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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 SMYD3 |
 Gene summary |
| Gene information | Gene symbol | SMYD3 | Gene ID | 64754 |
| Gene name | SET and MYND domain containing 3 | |
| Synonyms | KMT3E|ZMYND1|ZNFN3A1|bA74P14.1 | |
| Cytomap | 1q44 | |
| Type of gene | protein-coding | |
| Description | histone-lysine N-methyltransferase SMYD3SET and MYND domain-containing protein 3bA74P14.1 (novel protein)zinc finger MYND domain-containing protein 1zinc finger protein, subfamily 3A (MYND domain containing), 1zinc finger, MYND domain containing 1 | |
| Modification date | 20200320 | |
| 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 SMYD3 |
| 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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ENSG00000185420
| 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 | ENST00000391836.3 | SMYD3-203:protein_coding:SMYD3 | 3.440187e+00 | 1.011013e+00 | 3.629147e-05 | 3.136533e-04 |
| CB | DOWN | ENST00000482592.5 | SMYD3-211:lncRNA:SMYD3 | 3.411784e+01 | -1.488856e+00 | 2.666821e-04 | 1.698734e-03 |
| TC | UP | ENST00000462422.5 | SMYD3-207:lncRNA:SMYD3 | 1.287255e+00 | 8.440906e-01 | 5.594519e-03 | 3.642541e-02 |
| 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 SMYD3 |
| 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_133749 | chr1 | 245915530:245915640:245927931:245928033:245929870:245929937 | 245927931:245928033 |
| exon_skip_145487 | chr1 | 245749351:245749664:245764041:245764149:245858496:245858647 | 245764041:245764149 |
| exon_skip_167220 | chr1 | 245764041:245764149:245814342:245814415:245858496:245858647 | 245814342:245814415 |
| exon_skip_236697 | chr1 | 245749367:245749664:245764041:245764149:245814342:245814411 | 245764041:245764149 |
| exon_skip_275164 | chr1 | 245863809:245863886:245915530:245915640:245927931:245928033 | 245915530:245915640 |
| exon_skip_282135 | chr1 | 245749367:245749664:245764041:245764149:245858496:245858647 | 245764041:245764149 |
| exon_skip_46940 | chr1 | 245749541:245749664:245764041:245764149:245858496:245858647 | 245764041:245764149 |
| exon_skip_85045 | chr1 | 245764076:245764149:245814342:245814415:245858496:245858647 | 245814342:245814415 |
| exon_skip_90132 | chr1 | 246330480:246330537:246335367:246335474:246355031:246355094 | 246335367:246335474 |
| 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 SMYD3 |
| 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 |
| ENST00000490107 | 245764041 | 245764149 | Frame-shift |
| ENST00000490107 | 245915530 | 245915640 | 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 |
| ENST00000490107 | 245764041 | 245764149 | Frame-shift |
| ENST00000490107 | 245915530 | 245915640 | 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 |
| ENST00000490107 | 245764041 | 245764149 | Frame-shift |
| ENST00000490107 | 245927931 | 245928033 | Frame-shift |
| ENST00000490107 | 245915530 | 245915640 | In-frame |
| ENST00000490107 | 246335367 | 246335474 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMYD3 |
p-ENSG00000185420_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 |
| ENST00000490107 | 1565 | 428 | 245915530 | 245915640 | 743 | 852 | 234 | 270 |
| 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 |
| ENST00000490107 | 1565 | 428 | 245915530 | 245915640 | 743 | 852 | 234 | 270 |
| 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 |
| ENST00000490107 | 1565 | 428 | 246335367 | 246335474 | 269 | 375 | 76 | 111 |
| ENST00000490107 | 1565 | 428 | 245915530 | 245915640 | 743 | 852 | 234 | 270 |
| 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 |
| Q9H7B4 | 234 | 270 | 234 | 237 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 239 | 239 | Binding site | Note=S-adenosyl-L-methionine;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00190,ECO:0000269|Ref.12 |
| Q9H7B4 | 234 | 270 | 259 | 259 | Binding site | Note=S-adenosyl-L-methionine;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00190,ECO:0000269|Ref.12 |
| Q9H7B4 | 234 | 270 | 1 | 428 | Chain | ID=PRO_0000218312;Note=Histone-lysine N-methyltransferase SMYD3 |
| Q9H7B4 | 234 | 270 | 4 | 240 | Domain | Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00190 |
| Q9H7B4 | 234 | 270 | 246 | 255 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 264 | 268 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 269 | 271 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| 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 |
| Q9H7B4 | 234 | 270 | 234 | 237 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 239 | 239 | Binding site | Note=S-adenosyl-L-methionine;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00190,ECO:0000269|Ref.12 |
| Q9H7B4 | 234 | 270 | 259 | 259 | Binding site | Note=S-adenosyl-L-methionine;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00190,ECO:0000269|Ref.12 |
| Q9H7B4 | 234 | 270 | 1 | 428 | Chain | ID=PRO_0000218312;Note=Histone-lysine N-methyltransferase SMYD3 |
| Q9H7B4 | 234 | 270 | 4 | 240 | Domain | Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00190 |
| Q9H7B4 | 234 | 270 | 246 | 255 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 264 | 268 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 269 | 271 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| 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 |
| Q9H7B4 | 76 | 111 | 1 | 170 | Alternative sequence | ID=VSP_012416;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| Q9H7B4 | 76 | 111 | 1 | 428 | Chain | ID=PRO_0000218312;Note=Histone-lysine N-methyltransferase SMYD3 |
| Q9H7B4 | 76 | 111 | 4 | 240 | Domain | Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00190 |
| Q9H7B4 | 76 | 111 | 73 | 78 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 76 | 111 | 80 | 93 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 76 | 111 | 100 | 114 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 76 | 111 | 49 | 87 | Zinc finger | Note=MYND-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00134 |
| Q9H7B4 | 234 | 270 | 234 | 237 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 239 | 239 | Binding site | Note=S-adenosyl-L-methionine;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00190,ECO:0000269|Ref.12 |
| Q9H7B4 | 234 | 270 | 259 | 259 | Binding site | Note=S-adenosyl-L-methionine;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00190,ECO:0000269|Ref.12 |
| Q9H7B4 | 234 | 270 | 1 | 428 | Chain | ID=PRO_0000218312;Note=Histone-lysine N-methyltransferase SMYD3 |
| Q9H7B4 | 234 | 270 | 4 | 240 | Domain | Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00190 |
| Q9H7B4 | 234 | 270 | 246 | 255 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 264 | 268 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
| Q9H7B4 | 234 | 270 | 269 | 271 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5V37 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SMYD3 |
| 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 SMYD3 |
| - 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 SMYD3 |
| 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 SMYD3 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_275164 | rs2185075 | chr1:245961765 | 1.912992e-04 | 2.882831e-02 |
| CB | exon_skip_275164 | rs9659850 | chr1:245962516 | 1.912992e-04 | 2.882831e-02 |
| CB | exon_skip_275164 | rs1890329 | chr1:245998492 | 2.045818e-04 | 3.039726e-02 |
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Correlation with RNA binding proteins (RBPs) for SMYD3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SMYD3 |
| 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 SMYD3 |
| 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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