|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
Gene summary for SNAPC3 |
 Gene summary |
| Gene information | Gene symbol | SNAPC3 | Gene ID | 6619 |
| Gene name | small nuclear RNA activating complex polypeptide 3 | |
| Synonyms | PTFbeta|SNAP50 | |
| Cytomap | 9p22.3 | |
| Type of gene | protein-coding | |
| Description | snRNA-activating protein complex subunit 3PSE-binding factor subunit betaPTF subunit betaSNAPc 50 kDa subunitSNAPc subunit 3proximal sequence element-binding transcription factor subunit betasmall nuclear RNA activating complex, polypeptide 3, 50kD | |
| 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 |
Top |
Gene structures and expression levels for SNAPC3 |
| 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. |
 |
ENSG00000164975
| 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. |
 |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000421710.5 | SNAPC3-203:protein_coding:SNAPC3 | 9.947769e+00 | 1.078626e+00 | 3.419845e-08 | 8.566469e-07 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SNAPC3 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_115599 | chr9 | 15433552:15433636:15444602:15444706:15451320:15451402 | 15444602:15444706 |
| exon_skip_175148 | chr9 | 15447112:15447244:15451320:15451402:15453041:15453104 | 15451320:15451402 |
| exon_skip_197069 | chr9 | 15444602:15444706:15451320:15451402:15453041:15453104 | 15451320:15451402 |
| exon_skip_219365 | chr9 | 15423909:15423986:15433552:15433636:15444602:15444706 | 15433552:15433636 |
| exon_skip_230654 | chr9 | 15461631:15461805:15462865:15462990:15465510:15465832 | 15462865:15462990 |
| exon_skip_24494 | chr9 | 15451320:15451402:15453041:15453205:15457960:15458067 | 15453041:15453205 |
| exon_skip_292395 | chr9 | 15444602:15444706:15447095:15447244:15451320:15451402 | 15447095:15447244 |
| exon_skip_87741 | chr9 | 15457960:15458067:15459719:15460313:15461631:15461805 | 15459719:15460313 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SNAPC3 |
| 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 |
| ENST00000610884 | 15459719 | 15460313 | 3UTR-3CDS |
| ENST00000610884 | 15462865 | 15462990 | 3UTR-3UTR |
| ENST00000380821 | 15451320 | 15451402 | Frame-shift |
| ENST00000610884 | 15451320 | 15451402 | Frame-shift |
| ENST00000380821 | 15447095 | 15447244 | In-frame |
| ENST00000610884 | 15447095 | 15447244 | In-frame |
| ENST00000380821 | 15453041 | 15453205 | In-frame |
| ENST00000610884 | 15453041 | 15453205 | 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 |
| ENST00000610884 | 15459719 | 15460313 | 3UTR-3CDS |
| ENST00000380821 | 15451320 | 15451402 | Frame-shift |
| ENST00000610884 | 15451320 | 15451402 | Frame-shift |
| ENST00000380821 | 15447095 | 15447244 | In-frame |
| ENST00000610884 | 15447095 | 15447244 | In-frame |
| ENST00000380821 | 15453041 | 15453205 | In-frame |
| ENST00000610884 | 15453041 | 15453205 | 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 |
| ENST00000610884 | 15459719 | 15460313 | 3UTR-3CDS |
| ENST00000610884 | 15462865 | 15462990 | 3UTR-3UTR |
| ENST00000380821 | 15433552 | 15433636 | Frame-shift |
| ENST00000610884 | 15433552 | 15433636 | Frame-shift |
| ENST00000380821 | 15451320 | 15451402 | Frame-shift |
| ENST00000610884 | 15451320 | 15451402 | Frame-shift |
| ENST00000380821 | 15447095 | 15447244 | In-frame |
| ENST00000610884 | 15447095 | 15447244 | In-frame |
| ENST00000380821 | 15453041 | 15453205 | In-frame |
| ENST00000610884 | 15453041 | 15453205 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SNAPC3 |
p-ENSG00000164975_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 |
| ENST00000380821 | 5697 | 411 | 15447095 | 15447244 | 760 | 908 | 194 | 244 |
| ENST00000610884 | 2470 | 411 | 15447095 | 15447244 | 730 | 878 | 194 | 244 |
| ENST00000380821 | 5697 | 411 | 15453041 | 15453205 | 993 | 1156 | 272 | 326 |
| ENST00000610884 | 2470 | 411 | 15453041 | 15453205 | 963 | 1126 | 272 | 326 |
| 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 |
| ENST00000380821 | 5697 | 411 | 15447095 | 15447244 | 760 | 908 | 194 | 244 |
| ENST00000610884 | 2470 | 411 | 15447095 | 15447244 | 730 | 878 | 194 | 244 |
| ENST00000380821 | 5697 | 411 | 15453041 | 15453205 | 993 | 1156 | 272 | 326 |
| ENST00000610884 | 2470 | 411 | 15453041 | 15453205 | 963 | 1126 | 272 | 326 |
| 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 |
| ENST00000380821 | 5697 | 411 | 15447095 | 15447244 | 760 | 908 | 194 | 244 |
| ENST00000610884 | 2470 | 411 | 15447095 | 15447244 | 730 | 878 | 194 | 244 |
| ENST00000380821 | 5697 | 411 | 15453041 | 15453205 | 993 | 1156 | 272 | 326 |
| ENST00000610884 | 2470 | 411 | 15453041 | 15453205 | 963 | 1126 | 272 | 326 |
| 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 |
| Q92966 | 194 | 244 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 194 | 244 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 272 | 326 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 272 | 326 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| 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 |
| Q92966 | 194 | 244 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 194 | 244 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 272 | 326 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 272 | 326 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| 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 |
| Q92966 | 194 | 244 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 194 | 244 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 272 | 326 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
| Q92966 | 272 | 326 | 1 | 411 | Chain | ID=PRO_0000072024;Note=snRNA-activating protein complex subunit 3 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in SNAPC3 |
| 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 |
| Mayo | ENST00000610884 | 15462865 | 15462990 | hsa-miR-618 | chr9:15462895-15462902 | 8mer-1a | chr9:15462879-15462902 | 159.00 | -15.94 |
| Mayo | ENST00000610884 | 15462865 | 15462990 | hsa-miR-4721 | chr9:15462907-15462914 | 8mer-1a | chr9:15462888-15462915 | 150.00 | -24.34 |
| Mayo | ENST00000610884 | 15462865 | 15462990 | hsa-miR-5683 | chr9:15462978-15462985 | 8mer-1a | chr9:15462968-15462990 | 146.00 | -17.52 |
| Mayo | ENST00000610884 | 15462865 | 15462990 | hsa-miR-335-3p | chr9:15462924-15462931 | 8mer-1a | chr9:15462922-15462942 | 150.00 | -12.18 |
| ROSMAP | ENST00000610884 | 15462865 | 15462990 | hsa-miR-618 | chr9:15462895-15462902 | 8mer-1a | chr9:15462879-15462902 | 159.00 | -15.94 |
| ROSMAP | ENST00000610884 | 15462865 | 15462990 | hsa-miR-4721 | chr9:15462907-15462914 | 8mer-1a | chr9:15462888-15462915 | 150.00 | -24.34 |
| ROSMAP | ENST00000610884 | 15462865 | 15462990 | hsa-miR-5683 | chr9:15462978-15462985 | 8mer-1a | chr9:15462968-15462990 | 146.00 | -17.52 |
| ROSMAP | ENST00000610884 | 15462865 | 15462990 | hsa-miR-335-3p | chr9:15462924-15462931 | 8mer-1a | chr9:15462922-15462942 | 150.00 | -12.18 |
Top |
SNVs in the skipped exons for SNAPC3 |
| - 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 |
Top |
AD stage-associated exon skippint events for SNAPC3 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SNAPC3 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for SNAPC3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | ZNF638 | exon_skip_292395 | -4.453273e-01 | 4.059115e-09 |
| CB | CNOT4 | exon_skip_292395 | -4.270554e-01 | 1.980478e-08 |
| CB | PCBP1 | exon_skip_292395 | -4.004130e-01 | 1.698244e-07 |
| CB | TRA2A | exon_skip_292395 | -4.836352e-01 | 1.062977e-10 |
| CB | FUBP1 | exon_skip_175148 | -4.613215e-01 | 9.367778e-10 |
Top |
RelatedDrugs for SNAPC3 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for SNAPC3 |
| 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)
|