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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 NPM1 |
 Gene summary |
| Gene information | Gene symbol | NPM1 | Gene ID | 4869 |
| Gene name | nucleophosmin 1 | |
| Synonyms | B23|NPM | |
| Cytomap | 5q35.1 | |
| Type of gene | protein-coding | |
| Description | nucleophosminnucleolar protein NO38nucleophosmin (nucleolar phosphoprotein B23, numatrin)nucleophosmin/nucleoplasmin family, member 1testicular tissue protein Li 128 | |
| Modification date | 20180523 | |
| UniProtAcc | P06748 | |
| Context | PubMed: NPM1 [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 |
| NPM1 | GO:0006281 | DNA repair | 19188445 |
| NPM1 | GO:0006334 | nucleosome assembly | 11602260 |
| NPM1 | GO:0006913 | nucleocytoplasmic transport | 16041368 |
| NPM1 | GO:0008104 | protein localization | 18420587 |
| NPM1 | GO:0008284 | positive regulation of cell proliferation | 22528486 |
| NPM1 | GO:0032071 | regulation of endodeoxyribonuclease activity | 19188445 |
| NPM1 | GO:0034644 | cellular response to UV | 19160485 |
| NPM1 | GO:0043066 | negative regulation of apoptotic process | 12882984 |
| NPM1 | GO:0044387 | negative regulation of protein kinase activity by regulation of protein phosphorylation | 12882984 |
| NPM1 | GO:0045727 | positive regulation of translation | 12882984 |
| NPM1 | GO:0045893 | positive regulation of transcription, DNA-templated | 22528486 |
| NPM1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19160485 |
| NPM1 | GO:0051259 | protein complex oligomerization | 18809582 |
| NPM1 | GO:0060699 | regulation of endoribonuclease activity | 19188445 |
| NPM1 | GO:0060735 | regulation of eIF2 alpha phosphorylation by dsRNA | 12882984 |
| NPM1 | GO:1902751 | positive regulation of cell cycle G2/M phase transition | 22528486 |
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Exon skipping events across known transcript of Ensembl for NPM1 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 NPM1 |
| 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 NPM1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_439597 | 5 | 170814936:170815010:170817054:170817134:170818308:170818373 | 170817054:170817134 | ENSG00000181163.9 | ENST00000351986.6,ENST00000296930.5,ENST00000518587.1,ENST00000393820.2,ENST00000517671.1 |
| exon_skip_439602 | 5 | 170814936:170815010:170817078:170817134:170818308:170818373 | 170817078:170817134 | ENSG00000181163.9 | ENST00000523622.1 |
| exon_skip_439604 | 5 | 170814936:170815010:170818308:170818428:170818709:170818753 | 170818308:170818428 | ENSG00000181163.9 | ENST00000521672.1 |
| exon_skip_439615 | 5 | 170817097:170817134:170818308:170818428:170818709:170818753 | 170818308:170818428 | ENSG00000181163.9 | ENST00000351986.6,ENST00000296930.5,ENST00000518587.1,ENST00000393820.2,ENST00000517671.1 |
| exon_skip_439616 | 5 | 170818308:170818428:170818709:170818803:170819713:170819820 | 170818709:170818803 | ENSG00000181163.9 | ENST00000351986.6,ENST00000296930.5,ENST00000521672.1,ENST00000518587.1,ENST00000393820.2,ENST00000517671.1 |
| exon_skip_439621 | 5 | 170819917:170819982:170827156:170827214:170827842:170827929 | 170827156:170827214 | ENSG00000181163.9 | ENST00000296930.5,ENST00000393820.2,ENST00000517671.1 |
| exon_skip_439622 | 5 | 170819917:170819982:170827156:170827214:170832305:170832392 | 170827156:170827214 | ENSG00000181163.9 | ENST00000351986.6 |
| exon_skip_439641 | 5 | 170827156:170827214:170827842:170827929:170832305:170832392 | 170827842:170827929 | ENSG00000181163.9 | ENST00000296930.5,ENST00000393820.2,ENST00000517671.1 |
| exon_skip_439648 | 5 | 170827156:170827214:170832305:170832407:170834703:170834778 | 170832305:170832407 | ENSG00000181163.9 | ENST00000351986.6 |
| exon_skip_439657 | 5 | 170827842:170827929:170832305:170832407:170834703:170834778 | 170832305:170832407 | ENSG00000181163.9 | ENST00000296930.5,ENST00000517671.1 |
| exon_skip_439665 | 5 | 170832305:170832407:170834703:170834778:170837530:170837887 | 170834703:170834778 | ENSG00000181163.9 | ENST00000351986.6,ENST00000296930.5,ENST00000517671.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for NPM1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_439597 | 5 | 170814936:170815010:170817054:170817134:170818308:170818373 | 170817054:170817134 | ENSG00000181163.9 | ENST00000517671.1,ENST00000296930.5,ENST00000351986.6,ENST00000393820.2,ENST00000518587.1 |
| exon_skip_439602 | 5 | 170814936:170815010:170817078:170817134:170818308:170818373 | 170817078:170817134 | ENSG00000181163.9 | ENST00000523622.1 |
| exon_skip_439604 | 5 | 170814936:170815010:170818308:170818428:170818709:170818753 | 170818308:170818428 | ENSG00000181163.9 | ENST00000521672.1 |
| exon_skip_439615 | 5 | 170817097:170817134:170818308:170818428:170818709:170818753 | 170818308:170818428 | ENSG00000181163.9 | ENST00000517671.1,ENST00000296930.5,ENST00000351986.6,ENST00000393820.2,ENST00000518587.1 |
| exon_skip_439616 | 5 | 170818308:170818428:170818709:170818803:170819713:170819820 | 170818709:170818803 | ENSG00000181163.9 | ENST00000517671.1,ENST00000296930.5,ENST00000521672.1,ENST00000351986.6,ENST00000393820.2,ENST00000518587.1 |
| exon_skip_439621 | 5 | 170819917:170819982:170827156:170827214:170827842:170827929 | 170827156:170827214 | ENSG00000181163.9 | ENST00000517671.1,ENST00000296930.5,ENST00000393820.2 |
| exon_skip_439622 | 5 | 170819917:170819982:170827156:170827214:170832305:170832392 | 170827156:170827214 | ENSG00000181163.9 | ENST00000351986.6 |
| exon_skip_439641 | 5 | 170827156:170827214:170827842:170827929:170832305:170832392 | 170827842:170827929 | ENSG00000181163.9 | ENST00000517671.1,ENST00000296930.5,ENST00000393820.2 |
| exon_skip_439648 | 5 | 170827156:170827214:170832305:170832407:170834703:170834778 | 170832305:170832407 | ENSG00000181163.9 | ENST00000351986.6 |
| exon_skip_439657 | 5 | 170827842:170827929:170832305:170832407:170834703:170834778 | 170832305:170832407 | ENSG00000181163.9 | ENST00000517671.1,ENST00000296930.5 |
| exon_skip_439665 | 5 | 170832305:170832407:170834703:170834778:170837530:170837887 | 170834703:170834778 | ENSG00000181163.9 | ENST00000517671.1,ENST00000296930.5,ENST00000351986.6 |
| 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 NPM1 |
| 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 |
| ENST00000296930 | 170817054 | 170817134 | Frame-shift |
| ENST00000517671 | 170817054 | 170817134 | Frame-shift |
| ENST00000296930 | 170818709 | 170818803 | Frame-shift |
| ENST00000517671 | 170818709 | 170818803 | Frame-shift |
| ENST00000296930 | 170827156 | 170827214 | Frame-shift |
| ENST00000517671 | 170827156 | 170827214 | Frame-shift |
| ENST00000296930 | 170818308 | 170818428 | In-frame |
| ENST00000517671 | 170818308 | 170818428 | In-frame |
| ENST00000296930 | 170827842 | 170827929 | In-frame |
| ENST00000517671 | 170827842 | 170827929 | In-frame |
| ENST00000296930 | 170832305 | 170832407 | In-frame |
| ENST00000517671 | 170832305 | 170832407 | In-frame |
| ENST00000296930 | 170834703 | 170834778 | In-frame |
| ENST00000517671 | 170834703 | 170834778 | 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 |
| ENST00000296930 | 170817054 | 170817134 | Frame-shift |
| ENST00000517671 | 170817054 | 170817134 | Frame-shift |
| ENST00000296930 | 170818709 | 170818803 | Frame-shift |
| ENST00000517671 | 170818709 | 170818803 | Frame-shift |
| ENST00000296930 | 170827156 | 170827214 | Frame-shift |
| ENST00000517671 | 170827156 | 170827214 | Frame-shift |
| ENST00000296930 | 170818308 | 170818428 | In-frame |
| ENST00000517671 | 170818308 | 170818428 | In-frame |
| ENST00000296930 | 170827842 | 170827929 | In-frame |
| ENST00000517671 | 170827842 | 170827929 | In-frame |
| ENST00000296930 | 170832305 | 170832407 | In-frame |
| ENST00000517671 | 170832305 | 170832407 | In-frame |
| ENST00000296930 | 170834703 | 170834778 | In-frame |
| ENST00000517671 | 170834703 | 170834778 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NPM1 |
| 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 |
| ENST00000296930 | 1775 | 294 | 170818308 | 170818428 | 440 | 559 | 46 | 86 |
| ENST00000517671 | 1355 | 294 | 170818308 | 170818428 | 274 | 393 | 46 | 86 |
| ENST00000296930 | 1775 | 294 | 170827842 | 170827929 | 884 | 970 | 194 | 223 |
| ENST00000517671 | 1355 | 294 | 170827842 | 170827929 | 718 | 804 | 194 | 223 |
| ENST00000296930 | 1775 | 294 | 170832305 | 170832407 | 971 | 1072 | 223 | 257 |
| ENST00000517671 | 1355 | 294 | 170832305 | 170832407 | 805 | 906 | 223 | 257 |
| ENST00000296930 | 1775 | 294 | 170834703 | 170834778 | 1073 | 1147 | 257 | 282 |
| ENST00000517671 | 1355 | 294 | 170834703 | 170834778 | 907 | 981 | 257 | 282 |
| 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 |
| ENST00000296930 | 1775 | 294 | 170818308 | 170818428 | 440 | 559 | 46 | 86 |
| ENST00000517671 | 1355 | 294 | 170818308 | 170818428 | 274 | 393 | 46 | 86 |
| ENST00000296930 | 1775 | 294 | 170827842 | 170827929 | 884 | 970 | 194 | 223 |
| ENST00000517671 | 1355 | 294 | 170827842 | 170827929 | 718 | 804 | 194 | 223 |
| ENST00000296930 | 1775 | 294 | 170832305 | 170832407 | 971 | 1072 | 223 | 257 |
| ENST00000517671 | 1355 | 294 | 170832305 | 170832407 | 805 | 906 | 223 | 257 |
| ENST00000296930 | 1775 | 294 | 170834703 | 170834778 | 1073 | 1147 | 257 | 282 |
| ENST00000517671 | 1355 | 294 | 170834703 | 170834778 | 907 | 981 | 257 | 282 |
| 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 |
| 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 |
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SNVs in the skipped exons for NPM1 |
| - 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 |
| KIRP | TCGA-UZ-A9PS-01 | exon_skip_439604 exon_skip_439615 | 170818309 | 170818428 | 170818328 | 170818329 | Frame_Shift_Ins | - | A | p.A53fs |
| LGG | TCGA-DU-6392-01 | exon_skip_439641 | 170827843 | 170827929 | 170827849 | 170827849 | Nonsense_Mutation | C | T | p.R197* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-UZ-A9PS-01 |
| Cancer type: KIRP | |
| ESID: exon_skip_439615 | |
| Skipped exon start: 170818309 | |
| Skipped exon end: 170818428 | |
| Mutation start: 170818328 | |
| Mutation end: 170818329 | |
| Mutation type: Frame_Shift_Ins | |
| Reference seq: - | |
| Mutation seq: A | |
| AAchange: p.A53fs | |
exon_skip_425876_KIRP_TCGA-UZ-A9PS-01.png | |
exon_skip_438605_KIRP_TCGA-UZ-A9PS-01.png | |
exon_skip_439615_KIRP_TCGA-UZ-A9PS-01.png | |
| - 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 |
| HEC1A_ENDOMETRIUM | 170832306 | 170832407 | 170832382 | 170832383 | Frame_Shift_Ins | - | A | p.AK249fs |
| HS683_CENTRAL_NERVOUS_SYSTEM | 170817079 | 170817134 | 170817108 | 170817108 | Missense_Mutation | A | G | p.N38D |
| HS683_CENTRAL_NERVOUS_SYSTEM | 170817055 | 170817134 | 170817108 | 170817108 | Missense_Mutation | A | G | p.N38D |
| DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170818309 | 170818428 | 170818363 | 170818363 | Missense_Mutation | A | C | p.M65L |
| MZ7MEL_SKIN | 170818309 | 170818428 | 170818376 | 170818376 | Missense_Mutation | G | A | p.G69D |
| NCIBL2122_MATCHED_NORMAL_TISSUE | 170827157 | 170827214 | 170827179 | 170827179 | Missense_Mutation | G | A | p.D183N |
| TYKNU_OVARY | 170827157 | 170827214 | 170827189 | 170827189 | Missense_Mutation | C | T | p.A186V |
| KALS1_CENTRAL_NERVOUS_SYSTEM | 170827843 | 170827929 | 170827889 | 170827889 | Missense_Mutation | A | G | p.N210S |
| CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170827843 | 170827929 | 170827919 | 170827919 | Missense_Mutation | C | T | p.P220L |
| WM278_SKIN | 170832306 | 170832407 | 170832339 | 170832339 | Missense_Mutation | C | T | p.P235S |
| SNU1040_LARGE_INTESTINE | 170834704 | 170834778 | 170834761 | 170834761 | Missense_Mutation | C | T | p.R277W |
| NB69_AUTONOMIC_GANGLIA | 170834704 | 170834778 | 170834777 | 170834777 | Splice_Site | A | T | p.E282V |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NPM1 |
| 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 NPM1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NPM1 |
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RelatedDrugs for NPM1 |
| 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 NPM1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| NPM1 | C0023467 | Leukemia, Myelocytic, Acute | 3 | CTD_human |
| NPM1 | C0023487 | Acute Promyelocytic Leukemia | 2 | CTD_human;ORPHANET |
| NPM1 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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