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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 NBEA |
 Gene summary |
| Gene information | Gene symbol | NBEA | Gene ID | 26960 |
| Gene name | neurobeachin | |
| Synonyms | BCL8B|LYST2 | |
| Cytomap | 13q13.3 | |
| Type of gene | protein-coding | |
| Description | neurobeachinlysosomal-trafficking regulator 2 | |
| Modification date | 20200328 | |
| 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 |
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Gene structures and expression levels for NBEA |
| 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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ENSG00000172915
| 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 | DOWN | ENST00000379922.3 | NBEA-202:protein_coding:NBEA | 6.434858e+02 | -9.623959e-01 | 5.977580e-07 | 9.674838e-06 |
| 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 NBEA |
| 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_111699 | chr13 | 35110810:35110978:35117414:35117493:35118228:35118290 | 35117414:35117493 |
| exon_skip_124443 | chr13 | 35123482:35123574:35142269:35142377:35155774:35155855 | 35142269:35142377 |
| exon_skip_131798 | chr13 | 35432269:35432393:35452092:35452235:35472400:35472536 | 35452092:35452235 |
| exon_skip_134920 | chr13 | 35628081:35628248:35645869:35645931:35646259:35646348 | 35645869:35645931 |
| exon_skip_144722 | chr13 | 35665085:35665186:35667374:35667570:35668368:35668519 | 35667374:35667570 |
| exon_skip_153557 | chr13 | 35290389:35290450:35309528:35309592:35349108:35349216 | 35309528:35309592 |
| exon_skip_156051 | chr13 | 35164356:35164509:35168987:35168995:35171272:35171452 | 35168987:35168995 |
| exon_skip_181189 | chr13 | 35040933:35041164:35044947:35045047:35045306:35045401 | 35044947:35045047 |
| exon_skip_19088 | chr13 | 35173464:35173594:35176996:35177103:35182360:35182528 | 35176996:35177103 |
| exon_skip_195228 | chr13 | 35628088:35628248:35645869:35645931:35646259:35646348 | 35645869:35645931 |
| exon_skip_256533 | chr13 | 35156083:35156206:35157078:35157270:35159016:35160032 | 35157078:35157270 |
| exon_skip_266725 | chr13 | 35583898:35584038:35593328:35593447:35606426:35606578 | 35593328:35593447 |
| exon_skip_286187 | chr13 | 35070719:35070852:35098297:35098405:35109290:35109442 | 35098297:35098405 |
| exon_skip_51688 | chr13 | 35667374:35667570:35668368:35668519:35670901:35672735 | 35668368:35668519 |
| exon_skip_60021 | chr13 | 35117414:35117493:35118228:35118290:35118377:35118474 | 35118228:35118290 |
| exon_skip_60405 | chr13 | 35352157:35352323:35432269:35432393:35452092:35452235 | 35432269:35432393 |
| exon_skip_71376 | chr13 | 35452092:35452235:35472400:35472536:35550477:35550594 | 35472400:35472536 |
| exon_skip_80795 | chr13 | 35118377:35118474:35123482:35123574:35142269:35142377 | 35123482:35123574 |
| 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 NBEA |
| 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 |
| ENST00000400445 | 35044947 | 35045047 | Frame-shift |
| ENST00000400445 | 35098297 | 35098405 | Frame-shift |
| ENST00000400445 | 35117414 | 35117493 | Frame-shift |
| ENST00000400445 | 35142269 | 35142377 | Frame-shift |
| ENST00000400445 | 35432269 | 35432393 | Frame-shift |
| ENST00000400445 | 35668368 | 35668519 | Frame-shift |
| ENST00000400445 | 35118228 | 35118290 | In-frame |
| ENST00000400445 | 35123482 | 35123574 | In-frame |
| ENST00000400445 | 35168987 | 35168995 | In-frame |
| ENST00000400445 | 35452092 | 35452235 | In-frame |
| ENST00000400445 | 35593328 | 35593447 | 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 |
| ENST00000400445 | 35098297 | 35098405 | Frame-shift |
| ENST00000400445 | 35117414 | 35117493 | Frame-shift |
| ENST00000400445 | 35142269 | 35142377 | Frame-shift |
| ENST00000400445 | 35157078 | 35157270 | Frame-shift |
| ENST00000400445 | 35118228 | 35118290 | In-frame |
| ENST00000400445 | 35123482 | 35123574 | In-frame |
| ENST00000400445 | 35168987 | 35168995 | In-frame |
| ENST00000400445 | 35176996 | 35177103 | 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 |
| ENST00000400445 | 35044947 | 35045047 | Frame-shift |
| ENST00000400445 | 35117414 | 35117493 | Frame-shift |
| ENST00000400445 | 35142269 | 35142377 | Frame-shift |
| ENST00000400445 | 35157078 | 35157270 | Frame-shift |
| ENST00000400445 | 35309528 | 35309592 | Frame-shift |
| ENST00000400445 | 35432269 | 35432393 | Frame-shift |
| ENST00000400445 | 35472400 | 35472536 | Frame-shift |
| ENST00000400445 | 35667374 | 35667570 | Frame-shift |
| ENST00000400445 | 35118228 | 35118290 | In-frame |
| ENST00000400445 | 35123482 | 35123574 | In-frame |
| ENST00000400445 | 35168987 | 35168995 | In-frame |
| ENST00000400445 | 35593328 | 35593447 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NBEA |
p-ENSG00000172915_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 |
| ENST00000400445 | 11136 | 2946 | 35118228 | 35118290 | 2618 | 2679 | 694 | 715 |
| ENST00000400445 | 11136 | 2946 | 35123482 | 35123574 | 2779 | 2870 | 748 | 778 |
| ENST00000400445 | 11136 | 2946 | 35452092 | 35452235 | 6840 | 6982 | 2102 | 2149 |
| ENST00000400445 | 11136 | 2946 | 35593328 | 35593447 | 7712 | 7830 | 2392 | 2432 |
| 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 |
| ENST00000400445 | 11136 | 2946 | 35118228 | 35118290 | 2618 | 2679 | 694 | 715 |
| ENST00000400445 | 11136 | 2946 | 35123482 | 35123574 | 2779 | 2870 | 748 | 778 |
| ENST00000400445 | 11136 | 2946 | 35176996 | 35177103 | 5090 | 5196 | 1518 | 1554 |
| 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 |
| ENST00000400445 | 11136 | 2946 | 35118228 | 35118290 | 2618 | 2679 | 694 | 715 |
| ENST00000400445 | 11136 | 2946 | 35123482 | 35123574 | 2779 | 2870 | 748 | 778 |
| ENST00000400445 | 11136 | 2946 | 35593328 | 35593447 | 7712 | 7830 | 2392 | 2432 |
| 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 |
| Q8NFP9 | 694 | 715 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 694 | 715 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 694 | 715 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 748 | 778 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 748 | 778 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 748 | 778 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 2102 | 2149 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 2102 | 2149 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 2102 | 2149 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 2102 | 2149 | 2147 | 2255 | Domain | Note=BEACH-type PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01119 |
| Q8NFP9 | 2102 | 2149 | 2138 | 2138 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPN1 |
| Q8NFP9 | 2392 | 2432 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 2392 | 2432 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 2392 | 2432 | 2274 | 2563 | Domain | Note=BEACH;Ontology_term=ECO:0000255,ECO:0000305;evidence=ECO:0000255|PROSITE-ProRule:PRU00026,ECO:0000305 |
| Q8NFP9 | 2392 | 2432 | 2395 | 2401 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
| Q8NFP9 | 2392 | 2432 | 2417 | 2426 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
| Q8NFP9 | 2392 | 2432 | 2402 | 2405 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
| Q8NFP9 | 2392 | 2432 | 2410 | 2412 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
| 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 |
| Q8NFP9 | 694 | 715 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 694 | 715 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 694 | 715 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 748 | 778 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 748 | 778 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 748 | 778 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 1518 | 1554 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 1518 | 1554 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 1518 | 1554 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 1518 | 1554 | 1529 | 1529 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9EPN1 |
| 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 |
| Q8NFP9 | 694 | 715 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 694 | 715 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 694 | 715 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 748 | 778 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 748 | 778 | 1 | 2207 | Alternative sequence | ID=VSP_046397;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8NFP9 | 748 | 778 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 2392 | 2432 | 1 | 2443 | Alternative sequence | ID=VSP_050538;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8NFP9 | 2392 | 2432 | 1 | 2946 | Chain | ID=PRO_0000051089;Note=Neurobeachin |
| Q8NFP9 | 2392 | 2432 | 2274 | 2563 | Domain | Note=BEACH;Ontology_term=ECO:0000255,ECO:0000305;evidence=ECO:0000255|PROSITE-ProRule:PRU00026,ECO:0000305 |
| Q8NFP9 | 2392 | 2432 | 2395 | 2401 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
| Q8NFP9 | 2392 | 2432 | 2417 | 2426 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
| Q8NFP9 | 2392 | 2432 | 2402 | 2405 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
| Q8NFP9 | 2392 | 2432 | 2410 | 2412 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1MI1 |
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3'-UTR located exon skipping events that lost miRNA binding sites in NBEA |
| 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 NBEA |
| - 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 NBEA |
| 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 |
| ADstage | MSBB | IFG | exon_skip_292840 | 4.018597e-01 | 3.402447e-02 | chr13 | + | 35159016 | 35160032 | 35160423 | 35160592 | 35161750 | 35161967 |
| CDR | MSBB | IFG | exon_skip_292840 | 4.310191e-01 | 2.202812e-02 | chr13 | + | 35159016 | 35160032 | 35160423 | 35160592 | 35161750 | 35161967 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NBEA |
| 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 NBEA |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TRA2A | exon_skip_60021 | -5.938783e-01 | 5.380315e-15 |
| CB | HNRNPDL | exon_skip_60021 | 4.619094e-01 | 6.362694e-09 |
| CB | RBM45 | exon_skip_60021 | 7.118945e-01 | 2.136737e-23 |
| CB | NUP42 | exon_skip_60021 | 5.199519e-01 | 2.833537e-11 |
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RelatedDrugs for NBEA |
| 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 NBEA |
| 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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