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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for FXN |
 Gene summary |
| Gene information | Gene symbol | FXN | Gene ID | 2395 |
| Gene name | frataxin | |
| Synonyms | CyaY|FA|FARR|FRDA|X25 | |
| Cytomap | 9q21.11 | |
| Type of gene | protein-coding | |
| Description | frataxin, mitochondrialFriedreich ataxia protein | |
| Modification date | 20180523 | |
| UniProtAcc | Q16595 | |
| Context | PubMed: FXN [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| FXN | GO:0010722 | regulation of ferrochelatase activity | 15123683 |
| FXN | GO:0016540 | protein autoprocessing | 12785837 |
| FXN | GO:0018283 | iron incorporation into metallo-sulfur cluster | 12785837 |
| FXN | GO:0051349 | positive regulation of lyase activity | 20053667 |
| FXN | GO:0070301 | cellular response to hydrogen peroxide | 15641778 |
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Exon skipping events across known transcript of Ensembl for FXN from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for FXN |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for FXN |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_496298 | 9 | 71650677:71650863:71661300:71661398:71668055:71668176 | 71661300:71661398 | ENSG00000165060.7 | ENST00000396366.2,ENST00000396364.3 |
| exon_skip_496301 | 9 | 71661322:71661398:71668055:71668176:71679853:71679951 | 71668055:71668176 | ENSG00000165060.7 | ENST00000396366.2,ENST00000396364.3,ENST00000377270.3,ENST00000498653.1 |
| exon_skip_496303 | 9 | 71668055:71668176:71679853:71679951:71687527:71687712 | 71679853:71679951 | ENSG00000165060.7 | ENST00000377270.3,ENST00000498653.1 |
| exon_skip_496304 | 9 | 71668055:71668176:71679853:71679951:71714816:71715094 | 71679853:71679951 | ENSG00000165060.7 | ENST00000396364.3 |
| exon_skip_496305 | 9 | 71668055:71668176:71679853:71679959:71687527:71687712 | 71679853:71679959 | ENSG00000165060.7 | ENST00000396366.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for FXN |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_496298 | 9 | 71650677:71650863:71661300:71661398:71668055:71668176 | 71661300:71661398 | ENSG00000165060.7 | ENST00000396364.3,ENST00000396366.2 |
| exon_skip_496301 | 9 | 71661322:71661398:71668055:71668176:71679853:71679951 | 71668055:71668176 | ENSG00000165060.7 | ENST00000377270.3,ENST00000396364.3,ENST00000396366.2,ENST00000498653.1 |
| exon_skip_496303 | 9 | 71668055:71668176:71679853:71679951:71687527:71687712 | 71679853:71679951 | ENSG00000165060.7 | ENST00000377270.3,ENST00000498653.1 |
| exon_skip_496304 | 9 | 71668055:71668176:71679853:71679951:71714816:71715094 | 71679853:71679951 | ENSG00000165060.7 | ENST00000396364.3 |
| exon_skip_496305 | 9 | 71668055:71668176:71679853:71679959:71687527:71687712 | 71679853:71679959 | ENSG00000165060.7 | ENST00000396366.2 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for FXN |
| Open reading frame (ORF) of individual exon skipping events in TCGA 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 GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
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Infer the effects of exon skipping event on protein functional features for FXN |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 GTEx 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 TCGA. |
| 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 GTEx. |
| 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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SNVs in the skipped exons for FXN |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| KICH | TCGA-KN-8428-01 | exon_skip_496301 | 71668056 | 71668176 | 71668178 | 71668178 | Splice_Site | T | C | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| SCABER_URINARY_TRACT | 71661301 | 71661398 | 71661369 | 71661369 | Missense_Mutation | G | C | p.L78F |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71668056 | 71668176 | 71668068 | 71668068 | Missense_Mutation | G | C | p.E92D |
| NCIH1975_LUNG | 71668056 | 71668176 | 71668084 | 71668084 | Missense_Mutation | C | A | p.L98I |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71668056 | 71668176 | 71668097 | 71668097 | Missense_Mutation | C | T | p.T102M |
| MCC13_SKIN | 71668056 | 71668176 | 71668114 | 71668114 | Missense_Mutation | G | A | p.E108K |
| SNU324_PANCREAS | 71679854 | 71679951 | 71679917 | 71679917 | Missense_Mutation | C | T | p.P150S |
| SNU324_PANCREAS | 71679854 | 71679959 | 71679917 | 71679917 | Missense_Mutation | C | T | p.P150S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FXN |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FXN |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FXN |
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RelatedDrugs for FXN |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q16595 | DB01592 | Iron | Frataxin, mitochondrial | small molecule | approved | |
| Q16595 | DB14488 | Ferrous gluconate | Frataxin, mitochondrial | small molecule | approved | |
| Q16595 | DB14489 | Ferrous succinate | Frataxin, mitochondrial | small molecule | approved | |
| Q16595 | DB14490 | Ferrous ascorbate | Frataxin, mitochondrial | small molecule | approved | |
| Q16595 | DB14491 | Ferrous fumarate | Frataxin, mitochondrial | small molecule | approved | |
| Q16595 | DB14501 | Ferrous glycine sulfate | Frataxin, mitochondrial | small molecule | approved |
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RelatedDiseases for FXN |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| FXN | C0016719 | Friedreich Ataxia | 8 | CTD_human;ORPHANET |
| FXN | C1856689 | FRIEDREICH ATAXIA 1 | 6 | CTD_human;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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