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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 DNMT3A |
 Gene summary |
| Gene information | Gene symbol | DNMT3A | Gene ID | 1788 |
| Gene name | DNA methyltransferase 3 alpha | |
| Synonyms | DNMT3A2|HESJAS|M.HsaIIIA|TBRS | |
| Cytomap | 2p23.3 | |
| Type of gene | protein-coding | |
| Description | DNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5-)-methyltransferase 3 alphaDNA MTase HsaIIIADNA cytosine methyltransferase 3A2 | |
| Modification date | 20200322 | |
| 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 |
| DNMT3A | GO:0006306 | DNA methylation | 12138111|19786833|23042785 |
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Gene structures and expression levels for DNMT3A |
| 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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ENSG00000119772
| 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 | ENST00000380756.7 | DNMT3A-204:nonsense_mediated_decay:DNMT3A | 1.752232e+01 | 1.129008e+00 | 4.258520e-10 | 2.164094e-08 |
| CB | UP | ENST00000474887.5 | DNMT3A-211:lncRNA:DNMT3A | 9.381541e+00 | 8.069317e-01 | 1.852576e-07 | 3.576192e-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 DNMT3A |
| 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_110318 | chr2 | 25239176:25239215:25239315:25239513:25240302:25240450 | 25239315:25239513 |
| exon_skip_110685 | chr2 | 25236974:25237005:25239130:25239215:25240302:25240450 | 25239130:25239215 |
| exon_skip_157081 | chr2 | 25239130:25239215:25239315:25239513:25240302:25240450 | 25239315:25239513 |
| exon_skip_177168 | chr2 | 25240640:25240730:25241562:25241707:25243898:25243979 | 25241562:25241707 |
| exon_skip_202251 | chr2 | 25248037:25248252:25249657:25249724:25252194:25252311 | 25249657:25249724 |
| exon_skip_202271 | chr2 | 25236974:25237005:25239130:25239215:25240640:25240730 | 25239130:25239215 |
| exon_skip_210842 | chr2 | 25240640:25240730:25241562:25241777:25243898:25243982 | 25241562:25241777 |
| exon_skip_214237 | chr2 | 25235706:25235825:25236936:25237005:25239130:25239215 | 25236936:25237005 |
| exon_skip_264442 | chr2 | 25235785:25235825:25236936:25237005:25239130:25239215 | 25236936:25237005 |
| exon_skip_279756 | chr2 | 25240640:25240730:25241562:25241707:25243898:25243970 | 25241562:25241707 |
| exon_skip_42591 | chr2 | 25239176:25239215:25240302:25240450:25240640:25240730 | 25240302:25240450 |
| exon_skip_52265 | chr2 | 25247051:25247158:25247591:25247749:25248037:25248252 | 25247591:25247749 |
| 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 DNMT3A |
| 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 |
| ENST00000264709 | 25236936 | 25237005 | Frame-shift |
| ENST00000321117 | 25236936 | 25237005 | Frame-shift |
| ENST00000264709 | 25240302 | 25240450 | Frame-shift |
| ENST00000321117 | 25240302 | 25240450 | Frame-shift |
| ENST00000264709 | 25241562 | 25241707 | Frame-shift |
| ENST00000321117 | 25241562 | 25241707 | Frame-shift |
| 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 |
| ENST00000264709 | 25236936 | 25237005 | Frame-shift |
| ENST00000321117 | 25236936 | 25237005 | Frame-shift |
| ENST00000264709 | 25241562 | 25241707 | Frame-shift |
| ENST00000321117 | 25241562 | 25241707 | Frame-shift |
| 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 |
| ENST00000264709 | 25236936 | 25237005 | Frame-shift |
| ENST00000321117 | 25236936 | 25237005 | Frame-shift |
| ENST00000264709 | 25239130 | 25239215 | Frame-shift |
| ENST00000321117 | 25239130 | 25239215 | Frame-shift |
| ENST00000264709 | 25240302 | 25240450 | Frame-shift |
| ENST00000321117 | 25240302 | 25240450 | Frame-shift |
| ENST00000264709 | 25241562 | 25241707 | Frame-shift |
| ENST00000321117 | 25241562 | 25241707 | Frame-shift |
| ENST00000264709 | 25247591 | 25247749 | In-frame |
| ENST00000321117 | 25247591 | 25247749 | In-frame |
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Infer the effects of exon skipping event on protein functional features for DNMT3A |
p-ENSG00000119772_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 |
| 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 |
| 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 |
| ENST00000264709 | 9518 | 912 | 25247591 | 25247749 | 1194 | 1351 | 285 | 337 |
| ENST00000321117 | 4296 | 912 | 25247591 | 25247749 | 1093 | 1250 | 285 | 337 |
| 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 |
| 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 |
| 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 |
| Q9Y6K1 | 285 | 337 | 167 | 912 | Alternative sequence | ID=VSP_040999;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9Y6K1 | 285 | 337 | 167 | 912 | Alternative sequence | ID=VSP_040999;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9Y6K1 | 285 | 337 | 295 | 298 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 295 | 298 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 306 | 311 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 306 | 311 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 325 | 330 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 325 | 330 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 336 | 340 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 336 | 340 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 1 | 912 | Chain | ID=PRO_0000088043;Note=DNA (cytosine-5)-methyltransferase 3A |
| Q9Y6K1 | 285 | 337 | 1 | 912 | Chain | ID=PRO_0000088043;Note=DNA (cytosine-5)-methyltransferase 3A |
| Q9Y6K1 | 285 | 337 | 292 | 350 | Domain | Note=PWWP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00162 |
| Q9Y6K1 | 285 | 337 | 292 | 350 | Domain | Note=PWWP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00162 |
| Q9Y6K1 | 285 | 337 | 313 | 315 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 313 | 315 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 310 | 310 | Natural variant | ID=VAR_071463;Note=In TBRS%3B somatic mutation. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24614070;Dbxref=dbSNP:rs587777508,PMID:24614070 |
| Q9Y6K1 | 285 | 337 | 310 | 310 | Natural variant | ID=VAR_071463;Note=In TBRS%3B somatic mutation. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24614070;Dbxref=dbSNP:rs587777508,PMID:24614070 |
| Q9Y6K1 | 285 | 337 | 199 | 403 | Region | Note=Interaction with DNMT1 and DNMT3B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12145218;Dbxref=PMID:12145218 |
| Q9Y6K1 | 285 | 337 | 199 | 403 | Region | Note=Interaction with DNMT1 and DNMT3B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12145218;Dbxref=PMID:12145218 |
| Q9Y6K1 | 285 | 337 | 331 | 333 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
| Q9Y6K1 | 285 | 337 | 331 | 333 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LLR |
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3'-UTR located exon skipping events that lost miRNA binding sites in DNMT3A |
| 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 DNMT3A |
| - 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 DNMT3A |
| 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 DNMT3A |
| 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 DNMT3A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_264442 | -4.152817e-01 | 7.021954e-08 |
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RelatedDrugs for DNMT3A |
| 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 DNMT3A |
| 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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