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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 NBN |
 Gene summary |
| Gene information | Gene symbol | NBN | Gene ID | 4683 |
| Gene name | nibrin | |
| Synonyms | AT-V1|AT-V2|ATV|NBS|NBS1|P95 | |
| Cytomap | 8q21.3 | |
| Type of gene | protein-coding | |
| Description | nibrinNijmegen breakage syndrome 1 (nibrin)cell cycle regulatory protein p95p95 protein of the MRE11/RAD50 complex | |
| Modification date | 20200315 | |
| UniProtAcc | A0A087X1V5, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| NBN | GO:0000077 | DNA damage checkpoint | 12529385 |
| NBN | GO:0006302 | double-strand break repair | 9590181 |
| NBN | GO:0007093 | mitotic cell cycle checkpoint | 10766245 |
| NBN | GO:0007095 | mitotic G2 DNA damage checkpoint | 11438675 |
| NBN | GO:0031954 | positive regulation of protein autophosphorylation | 15790808 |
| NBN | GO:0033674 | positive regulation of kinase activity | 15790808 |
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Gene structures and expression levels for NBN |
| 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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ENSG00000104320
| 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 | ENST00000519426.5 | NBN-208:protein_coding:NBN | 1.427321e+00 | 2.308961e+00 | 4.094199e-09 | 1.424184e-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 NBN |
| 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_113988 | chr8 | 89980734:89980893:89981375:89981523:89982722:89982855 | 89981375:89981523 |
| exon_skip_13910 | chr8 | 89982722:89982855:89984525:89984733:89984917:89984973 | 89984525:89984733 |
| exon_skip_142302 | chr8 | 89937026:89937075:89943253:89943366:89947824:89947892 | 89943253:89943366 |
| exon_skip_146784 | chr8 | 89935432:89935612:89937026:89937075:89943253:89943366 | 89937026:89937075 |
| exon_skip_1520 | chr8 | 89955283:89955555:89958725:89958854:89964410:89964507 | 89958725:89958854 |
| exon_skip_181791 | chr8 | 89981375:89981523:89981953:89982002:89982722:89982855 | 89981953:89982002 |
| exon_skip_196352 | chr8 | 89946140:89946295:89947824:89947892:89953244:89953354 | 89947824:89947892 |
| exon_skip_209630 | chr8 | 89978282:89978323:89980734:89980893:89981375:89981523 | 89980734:89980893 |
| exon_skip_228412 | chr8 | 89943359:89943366:89947824:89947892:89953244:89953354 | 89947824:89947892 |
| exon_skip_247134 | chr8 | 89935544:89935612:89937026:89937075:89943253:89943366 | 89937026:89937075 |
| exon_skip_249001 | chr8 | 89943253:89943366:89946140:89946295:89947824:89947892 | 89946140:89946295 |
| exon_skip_251000 | chr8 | 89943359:89943366:89946140:89946295:89947824:89947892 | 89946140:89946295 |
| exon_skip_251257 | chr8 | 89981375:89981523:89982722:89982855:89984525:89984619 | 89982722:89982855 |
| exon_skip_265601 | chr8 | 89970520:89970557:89971173:89971290:89978220:89978323 | 89971173:89971290 |
| exon_skip_284456 | chr8 | 89937026:89937075:89943253:89943366:89946140:89946295 | 89943253:89943366 |
| exon_skip_288701 | chr8 | 89970520:89970557:89971173:89971290:89981375:89981523 | 89971173:89971290 |
| exon_skip_293038 | chr8 | 89978282:89978323:89980734:89980852:89981375:89981523 | 89980734:89980852 |
| exon_skip_33121 | chr8 | 89980734:89980893:89981375:89981523:89981953:89982002 | 89981375:89981523 |
| exon_skip_48922 | chr8 | 89971173:89971290:89978220:89978323:89980734:89980852 | 89978220:89978323 |
| exon_skip_63971 | chr8 | 89981469:89981523:89981953:89982002:89982722:89982855 | 89981953:89982002 |
| 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 NBN |
| 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 |
| ENST00000265433 | 89937026 | 89937075 | Frame-shift |
| ENST00000265433 | 89971173 | 89971290 | Frame-shift |
| ENST00000265433 | 89978220 | 89978323 | Frame-shift |
| ENST00000265433 | 89980734 | 89980893 | Frame-shift |
| ENST00000265433 | 89981375 | 89981523 | Frame-shift |
| ENST00000265433 | 89946140 | 89946295 | In-frame |
| ENST00000265433 | 89947824 | 89947892 | 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 |
| ENST00000265433 | 89937026 | 89937075 | Frame-shift |
| ENST00000265433 | 89978220 | 89978323 | Frame-shift |
| ENST00000265433 | 89980734 | 89980893 | Frame-shift |
| ENST00000265433 | 89947824 | 89947892 | 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 |
| ENST00000265433 | 89937026 | 89937075 | Frame-shift |
| ENST00000265433 | 89958725 | 89958854 | Frame-shift |
| ENST00000265433 | 89971173 | 89971290 | Frame-shift |
| ENST00000265433 | 89978220 | 89978323 | Frame-shift |
| ENST00000265433 | 89980734 | 89980893 | Frame-shift |
| ENST00000265433 | 89981375 | 89981523 | Frame-shift |
| ENST00000265433 | 89943253 | 89943366 | In-frame |
| ENST00000265433 | 89946140 | 89946295 | In-frame |
| ENST00000265433 | 89947824 | 89947892 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NBN |
p-ENSG00000104320_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 |
| ENST00000265433 | 4683 | 754 | 89947824 | 89947892 | 2001 | 2068 | 615 | 637 |
| ENST00000265433 | 4683 | 754 | 89946140 | 89946295 | 2070 | 2224 | 638 | 689 |
| 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 |
| ENST00000265433 | 4683 | 754 | 89947824 | 89947892 | 2001 | 2068 | 615 | 637 |
| 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 |
| ENST00000265433 | 4683 | 754 | 89947824 | 89947892 | 2001 | 2068 | 615 | 637 |
| ENST00000265433 | 4683 | 754 | 89946140 | 89946295 | 2070 | 2224 | 638 | 689 |
| ENST00000265433 | 4683 | 754 | 89943253 | 89943366 | 2226 | 2338 | 690 | 727 |
| 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 |
| O60934 | 615 | 637 | 1 | 754 | Chain | ID=PRO_0000231043;Note=Nibrin |
| O60934 | 615 | 637 | 615 | 615 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10839545;Dbxref=PMID:10839545 |
| O60934 | 615 | 637 | 615 | 615 | Mutagenesis | Note=Abrogates ATM-dependent phosphorylation. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10839545;Dbxref=PMID:10839545 |
| O60934 | 638 | 689 | 1 | 754 | Chain | ID=PRO_0000231043;Note=Nibrin |
| O60934 | 638 | 689 | 673 | 673 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| O60934 | 638 | 689 | 679 | 679 | Natural variant | ID=VAR_064738;Note=Found in a renal cell carcinoma sample%3B somatic mutation. Y->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21248752;Dbxref=PMID:21248752 |
| 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 |
| O60934 | 615 | 637 | 1 | 754 | Chain | ID=PRO_0000231043;Note=Nibrin |
| O60934 | 615 | 637 | 615 | 615 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10839545;Dbxref=PMID:10839545 |
| O60934 | 615 | 637 | 615 | 615 | Mutagenesis | Note=Abrogates ATM-dependent phosphorylation. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10839545;Dbxref=PMID:10839545 |
| 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 |
| O60934 | 615 | 637 | 1 | 754 | Chain | ID=PRO_0000231043;Note=Nibrin |
| O60934 | 615 | 637 | 615 | 615 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10839545;Dbxref=PMID:10839545 |
| O60934 | 615 | 637 | 615 | 615 | Mutagenesis | Note=Abrogates ATM-dependent phosphorylation. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10839545;Dbxref=PMID:10839545 |
| O60934 | 638 | 689 | 1 | 754 | Chain | ID=PRO_0000231043;Note=Nibrin |
| O60934 | 638 | 689 | 673 | 673 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| O60934 | 638 | 689 | 679 | 679 | Natural variant | ID=VAR_064738;Note=Found in a renal cell carcinoma sample%3B somatic mutation. Y->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21248752;Dbxref=PMID:21248752 |
| O60934 | 690 | 727 | 1 | 754 | Chain | ID=PRO_0000231043;Note=Nibrin |
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3'-UTR located exon skipping events that lost miRNA binding sites in NBN |
| 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 NBN |
| - 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 NBN |
| 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 NBN |
| 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 NBN |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TRA2A | exon_skip_146784 | -4.953099e-01 | 3.687134e-11 |
| CB | TRA2A | exon_skip_196352 | -6.360648e-01 | 4.586294e-19 |
| CB | NUP42 | exon_skip_196352 | 4.093715e-01 | 1.118527e-07 |
| CB | CNOT4 | exon_skip_209630 | -4.486192e-01 | 2.191668e-07 |
| CB | TRA2A | exon_skip_209630 | -4.198583e-01 | 1.478380e-06 |
| CB | RBM4 | exon_skip_209630 | -4.783715e-01 | 2.506680e-08 |
| IFG | PABPC3 | exon_skip_181791 | -4.207422e-01 | 2.886137e-02 |
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RelatedDrugs for NBN |
| 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 NBN |
| 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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