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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 RBFOX3 |
Gene summary |
Gene information | Gene symbol | RBFOX3 | Gene ID | 146713 |
Gene name | RNA binding fox-1 homolog 3 | |
Synonyms | FOX-3|FOX3|HRNBP3|NEUN | |
Cytomap | 17q25.3 | |
Type of gene | protein-coding | |
Description | RNA binding protein fox-1 homolog 3RNA binding protein, fox-1 homolog 3fox-1 homolog Chexaribonucleotide binding protein 3neuN antigenneuronal nuclei antigen | |
Modification date | 20200313 | |
UniProtAcc | ||
Context | - 30475774(Rbfox3/NeuN Regulates Alternative Splicing of Tau Exon 10) |
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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Gene structures and expression levels for RBFOX3 |
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 |
STG | UP | ENST00000578887.1 | RBFOX3-201:lncRNA:RBFOX3 | 3.469364e+01 | 8.163405e-01 | 8.212540e-05 | 9.858054e-03 |
STG | UP | ENST00000582880.6 | RBFOX3-209:protein_coding:RBFOX3 | 1.049104e+01 | 8.156414e-01 | 8.679082e-05 | 1.007868e-02 |
CB | UP | ENST00000580508.1 | RBFOX3-204:protein_coding:RBFOX3 | 1.143991e+01 | 9.250286e-01 | 1.863642e-05 | 1.783120e-04 |
CB | DOWN | ENST00000581393.5 | RBFOX3-205:retained_intron:RBFOX3 | 6.755837e+01 | -8.776667e-01 | 2.040025e-04 | 1.353296e-03 |
CB | DOWN | ENST00000582894.5 | RBFOX3-210:protein_coding:RBFOX3 | 9.871822e+00 | -1.165794e+00 | 2.276571e-03 | 1.025760e-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 RBFOX3 |
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_140324 | chr17 | 79090847:79090885:79094451:79094529:79095513:79095574 | 79094451:79094529 |
exon_skip_150097 | chr17 | 79104073:79104126:79106651:79106788:79115494:79115580 | 79106651:79106788 |
exon_skip_166594 | chr17 | 79106651:79106788:79115494:79115748:79235766:79235805 | 79115494:79115748 |
exon_skip_246437 | chr17 | 79096653:79096692:79097292:79097424:79097692:79097726 | 79097292:79097424 |
exon_skip_267987 | chr17 | 79115703:79115748:79235766:79235805:79307724:79307824 | 79235766:79235805 |
exon_skip_283758 | chr17 | 79101584:79101644:79104073:79104126:79106651:79106785 | 79104073:79104126 |
exon_skip_284771 | chr17 | 79103162:79103254:79104073:79104126:79106651:79106785 | 79104073:79104126 |
exon_skip_32394 | chr17 | 79235766:79235805:79307724:79307824:79482454:79482598 | 79307724:79307824 |
exon_skip_45321 | chr17 | 79104073:79104126:79106651:79106785:79115494:79115580 | 79106651:79106785 |
exon_skip_59039 | chr17 | 79106651:79106785:79115494:79115748:79235766:79235805 | 79115494:79115748 |
exon_skip_63239 | chr17 | 79101584:79101644:79103162:79103254:79104073:79104126 | 79103162:79103254 |
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 RBFOX3 |
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 |
ENST00000580155 | 79115494 | 79115748 | 3UTR-3CDS |
ENST00000580155 | 79235766 | 79235805 | 3UTR-3UTR |
ENST00000580155 | 79307724 | 79307824 | 3UTR-3UTR |
ENST00000580155 | 79094451 | 79094529 | Frame-shift |
ENST00000580155 | 79097292 | 79097424 | Frame-shift |
ENST00000580155 | 79103162 | 79103254 | In-frame |
ENST00000580155 | 79104073 | 79104126 | In-frame |
ENST00000580155 | 79106651 | 79106788 | 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 |
ENST00000580155 | 79235766 | 79235805 | 3UTR-3UTR |
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 |
ENST00000580155 | 79115494 | 79115748 | 3UTR-3CDS |
ENST00000580155 | 79235766 | 79235805 | 3UTR-3UTR |
ENST00000580155 | 79307724 | 79307824 | 3UTR-3UTR |
ENST00000580155 | 79094451 | 79094529 | Frame-shift |
ENST00000580155 | 79097292 | 79097424 | Frame-shift |
ENST00000580155 | 79103162 | 79103254 | In-frame |
ENST00000580155 | 79104073 | 79104126 | In-frame |
ENST00000580155 | 79106651 | 79106788 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RBFOX3 |
p-ENSG00000167281_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 |
ENST00000580155 | 1536 | 312 | 79106651 | 79106788 | 736 | 872 | 74 | 119 |
ENST00000580155 | 1536 | 312 | 79104073 | 79104126 | 874 | 926 | 120 | 137 |
ENST00000580155 | 1536 | 312 | 79103162 | 79103254 | 928 | 1019 | 138 | 168 |
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 |
ENST00000580155 | 1536 | 312 | 79106651 | 79106788 | 736 | 872 | 74 | 119 |
ENST00000580155 | 1536 | 312 | 79104073 | 79104126 | 874 | 926 | 120 | 137 |
ENST00000580155 | 1536 | 312 | 79103162 | 79103254 | 928 | 1019 | 138 | 168 |
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 |
A6NFN3 | 74 | 119 | 1 | 312 | Chain | ID=PRO_0000349207;Note=RNA binding protein fox-1 homolog 3 |
A6NFN3 | 74 | 119 | 100 | 175 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
A6NFN3 | 74 | 119 | 100 | 100 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 74 | 119 | 108 | 108 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 74 | 119 | 109 | 109 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 120 | 137 | 1 | 312 | Chain | ID=PRO_0000349207;Note=RNA binding protein fox-1 homolog 3 |
A6NFN3 | 120 | 137 | 100 | 175 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
A6NFN3 | 120 | 137 | 133 | 133 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 138 | 168 | 1 | 312 | Chain | ID=PRO_0000349207;Note=RNA binding protein fox-1 homolog 3 |
A6NFN3 | 138 | 168 | 100 | 175 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
A6NFN3 | 138 | 168 | 138 | 138 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 138 | 168 | 142 | 142 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 138 | 168 | 166 | 166 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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 |
A6NFN3 | 74 | 119 | 1 | 312 | Chain | ID=PRO_0000349207;Note=RNA binding protein fox-1 homolog 3 |
A6NFN3 | 74 | 119 | 100 | 175 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
A6NFN3 | 74 | 119 | 100 | 100 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 74 | 119 | 108 | 108 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 74 | 119 | 109 | 109 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 120 | 137 | 1 | 312 | Chain | ID=PRO_0000349207;Note=RNA binding protein fox-1 homolog 3 |
A6NFN3 | 120 | 137 | 100 | 175 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
A6NFN3 | 120 | 137 | 133 | 133 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 138 | 168 | 1 | 312 | Chain | ID=PRO_0000349207;Note=RNA binding protein fox-1 homolog 3 |
A6NFN3 | 138 | 168 | 100 | 175 | Domain | Note=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
A6NFN3 | 138 | 168 | 138 | 138 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 138 | 168 | 142 | 142 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
A6NFN3 | 138 | 168 | 166 | 166 | Site | Note=Interaction with RNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RBFOX3 |
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 | ENST00000580155 | 79307724 | 79307824 | hsa-miR-4254 | chr17:79307742-79307749 | 8mer-1a | chr17:79307729-79307750 | 155.00 | -32.52 |
Mayo | ENST00000580155 | 79307724 | 79307824 | hsa-miR-4726-3p | chr17:79307777-79307784 | 8mer-1a | chr17:79307776-79307799 | 159.00 | -23.26 |
Mayo | ENST00000580155 | 79307724 | 79307824 | hsa-miR-4727-5p | chr17:79307791-79307798 | 8mer-1a | chr17:79307776-79307799 | 159.00 | -23.26 |
Mayo | ENST00000580155 | 79307724 | 79307824 | hsa-miR-505-5p | chr17:79307739-79307746 | 8mer-1a | chr17:79307729-79307750 | 155.00 | -32.52 |
Mayo | ENST00000580155 | 79307724 | 79307824 | hsa-miR-1184 | chr17:79307770-79307777 | 8mer-1a | chr17:79307757-79307784 | 151.00 | -30.99 |
ROSMAP | ENST00000580155 | 79307724 | 79307824 | hsa-miR-4254 | chr17:79307742-79307749 | 8mer-1a | chr17:79307729-79307750 | 155.00 | -32.52 |
ROSMAP | ENST00000580155 | 79307724 | 79307824 | hsa-miR-4726-3p | chr17:79307777-79307784 | 8mer-1a | chr17:79307776-79307799 | 159.00 | -23.26 |
ROSMAP | ENST00000580155 | 79307724 | 79307824 | hsa-miR-4727-5p | chr17:79307791-79307798 | 8mer-1a | chr17:79307776-79307799 | 159.00 | -23.26 |
ROSMAP | ENST00000580155 | 79307724 | 79307824 | hsa-miR-505-5p | chr17:79307739-79307746 | 8mer-1a | chr17:79307729-79307750 | 155.00 | -32.52 |
ROSMAP | ENST00000580155 | 79307724 | 79307824 | hsa-miR-1184 | chr17:79307770-79307777 | 8mer-1a | chr17:79307757-79307784 | 151.00 | -30.99 |
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SNVs in the skipped exons for RBFOX3 |
- 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 RBFOX3 |
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 RBFOX3 |
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 RBFOX3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | CNOT4 | exon_skip_266183 | 4.045242e-01 | 2.884686e-06 |
CB | RBM4B | exon_skip_266183 | 5.510176e-01 | 2.769054e-11 |
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RelatedDrugs for RBFOX3 |
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 RBFOX3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |