533 | 1045 | 1088 | 1049 | 1049 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27720643;Dbxref=PMID:27720643 |
| 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 |
| O75533 | 1045 | 1088 | 145 | 1304 | Alternative sequence | ID=VSP_046183;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| O75533 | 1045 | 1088 | 1 | 1304 | Chain | ID=PRO_0000174323;Note=Splicing factor 3B subunit 1 |
| O75533 | 1045 | 1088 | 1029 | 1045 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1047 | 1049 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1052 | 1062 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1063 | 1067 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1071 | 1088 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IFE |
| O75533 | 1045 | 1088 | 1010 | 1048 | Repeat | Note=HEAT 8 |
| O75533 | 1045 | 1088 | 1052 | 1090 | Repeat | Note=HEAT 9 |
| O75533 | 1045 | 1088 | 1049 | 1049 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27720643;Dbxref=PMID:27720643 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SF3B1 |
| 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 SF3B1 |
| - 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 SF3B1 |
| 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 SF3B1 |
| 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 SF3B1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| DLPFC | RBM6 | exon_skip_127530 | 4.689636e-01 | 4.201004e-20 |
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RelatedDrugs for SF3B1 |
| 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 SF3B1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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