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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 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 | 20200313 | |
| 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 |
| RUFY3 | GO:0030335 | positive regulation of cell migration | 25766321 |
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Gene structures and expression levels for RUFY3 |
| 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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ENSG00000018189
| 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 |
| 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 RUFY3 |
| 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_110651 | chr4 | 70775168:70775233:70778369:70778438:70783091:70783183 | 70778369:70778438 |
| exon_skip_115422 | chr4 | 70778369:70778438:70783091:70783183:70784796:70784879 | 70783091:70783183 |
| exon_skip_132139 | chr4 | 70789495:70789592:70800141:70800205:70802956:70802983 | 70800141:70800205 |
| exon_skip_13815 | chr4 | 70734581:70734593:70741627:70741680:70762519:70762692 | 70741627:70741680 |
| exon_skip_146357 | chr4 | 70783091:70783183:70784796:70784879:70788806:70788973 | 70784796:70784879 |
| exon_skip_146836 | chr4 | 70802871:70803176:70804348:70804416:70806516:70806553 | 70804348:70804416 |
| exon_skip_180155 | chr4 | 70788939:70788973:70789495:70789592:70791225:70793557 | 70789495:70789592 |
| exon_skip_182384 | chr4 | 70794795:70794894:70800141:70800205:70802956:70802983 | 70800141:70800205 |
| exon_skip_203018 | chr4 | 70775169:70775233:70778369:70778438:70783091:70783183 | 70778369:70778438 |
| exon_skip_208257 | chr4 | 70799405:70799875:70800141:70800205:70802956:70802983 | 70800141:70800205 |
| exon_skip_208567 | chr4 | 70783091:70783183:70784796:70784879:70788806:70788824 | 70784796:70784879 |
| exon_skip_216992 | chr4 | 70775170:70775233:70778369:70778438:70783091:70783183 | 70778369:70778438 |
| exon_skip_221234 | chr4 | 70762519:70762692:70763552:70763669:70764475:70764576 | 70763552:70763669 |
| exon_skip_240908 | chr4 | 70800141:70800205:70802956:70802983:70806516:70806816 | 70802956:70802983 |
| exon_skip_252551 | chr4 | 70784866:70784879:70788806:70788973:70789495:70789592 | 70788806:70788973 |
| exon_skip_258085 | chr4 | 70800141:70800205:70802956:70802983:70806516:70806553 | 70802956:70802983 |
| exon_skip_260285 | chr4 | 70764475:70764576:70768538:70768661:70773511:70773572 | 70768538:70768661 |
| exon_skip_260549 | chr4 | 70789495:70789592:70793785:70793904:70794795:70794894 | 70793785:70793904 |
| exon_skip_280217 | chr4 | 70768538:70768661:70773511:70773572:70775168:70775206 | 70773511:70773572 |
| exon_skip_282723 | chr4 | 70800141:70800205:70802956:70802983:70804348:70804416 | 70802956:70802983 |
| exon_skip_51546 | chr4 | 70789495:70789592:70793765:70793904:70794795:70794894 | 70793765:70793904 |
| exon_skip_57986 | chr4 | 70734434:70734593:70741627:70741680:70762519:70762692 | 70741627:70741680 |
| exon_skip_77691 | chr4 | 70802956:70802983:70804348:70804416:70806516:70806553 | 70804348:70804416 |
| 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 RUFY3 |
| 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 |
| ENST00000226328 | 70768538 | 70768661 | Frame-shift |
| ENST00000226328 | 70778369 | 70778438 | Frame-shift |
| ENST00000226328 | 70783091 | 70783183 | In-frame |
| ENST00000226328 | 70784796 | 70784879 | In-frame |
| ENST00000226328 | 70788806 | 70788973 | 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 |
| ENST00000226328 | 70773511 | 70773572 | Frame-shift |
| ENST00000226328 | 70778369 | 70778438 | Frame-shift |
| ENST00000226328 | 70783091 | 70783183 | In-frame |
| ENST00000226328 | 70784796 | 70784879 | In-frame |
| 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 |
| ENST00000226328 | 70763552 | 70763669 | Frame-shift |
| ENST00000226328 | 70778369 | 70778438 | Frame-shift |
| ENST00000226328 | 70789495 | 70789592 | Frame-shift |
| ENST00000226328 | 70783091 | 70783183 | In-frame |
| ENST00000226328 | 70784796 | 70784879 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RUFY3 |
p-ENSG00000018189_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 |
| ENST00000226328 | 4250 | 469 | 70783091 | 70783183 | 1459 | 1550 | 298 | 329 |
| ENST00000226328 | 4250 | 469 | 70784796 | 70784879 | 1552 | 1634 | 329 | 357 |
| ENST00000226328 | 4250 | 469 | 70788806 | 70788973 | 1636 | 1802 | 357 | 413 |
| 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 |
| ENST00000226328 | 4250 | 469 | 70783091 | 70783183 | 1459 | 1550 | 298 | 329 |
| ENST00000226328 | 4250 | 469 | 70784796 | 70784879 | 1552 | 1634 | 329 | 357 |
| 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 |
| ENST00000226328 | 4250 | 469 | 70783091 | 70783183 | 1459 | 1550 | 298 | 329 |
| ENST00000226328 | 4250 | 469 | 70784796 | 70784879 | 1552 | 1634 | 329 | 357 |
| 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 |
| 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 |
| Q7L099 | 357 | 413 | 1 | 469 | Chain | ID=PRO_0000245833;Note=Protein RUFY3 |
| Q7L099 | 357 | 413 | 267 | 464 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q7L099 | 357 | 413 | 357 | 357 | Sequence conflict | Note=L->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| 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 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 |
| 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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3'-UTR located exon skipping events that lost miRNA binding sites in RUFY3 |
| 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 RUFY3 |
| - 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 RUFY3 |
| 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 RUFY3 |
| 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 RUFY3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | HNRNPA2B1 | exon_skip_23044 | 4.244090e-01 | 3.361022e-08 |
| CB | RBM4 | exon_skip_23044 | 4.781413e-01 | 2.745888e-10 |
| CB | TRA2A | exon_skip_77691 | -4.538209e-01 | 1.880879e-09 |
| FL | SRSF9 | exon_skip_152677 | -4.548760e-01 | 1.670366e-11 |
| TC | NOVA1 | exon_skip_77691 | 4.217856e-01 | 2.779696e-08 |
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RelatedDrugs for RUFY3 |
| 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 RUFY3 |
| 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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