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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 RFX3 |
 Gene summary |
| Gene information | Gene symbol | RFX3 | Gene ID | 5991 |
| Gene name | regulatory factor X3 | |
| Synonyms | - | |
| Cytomap | 9p24.2 | |
| Type of gene | protein-coding | |
| Description | transcription factor RFX3DNA binding protein RFX3regulatory factor X, 3 (influences HLA class II expression) | |
| Modification date | 20180523 | |
| UniProtAcc | P48380 | |
| Context | PubMed: RFX3 [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 |
| RFX3 | GO:0045892 | negative regulation of transcription, DNA-templated | 12411430 |
| RFX3 | GO:0045893 | positive regulation of transcription, DNA-templated | 20148032 |
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Exon skipping events across known transcript of Ensembl for RFX3 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 RFX3 |
| 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 RFX3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_502357 | 9 | 3266207:3266305:3270370:3270525:3271002:3271118 | 3270370:3270525 | ENSG00000080298.11 | ENST00000358730.2,ENST00000382004.3,ENST00000302303.1 |
| exon_skip_502359 | 9 | 3275499:3275612:3277339:3277461:3288130:3288250 | 3277339:3277461 | ENSG00000080298.11 | ENST00000358730.2,ENST00000382004.3,ENST00000302303.1 |
| exon_skip_502360 | 9 | 3277339:3277461:3288130:3288250:3293076:3293258 | 3288130:3288250 | ENSG00000080298.11 | ENST00000358730.2,ENST00000382004.3,ENST00000302303.1 |
| exon_skip_502361 | 9 | 3293083:3293258:3301545:3301620:3330258:3330517 | 3301545:3301620 | ENSG00000080298.11 | ENST00000358730.2,ENST00000382004.3,ENST00000302303.1 |
| exon_skip_502362 | 9 | 3330316:3330517:3346666:3346764:3395471:3395588 | 3346666:3346764 | ENSG00000080298.11 | ENST00000358730.2,ENST00000382004.3,ENST00000449190.1,ENST00000302303.1,ENST00000457373.1,ENST00000451859.1 |
| exon_skip_502364 | 9 | 3395471:3395596:3488775:3488895:3490278:3490345 | 3488775:3488895 | ENSG00000080298.11 | ENST00000449190.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RFX3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_502357 | 9 | 3266207:3266305:3270370:3270525:3271002:3271118 | 3270370:3270525 | ENSG00000080298.11 | ENST00000382004.3,ENST00000358730.2,ENST00000302303.1 |
| exon_skip_502359 | 9 | 3275499:3275612:3277339:3277461:3288130:3288250 | 3277339:3277461 | ENSG00000080298.11 | ENST00000382004.3,ENST00000358730.2,ENST00000302303.1 |
| exon_skip_502360 | 9 | 3277339:3277461:3288130:3288250:3293076:3293258 | 3288130:3288250 | ENSG00000080298.11 | ENST00000382004.3,ENST00000358730.2,ENST00000302303.1 |
| exon_skip_502361 | 9 | 3293083:3293258:3301545:3301620:3330258:3330517 | 3301545:3301620 | ENSG00000080298.11 | ENST00000382004.3,ENST00000358730.2,ENST00000302303.1 |
| exon_skip_502362 | 9 | 3330316:3330517:3346666:3346764:3395471:3395588 | 3346666:3346764 | ENSG00000080298.11 | ENST00000382004.3,ENST00000358730.2,ENST00000302303.1,ENST00000457373.1,ENST00000451859.1,ENST00000449190.1 |
| exon_skip_502364 | 9 | 3395471:3395596:3488775:3488895:3490278:3490345 | 3488775:3488895 | ENSG00000080298.11 | ENST00000449190.1 |
| 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 RFX3 |
| 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 |
| ENST00000382004 | 3270370 | 3270525 | Frame-shift |
| ENST00000382004 | 3277339 | 3277461 | Frame-shift |
| ENST00000382004 | 3346666 | 3346764 | Frame-shift |
| ENST00000382004 | 3288130 | 3288250 | In-frame |
| ENST00000382004 | 3301545 | 3301620 | In-frame |
| 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 |
| ENST00000382004 | 3270370 | 3270525 | Frame-shift |
| ENST00000382004 | 3277339 | 3277461 | Frame-shift |
| ENST00000382004 | 3346666 | 3346764 | Frame-shift |
| ENST00000382004 | 3288130 | 3288250 | In-frame |
| ENST00000382004 | 3301545 | 3301620 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RFX3 |
| 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 |
| ENST00000382004 | 9324 | 749 | 3301545 | 3301620 | 787 | 861 | 158 | 183 |
| ENST00000382004 | 9324 | 749 | 3288130 | 3288250 | 1044 | 1163 | 244 | 283 |
| 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 |
| ENST00000382004 | 9324 | 749 | 3301545 | 3301620 | 787 | 861 | 158 | 183 |
| ENST00000382004 | 9324 | 749 | 3288130 | 3288250 | 1044 | 1163 | 244 | 283 |
| 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 RFX3 |
| - 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 |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_502359 | 3277340 | 3277461 | 3277379 | 3277379 | Frame_Shift_Del | T | - | p.T312fs |
| BRCA | TCGA-B6-A0IH-01 | exon_skip_502362 | 3346667 | 3346764 | 3346744 | 3346745 | Frame_Shift_Del | CA | - | p.V46fs |
| STAD | TCGA-BR-4363-01 | exon_skip_502359 | 3277340 | 3277461 | 3277341 | 3277342 | Frame_Shift_Ins | - | A | p.L324fs |
| LIHC | TCGA-DD-A1EE-01 | exon_skip_502362 | 3346667 | 3346764 | 3346710 | 3346710 | Nonsense_Mutation | G | A | p.Q58X |
| LIHC | TCGA-G3-A25S-01 | exon_skip_502362 | 3346667 | 3346764 | 3346710 | 3346710 | Nonsense_Mutation | G | A | p.Q58* |
| - 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 |
| SCLC22H_LUNG | 3270371 | 3270525 | 3270432 | 3270432 | Missense_Mutation | G | C | p.D432E |
| SCLC21H_LUNG | 3270371 | 3270525 | 3270432 | 3270432 | Missense_Mutation | G | C | p.D432E |
| HS939T_SKIN | 3288131 | 3288250 | 3288212 | 3288212 | Missense_Mutation | T | G | p.K257T |
| MCC26_SKIN | 3288131 | 3288250 | 3288219 | 3288219 | Missense_Mutation | G | A | p.R255C |
| SARC9371_BONE | 3288131 | 3288250 | 3288242 | 3288242 | Missense_Mutation | G | A | p.S247F |
| SNU175_LARGE_INTESTINE | 3301546 | 3301620 | 3301559 | 3301559 | Missense_Mutation | A | G | p.L179P |
| TEN_ENDOMETRIUM | 3346667 | 3346764 | 3346688 | 3346688 | Missense_Mutation | G | A | p.T65I |
| SNU719_STOMACH | 3346667 | 3346764 | 3346719 | 3346719 | Missense_Mutation | C | A | p.A55S |
| SNU1040_LARGE_INTESTINE | 3288131 | 3288250 | 3288144 | 3288144 | Nonsense_Mutation | G | A | p.Q280* |
| NUGC3_STOMACH | 3288131 | 3288250 | 3288174 | 3288174 | Nonsense_Mutation | G | A | p.Q270* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RFX3 |
| 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 RFX3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RFX3 |
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RelatedDrugs for RFX3 |
| 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 |
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RelatedDiseases for RFX3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RFX3 | C0037274 | Dermatologic disorders | 1 | CTD_human |
| RFX3 | C0311375 | Arsenic Poisoning | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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