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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 FGD4 |
 Gene summary |
| Gene information | Gene symbol | FGD4 | Gene ID | 121512 |
| Gene name | FYVE, RhoGEF and PH domain containing 4 | |
| Synonyms | CMT4H|FRABP|ZFYVE6 | |
| Cytomap | 12p11.21 | |
| Type of gene | protein-coding | |
| Description | FYVE, RhoGEF and PH domain-containing protein 4FGD1 family, member 4FGD1-related F-actin-binding proteinactin-filament binding protein frabinzinc finger FYVE domain-containing protein 6 | |
| Modification date | 20200328 | |
| 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 |
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Gene structures and expression levels for FGD4 |
| 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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ENSG00000139132
| 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 |
| TC | UP | ENST00000525053.5 | FGD4-210:protein_coding:FGD4 | 4.673302e+00 | 1.217733e+00 | 7.723096e-06 | 2.104407e-04 |
| 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 FGD4 |
| 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_100983 | chr12 | 32598497:32598586:32601278:32601423:32602161:32602317 | 32601278:32601423 |
| exon_skip_10250 | chr12 | 32601278:32601423:32602161:32602317:32607957:32608095 | 32602161:32602317 |
| exon_skip_107435 | chr12 | 32624422:32624452:32624659:32624751:32624976:32625068 | 32624659:32624751 |
| exon_skip_121276 | chr12 | 32598497:32598586:32600410:32600509:32601278:32601334 | 32600410:32600509 |
| exon_skip_163415 | chr12 | 32633549:32633689:32637650:32637855:32638655:32638795 | 32637650:32637855 |
| exon_skip_223659 | chr12 | 32564137:32564289:32576266:32576449:32581960:32582251 | 32576266:32576449 |
| exon_skip_237399 | chr12 | 32564137:32564289:32576266:32576449:32598497:32598586 | 32576266:32576449 |
| exon_skip_240104 | chr12 | 32624422:32624452:32624659:32624751:32624976:32625062 | 32624659:32624751 |
| exon_skip_258027 | chr12 | 32640276:32640453:32642761:32642842:32644594:32644751 | 32642761:32642842 |
| exon_skip_259468 | chr12 | 32502217:32502338:32556874:32556995:32564137:32564289 | 32556874:32556995 |
| exon_skip_264188 | chr12 | 32576266:32576449:32581960:32582467:32598497:32598586 | 32581960:32582467 |
| exon_skip_291457 | chr12 | 32624976:32625068:32625654:32625779:32633549:32633689 | 32625654:32625779 |
| exon_skip_44185 | chr12 | 32611137:32611283:32619698:32619870:32624422:32624452 | 32619698:32619870 |
| exon_skip_60131 | chr12 | 32564137:32564289:32574726:32574868:32576266:32576298 | 32574726:32574868 |
| exon_skip_62071 | chr12 | 32564137:32564289:32581960:32582467:32598497:32598586 | 32581960:32582467 |
| exon_skip_62117 | chr12 | 32564141:32564289:32576266:32576449:32581960:32582251 | 32576266:32576449 |
| exon_skip_71939 | chr12 | 32598497:32598586:32600410:32600509:32601278:32601423 | 32600410:32600509 |
| 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 FGD4 |
| 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 |
| ENST00000427716 | 32576266 | 32576449 | 5CDS-5UTR |
| ENST00000427716 | 32581960 | 32582467 | Frame-shift |
| ENST00000427716 | 32601278 | 32601423 | Frame-shift |
| ENST00000427716 | 32602161 | 32602317 | Frame-shift |
| ENST00000427716 | 32625654 | 32625779 | 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 |
| ENST00000427716 | 32576266 | 32576449 | 5CDS-5UTR |
| ENST00000427716 | 32581960 | 32582467 | Frame-shift |
| ENST00000427716 | 32602161 | 32602317 | Frame-shift |
| ENST00000427716 | 32619698 | 32619870 | 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 |
| ENST00000427716 | 32576266 | 32576449 | 5CDS-5UTR |
| ENST00000427716 | 32581960 | 32582467 | Frame-shift |
| ENST00000427716 | 32602161 | 32602317 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for FGD4 |
p-ENSG00000139132_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 |
| ENST00000427716 | 8259 | 766 | 32625654 | 32625779 | 2061 | 2185 | 545 | 587 |
| 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 |
| Q96M96 | 545 | 587 | 208 | 766 | Alternative sequence | ID=VSP_013081;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q96M96 | 545 | 587 | 515 | 766 | Alternative sequence | ID=VSP_013082;Note=In isoform 2. ALQETIDAFHQRHETFRNAIAKDNDIHSEVSTAELGKRAPRWIRDNEVTMCMKCKEPFNALTRRRHHCRACGYVVCWKCSDYKAQLEYDGGKLSKVCKDCYQIISGFTDSEEKKRKGILEIESAEVSGNSVVCSFLQYMEKSKPWQKAWCVIPKQDPLVLYMYGAPQDVRAQATIPLLGYVVDEMPRSADLPHSFKLTQSKSVHSFAADSEELKQKWLKVIL |
| Q96M96 | 545 | 587 | 1 | 766 | Chain | ID=PRO_0000080947;Note=FYVE%2C RhoGEF and PH domain-containing protein 4 |
| Q96M96 | 545 | 587 | 559 | 619 | Zinc finger | Note=FYVE-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00091 |
| 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 FGD4 |
| 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 FGD4 |
| - 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 FGD4 |
| 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 FGD4 |
| 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 FGD4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| HCC | SFPQ | exon_skip_223659 | 4.307378e-01 | 7.493866e-13 |
| HCC | RBM6 | exon_skip_223659 | 4.634329e-01 | 7.107601e-15 |
| HCC | RBM5 | exon_skip_223659 | 4.340406e-01 | 4.786800e-13 |
| HCC | G3BP2 | exon_skip_223659 | -4.726759e-01 | 1.735899e-15 |
| HCC | KHDRBS3 | exon_skip_223659 | 4.049086e-01 | 2.118565e-11 |
| HCC | HNRNPF | exon_skip_223659 | 4.039489e-01 | 2.385670e-11 |
| IFG | SFPQ | exon_skip_223659 | 4.443215e-01 | 3.829276e-02 |
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RelatedDrugs for FGD4 |
| 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 FGD4 |
| 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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