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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 NSD3 |
 Gene summary |
| Gene information | Gene symbol | NSD3 | Gene ID | 54904 |
| Gene name | nuclear receptor binding SET domain protein 3 | |
| Synonyms | KMT3F|KMT3G|WHISTLE|WHSC1L1|pp14328 | |
| Cytomap | 8p11.23 | |
| Type of gene | protein-coding | |
| Description | histone-lysine N-methyltransferase NSD3WHSC1-like 1 isoform 9 with methyltransferase activity to lysineWolf-Hirschhorn syndrome candidate 1-like 1nuclear SET domain-containing protein 3protein whistle | |
| 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 |
| NSD3 | GO:0016571 | histone methylation | 16682010 |
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Gene structures and expression levels for NSD3 |
| 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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ENSG00000147548
| 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 | ENST00000433384.6 | NSD3-203:protein_coding:NSD3 | 1.133441e+01 | 9.140434e-01 | 3.696678e-04 | 2.233550e-03 |
| 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 NSD3 |
| 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_131854 | chr8 | 38290475:38290677:38295796:38295952:38299444:38299590 | 38295796:38295952 |
| exon_skip_145697 | chr8 | 38295796:38295952:38299444:38299590:38304587:38304757 | 38299444:38299590 |
| exon_skip_179097 | chr8 | 38295796:38295952:38304587:38304757:38305248:38305445 | 38304587:38304757 |
| exon_skip_190575 | chr8 | 38318895:38318940:38321072:38321172:38326730:38326835 | 38321072:38321172 |
| exon_skip_200372 | chr8 | 38288487:38288756:38289393:38289505:38290475:38290677 | 38289393:38289505 |
| exon_skip_202998 | chr8 | 38337369:38337467:38338536:38338607:38347497:38348215 | 38338536:38338607 |
| exon_skip_227690 | chr8 | 38321072:38321172:38326730:38326856:38329378:38329893 | 38326730:38326856 |
| 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 NSD3 |
| 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 |
| ENST00000317025 | 38321072 | 38321172 | Frame-shift |
| ENST00000317025 | 38326730 | 38326856 | Frame-shift |
| ENST00000317025 | 38299444 | 38299590 | In-frame |
| ENST00000317025 | 38338536 | 38338607 | 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 |
| ENST00000317025 | 38326730 | 38326856 | Frame-shift |
| ENST00000317025 | 38299444 | 38299590 | In-frame |
| ENST00000317025 | 38338536 | 38338607 | 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 |
| ENST00000317025 | 38289393 | 38289505 | Frame-shift |
| ENST00000317025 | 38295796 | 38295952 | Frame-shift |
| ENST00000317025 | 38321072 | 38321172 | Frame-shift |
| ENST00000317025 | 38326730 | 38326856 | Frame-shift |
| ENST00000317025 | 38299444 | 38299590 | In-frame |
| ENST00000317025 | 38338536 | 38338607 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NSD3 |
p-ENSG00000147548_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 |
| ENST00000317025 | 10793 | 1437 | 38338536 | 38338607 | 1194 | 1264 | 225 | 248 |
| ENST00000317025 | 10793 | 1437 | 38299444 | 38299590 | 3130 | 3275 | 870 | 919 |
| 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 |
| ENST00000317025 | 10793 | 1437 | 38338536 | 38338607 | 1194 | 1264 | 225 | 248 |
| ENST00000317025 | 10793 | 1437 | 38299444 | 38299590 | 3130 | 3275 | 870 | 919 |
| 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 |
| ENST00000317025 | 10793 | 1437 | 38338536 | 38338607 | 1194 | 1264 | 225 | 248 |
| ENST00000317025 | 10793 | 1437 | 38299444 | 38299590 | 3130 | 3275 | 870 | 919 |
| 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 |
| Q9BZ95 | 225 | 248 | 1 | 1437 | Chain | ID=PRO_0000259521;Note=Histone-lysine N-methyltransferase NSD3 |
| Q9BZ95 | 225 | 248 | 245 | 245 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:25772364,ECO:0000244|PubMed:28112733;Dbxref=PMID:25218447,PMID:25772364,PMI |
| Q9BZ95 | 870 | 919 | 646 | 1437 | Alternative sequence | ID=VSP_021429;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11374904,ECO:0000303|PubMed:11549311,ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|Ref.3;D |
| Q9BZ95 | 870 | 919 | 871 | 919 | Alternative sequence | ID=VSP_021430;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11374904;Dbxref=PMID:11374904 |
| Q9BZ95 | 870 | 919 | 1 | 1437 | Chain | ID=PRO_0000259521;Note=Histone-lysine N-methyltransferase NSD3 |
| Q9BZ95 | 870 | 919 | 862 | 955 | Zinc finger | Note=PHD-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00146 |
| 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 |
| Q9BZ95 | 225 | 248 | 1 | 1437 | Chain | ID=PRO_0000259521;Note=Histone-lysine N-methyltransferase NSD3 |
| Q9BZ95 | 225 | 248 | 245 | 245 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:25772364,ECO:0000244|PubMed:28112733;Dbxref=PMID:25218447,PMID:25772364,PMI |
| Q9BZ95 | 870 | 919 | 646 | 1437 | Alternative sequence | ID=VSP_021429;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11374904,ECO:0000303|PubMed:11549311,ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|Ref.3;D |
| Q9BZ95 | 870 | 919 | 871 | 919 | Alternative sequence | ID=VSP_021430;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11374904;Dbxref=PMID:11374904 |
| Q9BZ95 | 870 | 919 | 1 | 1437 | Chain | ID=PRO_0000259521;Note=Histone-lysine N-methyltransferase NSD3 |
| Q9BZ95 | 870 | 919 | 862 | 955 | Zinc finger | Note=PHD-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00146 |
| 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 |
| Q9BZ95 | 225 | 248 | 1 | 1437 | Chain | ID=PRO_0000259521;Note=Histone-lysine N-methyltransferase NSD3 |
| Q9BZ95 | 225 | 248 | 245 | 245 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:25772364,ECO:0000244|PubMed:28112733;Dbxref=PMID:25218447,PMID:25772364,PMI |
| Q9BZ95 | 870 | 919 | 646 | 1437 | Alternative sequence | ID=VSP_021429;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11374904,ECO:0000303|PubMed:11549311,ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|Ref.3;D |
| Q9BZ95 | 870 | 919 | 871 | 919 | Alternative sequence | ID=VSP_021430;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11374904;Dbxref=PMID:11374904 |
| Q9BZ95 | 870 | 919 | 1 | 1437 | Chain | ID=PRO_0000259521;Note=Histone-lysine N-methyltransferase NSD3 |
| Q9BZ95 | 870 | 919 | 862 | 955 | Zinc finger | Note=PHD-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00146 |
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3'-UTR located exon skipping events that lost miRNA binding sites in NSD3 |
| 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 NSD3 |
| - 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 NSD3 |
| 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 NSD3 |
| 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 NSD3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | TARDBP | exon_skip_145697 | 4.145886e-01 | 3.154266e-02 |
| IFG | RBM6 | exon_skip_145697 | 4.139758e-01 | 3.182031e-02 |
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RelatedDrugs for NSD3 |
| 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 NSD3 |
| 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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