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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 RUFY3 |
 Gene summary |
| Gene information | Gene symbol | RUFY3 | Gene ID | 22902 |
| Gene name | RUN and FYVE domain containing 3 | |
| Synonyms | RIPX|SINGAR1|ZFYVE30 | |
| Cytomap | 4q13.3 | |
| Type of gene | protein-coding | |
| Description | protein RUFY3rap2 interacting protein xsingle axon-regulated proteinsingle axon-related 1 | |
| Modification date | 20180523 | |
| UniProtAcc | Q7L099 | |
| Context | PubMed: RUFY3 [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 |
| RUFY3 | GO:0030335 | positive regulation of cell migration | 25766321 |
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Exon skipping events across known transcript of Ensembl for RUFY3 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 RUFY3 |
| 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 RUFY3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_424072 | 4 | 71588371:71588468:71607343:71607397:71628235:71628409 | 71607343:71607397 | ENSG00000018189.8 | ENST00000536664.1 |
| exon_skip_424074 | 4 | 71600150:71600310:71607343:71607397:71628235:71628409 | 71607343:71607397 | ENSG00000018189.8 | ENST00000502653.1 |
| exon_skip_424075 | 4 | 71630191:71630293:71634254:71634378:71639227:71639289 | 71634254:71634378 | ENSG00000018189.8 | ENST00000417478.2,ENST00000536664.1,ENST00000381006.3,ENST00000513597.1,ENST00000502653.1,ENST00000226328.4 |
| exon_skip_424076 | 4 | 71640884:71640950:71644085:71644155:71648807:71648900 | 71644085:71644155 | ENSG00000018189.8 | ENST00000417478.2,ENST00000536664.1,ENST00000381006.3,ENST00000502653.1,ENST00000226328.4 |
| exon_skip_424077 | 4 | 71644085:71644155:71648807:71648900:71650512:71650596 | 71648807:71648900 | ENSG00000018189.8 | ENST00000417478.2,ENST00000536664.1,ENST00000381006.3,ENST00000502653.1,ENST00000226328.4 |
| exon_skip_424078 | 4 | 71648807:71648900:71650512:71650596:71654522:71654690 | 71650512:71650596 | ENSG00000018189.8 | ENST00000417478.2,ENST00000536664.1,ENST00000381006.3,ENST00000502653.1,ENST00000226328.4 |
| exon_skip_424087 | 4 | 71655211:71655309:71659481:71659621:71660511:71660611 | 71659481:71659621 | ENSG00000018189.8 | ENST00000504805.2 |
| exon_skip_424091 | 4 | 71655211:71655309:71659501:71659621:71660511:71660611 | 71659501:71659621 | ENSG00000018189.8 | ENST00000381006.3,ENST00000502653.1 |
| exon_skip_424097 | 4 | 71655211:71655309:71665857:71665922:71668672:71668700 | 71665857:71665922 | ENSG00000018189.8 | ENST00000512103.1 |
| exon_skip_424105 | 4 | 71660511:71660611:71665857:71665922:71668672:71668700 | 71665857:71665922 | ENSG00000018189.8 | ENST00000503025.1,ENST00000381006.3,ENST00000502653.1 |
| exon_skip_424110 | 4 | 71665121:71665592:71665857:71665922:71668672:71668700 | 71665857:71665922 | ENSG00000018189.8 | ENST00000512331.1 |
| exon_skip_424111 | 4 | 71665857:71665922:71668672:71668700:71670064:71670133 | 71668672:71668700 | ENSG00000018189.8 | ENST00000503025.1,ENST00000381006.3,ENST00000512331.1,ENST00000502653.1,ENST00000515479.1 |
| exon_skip_424112 | 4 | 71665857:71665922:71668672:71668700:71672232:71672270 | 71668672:71668700 | ENSG00000018189.8 | ENST00000512103.1 |
| exon_skip_424116 | 4 | 71668672:71668700:71670064:71670133:71672232:71672270 | 71670064:71670133 | ENSG00000018189.8 | ENST00000503025.1,ENST00000381006.3,ENST00000512331.1,ENST00000502653.1,ENST00000515479.1 |
| exon_skip_424118 | 4 | 71668587:71668893:71670064:71670133:71672232:71672270 | 71670064:71670133 | ENSG00000018189.8 | ENST00000515442.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RUFY3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_424072 | 4 | 71588371:71588468:71607343:71607397:71628235:71628409 | 71607343:71607397 | ENSG00000018189.8 | ENST00000536664.1 |
| exon_skip_424074 | 4 | 71600150:71600310:71607343:71607397:71628235:71628409 | 71607343:71607397 | ENSG00000018189.8 | ENST00000502653.1 |
| exon_skip_424075 | 4 | 71630191:71630293:71634254:71634378:71639227:71639289 | 71634254:71634378 | ENSG00000018189.8 | ENST00000417478.2,ENST00000381006.3,ENST00000226328.4,ENST00000536664.1,ENST00000513597.1,ENST00000502653.1 |
| exon_skip_424076 | 4 | 71640884:71640950:71644085:71644155:71648807:71648900 | 71644085:71644155 | ENSG00000018189.8 | ENST00000417478.2,ENST00000381006.3,ENST00000226328.4,ENST00000536664.1,ENST00000502653.1 |
| exon_skip_424077 | 4 | 71644085:71644155:71648807:71648900:71650512:71650596 | 71648807:71648900 | ENSG00000018189.8 | ENST00000417478.2,ENST00000381006.3,ENST00000226328.4,ENST00000536664.1,ENST00000502653.1 |
| exon_skip_424078 | 4 | 71648807:71648900:71650512:71650596:71654522:71654690 | 71650512:71650596 | ENSG00000018189.8 | ENST00000417478.2,ENST00000381006.3,ENST00000226328.4,ENST00000536664.1,ENST00000502653.1 |
| exon_skip_424079 | 4 | 71654655:71654690:71655211:71655309:71665857:71665899 | 71655211:71655309 | ENSG00000018189.8 | ENST00000512103.1 |
| exon_skip_424087 | 4 | 71655211:71655309:71659481:71659621:71660511:71660611 | 71659481:71659621 | ENSG00000018189.8 | ENST00000504805.2 |
| exon_skip_424091 | 4 | 71655211:71655309:71659501:71659621:71660511:71660611 | 71659501:71659621 | ENSG00000018189.8 | ENST00000381006.3,ENST00000502653.1 |
| exon_skip_424097 | 4 | 71655211:71655309:71665857:71665922:71668672:71668700 | 71665857:71665922 | ENSG00000018189.8 | ENST00000512103.1 |
| exon_skip_424105 | 4 | 71660511:71660611:71665857:71665922:71668672:71668700 | 71665857:71665922 | ENSG00000018189.8 | ENST00000381006.3,ENST00000502653.1,ENST00000503025.1 |
| exon_skip_424110 | 4 | 71665121:71665592:71665857:71665922:71668672:71668700 | 71665857:71665922 | ENSG00000018189.8 | ENST00000512331.1 |
| exon_skip_424111 | 4 | 71665857:71665922:71668672:71668700:71670064:71670133 | 71668672:71668700 | ENSG00000018189.8 | ENST00000381006.3,ENST00000502653.1,ENST00000503025.1,ENST00000512331.1,ENST00000515479.1 |
| exon_skip_424112 | 4 | 71665857:71665922:71668672:71668700:71672232:71672270 | 71668672:71668700 | ENSG00000018189.8 | ENST00000512103.1 |
| exon_skip_424116 | 4 | 71668672:71668700:71670064:71670133:71672232:71672270 | 71670064:71670133 | ENSG00000018189.8 | ENST00000381006.3,ENST00000502653.1,ENST00000503025.1,ENST00000512331.1,ENST00000515479.1 |
| exon_skip_424118 | 4 | 71668587:71668893:71670064:71670133:71672232:71672270 | 71670064:71670133 | ENSG00000018189.8 | ENST00000515442.1 |
| 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 RUFY3 |
| 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 |
| ENST00000226328 | 71634254 | 71634378 | Frame-shift |
| ENST00000226328 | 71644085 | 71644155 | Frame-shift |
| ENST00000226328 | 71648807 | 71648900 | In-frame |
| ENST00000226328 | 71650512 | 71650596 | 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 |
| ENST00000226328 | 71634254 | 71634378 | Frame-shift |
| ENST00000226328 | 71644085 | 71644155 | Frame-shift |
| ENST00000226328 | 71648807 | 71648900 | In-frame |
| ENST00000226328 | 71650512 | 71650596 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RUFY3 |
| 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 |
| ENST00000226328 | 4250 | 469 | 71648807 | 71648900 | 1458 | 1550 | 298 | 329 |
| ENST00000226328 | 4250 | 469 | 71650512 | 71650596 | 1551 | 1634 | 329 | 357 |
| 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 |
| ENST00000226328 | 4250 | 469 | 71648807 | 71648900 | 1458 | 1550 | 298 | 329 |
| ENST00000226328 | 4250 | 469 | 71650512 | 71650596 | 1551 | 1634 | 329 | 357 |
| 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 |
| Q7L099 | 298 | 329 | 1 | 469 | Chain | ID=PRO_0000245833;Note=Protein RUFY3 |
| Q7L099 | 298 | 329 | 267 | 464 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7L099 | 329 | 357 | 1 | 469 | Chain | ID=PRO_0000245833;Note=Protein RUFY3 |
| Q7L099 | 329 | 357 | 267 | 464 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7L099 | 329 | 357 | 357 | 357 | Sequence conflict | Note=L->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q7L099 | 298 | 329 | 1 | 469 | Chain | ID=PRO_0000245833;Note=Protein RUFY3 |
| Q7L099 | 298 | 329 | 267 | 464 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7L099 | 329 | 357 | 1 | 469 | Chain | ID=PRO_0000245833;Note=Protein RUFY3 |
| Q7L099 | 329 | 357 | 267 | 464 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7L099 | 329 | 357 | 357 | 357 | Sequence conflict | Note=L->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for RUFY3 |
| - 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-DD-A39Y-01 | exon_skip_424078 | 71650513 | 71650596 | 71650572 | 71650572 | Frame_Shift_Del | A | - | p.L349fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_424087 | 71659482 | 71659621 | 71659569 | 71659569 | Frame_Shift_Del | G | - | p.G469fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_424091 | 71659502 | 71659621 | 71659569 | 71659569 | Frame_Shift_Del | G | - | p.G469fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_424110 exon_skip_424097 exon_skip_424105 | 71665858 | 71665922 | 71665883 | 71665883 | Frame_Shift_Del | A | - | p.E528fs |
| THYM | TCGA-XU-A92O-01 | exon_skip_424075 | 71634255 | 71634378 | 71634265 | 71634265 | Nonsense_Mutation | G | T | p.E255X |
| PAAD | TCGA-IB-7651-01 | exon_skip_424077 | 71648808 | 71648900 | 71648856 | 71648856 | Nonsense_Mutation | C | T | p.R315* |
| PAAD | TCGA-IB-7651-01 | exon_skip_424077 | 71648808 | 71648900 | 71648856 | 71648856 | Nonsense_Mutation | C | T | p.R375X |
| ESCA | TCGA-L5-A8NI-01 | exon_skip_424078 | 71650513 | 71650596 | 71650543 | 71650543 | Nonsense_Mutation | C | T | p.Q340* |
| ESCA | TCGA-L5-A8NI-01 | exon_skip_424078 | 71650513 | 71650596 | 71650543 | 71650543 | Nonsense_Mutation | C | T | p.Q400* |
| ESCA | TCGA-L5-A8NI-01 | exon_skip_424078 | 71650513 | 71650596 | 71650543 | 71650543 | Nonsense_Mutation | C | T | p.Q400X |
| UCEC | TCGA-D1-A17Q-01 | exon_skip_424087 | 71659482 | 71659621 | 71659518 | 71659518 | Nonsense_Mutation | C | T | p.R452* |
| UCEC | TCGA-D1-A17Q-01 | exon_skip_424091 | 71659502 | 71659621 | 71659518 | 71659518 | Nonsense_Mutation | C | T | p.R452* |
| TGCT | TCGA-SB-A6J6-01 | exon_skip_424087 | 71659482 | 71659621 | 71659590 | 71659590 | Nonsense_Mutation | C | T | p.Q476* |
| TGCT | TCGA-SB-A6J6-01 | exon_skip_424087 | 71659482 | 71659621 | 71659590 | 71659590 | Nonsense_Mutation | C | T | p.Q476X |
| TGCT | TCGA-SB-A6J6-01 | exon_skip_424091 | 71659502 | 71659621 | 71659590 | 71659590 | Nonsense_Mutation | C | T | p.Q476* |
| TGCT | TCGA-SB-A6J6-01 | exon_skip_424091 | 71659502 | 71659621 | 71659590 | 71659590 | Nonsense_Mutation | C | T | p.Q476X |
| KIRC | TCGA-B2-4099-01 | exon_skip_424077 | 71648808 | 71648900 | 71648807 | 71648807 | Splice_Site | G | T | . |
| - 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 |
| DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71668673 | 71668700 | 71668680 | 71668680 | Frame_Shift_Del | C | - | p.P544fs |
| HCC2998_LARGE_INTESTINE | 71634255 | 71634378 | 71634261 | 71634261 | Missense_Mutation | C | A | p.F193L |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71648808 | 71648900 | 71648868 | 71648868 | Missense_Mutation | G | A | p.E319K |
| TE1_OESOPHAGUS | 71648808 | 71648900 | 71648875 | 71648875 | Missense_Mutation | C | T | p.S321F |
| NCIH2286_LUNG | 71650513 | 71650596 | 71650574 | 71650574 | Missense_Mutation | A | T | p.K350I |
| JHUEM7_ENDOMETRIUM | 71665858 | 71665922 | 71665904 | 71665904 | Missense_Mutation | C | T | p.P535L |
| JHUEM7_ENDOMETRIUM | 71648808 | 71648900 | 71648847 | 71648847 | Nonsense_Mutation | G | T | p.E312* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RUFY3 |
| 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 RUFY3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RUFY3 |
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RelatedDrugs for RUFY3 |
| 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 RUFY3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RUFY3 | C0037274 | Dermatologic disorders | 1 | CTD_human |
| RUFY3 | C0311375 | Arsenic Poisoning | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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