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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 RUBCN |
 Gene summary |
| Gene information | Gene symbol | RUBCN | Gene ID | 9711 |
| Gene name | rubicon autophagy regulator | |
| Synonyms | KIAA0226|RUBICON|SCAR15 | |
| Cytomap | 3q29 | |
| Type of gene | protein-coding | |
| Description | run domain Beclin-1-interacting and cysteine-rich domain-containing proteinRUN and cysteine rich domain containing beclin 1 interacting proteinRUN domain and cysteine-rich domain containing, Beclin 1-interacting proteinbaronbeclin-1 associated RUN dom | |
| 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 |
| RUBCN | GO:0043553 | negative regulation of phosphatidylinositol 3-kinase activity | 21062745 |
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Gene structures and expression levels for RUBCN |
| 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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ENSG00000145016
| 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 |
| CB | UP | ENST00000447048.1 | RUBCN-205:protein_coding:RUBCN | 2.420527e+00 | 3.329549e+00 | 2.319575e-08 | 6.154688e-07 |
| 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 RUBCN |
| 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_134094 | chr3 | 197696954:197697049:197699187:197699231:197700613:197700765 | 197699187:197699231 |
| exon_skip_152849 | chr3 | 197695866:197695981:197696954:197697049:197700613:197700765 | 197696954:197697049 |
| exon_skip_182300 | chr3 | 197683307:197683439:197684157:197684217:197693715:197693816 | 197684157:197684217 |
| exon_skip_211975 | chr3 | 197705092:197705175:197717977:197718130:197736655:197736904 | 197717977:197718130 |
| exon_skip_238317 | chr3 | 197701860:197701864:197703548:197703654:197704542:197704701 | 197703548:197703654 |
| exon_skip_240531 | chr3 | 197696954:197697049:197699187:197699231:197700613:197700769 | 197699187:197699231 |
| exon_skip_251394 | chr3 | 197695866:197695981:197696954:197697049:197700613:197700769 | 197696954:197697049 |
| exon_skip_255183 | chr3 | 197695866:197695981:197699187:197699231:197700613:197700769 | 197699187:197699231 |
| exon_skip_259485 | chr3 | 197705092:197705175:197717977:197718130:197749269:197749347 | 197717977:197718130 |
| exon_skip_265562 | chr3 | 197705092:197705175:197717977:197718130:197736655:197736707 | 197717977:197718130 |
| exon_skip_37817 | chr3 | 197695866:197695981:197699187:197699231:197700613:197700765 | 197699187:197699231 |
| exon_skip_40570 | chr3 | 197684157:197684217:197691074:197691148:197693715:197693816 | 197691074:197691148 |
| exon_skip_4730 | chr3 | 197700613:197701146:197701708:197701864:197703548:197703654 | 197701708:197701864 |
| exon_skip_62654 | chr3 | 197695866:197695981:197696954:197697049:197699187:197699231 | 197696954:197697049 |
| exon_skip_70980 | chr3 | 197683307:197683439:197684157:197684217:197691074:197691148 | 197684157:197684217 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_134094 | Mayo_TC | 4.746341e-01 | 6.198649e-01 | -1.452307e-01 | 1.684096e-05 |
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Open reading frame (ORF) annotation in the exon skipping event for RUBCN |
| 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 |
| ENST00000296343 | 197701708 | 197701864 | Frame-shift |
| ENST00000296343 | 197703548 | 197703654 | Frame-shift |
| ENST00000296343 | 197696954 | 197697049 | 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 |
| ENST00000296343 | 197703548 | 197703654 | Frame-shift |
| ENST00000296343 | 197696954 | 197697049 | 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 |
| ENST00000296343 | 197684157 | 197684217 | Frame-shift |
| ENST00000296343 | 197696954 | 197697049 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RUBCN |
p-ENSG00000145016_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 |
| ENST00000296343 | 2936 | 972 | 197696954 | 197697049 | 1262 | 1356 | 420 | 452 |
| 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 |
| ENST00000296343 | 2936 | 972 | 197696954 | 197697049 | 1262 | 1356 | 420 | 452 |
| 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 |
| ENST00000296343 | 2936 | 972 | 197696954 | 197697049 | 1262 | 1356 | 420 | 452 |
| 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 |
| Q92622 | 420 | 452 | 420 | 420 | Alternative sequence | ID=VSP_039161;Note=In isoform 2. P->PGGPRNITIIVEDPIA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9039502;Dbxref=PMID:9039502 |
| Q92622 | 420 | 452 | 1 | 972 | Chain | ID=PRO_0000050736;Note=Run domain Beclin-1-interacting and cysteine-rich domain-containing protein |
| Q92622 | 420 | 452 | 204 | 447 | Compositional bias | Note=Ser-rich |
| Q92622 | 420 | 452 | 204 | 447 | Region | Note=Interaction with YWHAB;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22423967;Dbxref=PMID:22423967 |
| Q92622 | 420 | 452 | 300 | 600 | Region | Note=Interaction with UVRAG;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21062745;Dbxref=PMID:21062745 |
| 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 |
| Q92622 | 420 | 452 | 420 | 420 | Alternative sequence | ID=VSP_039161;Note=In isoform 2. P->PGGPRNITIIVEDPIA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9039502;Dbxref=PMID:9039502 |
| Q92622 | 420 | 452 | 1 | 972 | Chain | ID=PRO_0000050736;Note=Run domain Beclin-1-interacting and cysteine-rich domain-containing protein |
| Q92622 | 420 | 452 | 204 | 447 | Compositional bias | Note=Ser-rich |
| Q92622 | 420 | 452 | 204 | 447 | Region | Note=Interaction with YWHAB;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22423967;Dbxref=PMID:22423967 |
| Q92622 | 420 | 452 | 300 | 600 | Region | Note=Interaction with UVRAG;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21062745;Dbxref=PMID:21062745 |
| 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 |
| Q92622 | 420 | 452 | 420 | 420 | Alternative sequence | ID=VSP_039161;Note=In isoform 2. P->PGGPRNITIIVEDPIA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9039502;Dbxref=PMID:9039502 |
| Q92622 | 420 | 452 | 1 | 972 | Chain | ID=PRO_0000050736;Note=Run domain Beclin-1-interacting and cysteine-rich domain-containing protein |
| Q92622 | 420 | 452 | 204 | 447 | Compositional bias | Note=Ser-rich |
| Q92622 | 420 | 452 | 204 | 447 | Region | Note=Interaction with YWHAB;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22423967;Dbxref=PMID:22423967 |
| Q92622 | 420 | 452 | 300 | 600 | Region | Note=Interaction with UVRAG;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21062745;Dbxref=PMID:21062745 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RUBCN |
| 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 RUBCN |
| - 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 RUBCN |
| 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 RUBCN |
| 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 RUBCN |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| HCC | RBM5 | exon_skip_240531 | -5.704722e-01 | 5.095949e-24 |
| HCC | RC3H1 | exon_skip_240531 | -4.895409e-01 | 3.395289e-17 |
| HCC | RBM3 | exon_skip_265562 | -5.635080e-01 | 5.134624e-22 |
| IFG | PTBP3 | exon_skip_40570 | -4.740144e-01 | 1.249640e-02 |
| IFG | RBM25 | exon_skip_211975 | 4.536889e-01 | 3.885230e-02 |
| IFG | RBM5 | exon_skip_211975 | 4.335394e-01 | 4.960002e-02 |
| IFG | MBNL1 | exon_skip_211975 | 4.881380e-01 | 2.476643e-02 |
| IFG | PUM1 | exon_skip_211975 | 5.188558e-01 | 1.595004e-02 |
| PCC | RBM3 | exon_skip_265562 | -5.816363e-01 | 3.903346e-18 |
| TC | NOVA1 | exon_skip_40570 | -4.891322e-01 | 9.230408e-11 |
| TC | HNRNPA0 | exon_skip_134094 | 6.173218e-01 | 9.291243e-18 |
| TC | NOVA1 | exon_skip_134094 | 6.810801e-01 | 1.333239e-22 |
| TC | RBM3 | exon_skip_211975 | -4.482237e-01 | 2.223790e-08 |
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RelatedDrugs for RUBCN |
| 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 RUBCN |
| 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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