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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 SYP |
 Gene summary |
| Gene information | Gene symbol | SYP | Gene ID | 6855 |
| Gene name | synaptophysin | |
| Synonyms | MRX96|MRXSYP | |
| Cytomap | Xp11.23 | |
| Type of gene | protein-coding | |
| Description | synaptophysinmajor synaptic vesicle protein P38 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 27143853(Neuroprotective Effect of β-asarone Against Alzheimer's Disease: Regulation of Synaptic Plasticity by Increased Expression of SYP and GluR1) |
| 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 SYP |
| 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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ENSG00000102003
| 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 |
| PG | DOWN | ENST00000263233.8 | SYP-201:protein_coding:SYP | 2.170424e+03 | -8.592880e-01 | 2.062448e-06 | 1.553931e-04 |
| CB | UP | ENST00000472598.5 | SYP-205:protein_coding:SYP | 1.553832e+02 | 1.244136e+00 | 3.538740e-13 | 6.254073e-11 |
| CB | UP | ENST00000376303.6 | SYP-202:nonsense_mediated_decay:SYP | 1.721648e+02 | 9.305572e-01 | 2.054206e-09 | 7.916268e-08 |
| 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 SYP |
| 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_133066 | chrX | 49194311:49194361:49197539:49197839:49198968:49199033 | 49197539:49197839 |
| exon_skip_153516 | chrX | 49193272:49193463:49198968:49199033:49200151:49200176 | 49198968:49199033 |
| exon_skip_162152 | chrX | 49197715:49197839:49198968:49199033:49200151:49200176 | 49198968:49199033 |
| exon_skip_187738 | chrX | 49189253:49189282:49191433:49191763:49193272:49193463 | 49191433:49191763 |
| exon_skip_237246 | chrX | 49193366:49193463:49194166:49194361:49198968:49199033 | 49194166:49194361 |
| exon_skip_25809 | chrX | 49194191:49194361:49197539:49197839:49198968:49199033 | 49197539:49197839 |
| exon_skip_3067 | chrX | 49194311:49194361:49197487:49197839:49198968:49199033 | 49197487:49197839 |
| exon_skip_36819 | chrX | 49191433:49191763:49193272:49193463:49198968:49199033 | 49193272:49193463 |
| exon_skip_7016 | chrX | 49193272:49193463:49194166:49194361:49197715:49197839 | 49194166:49194361 |
| exon_skip_70267 | chrX | 49193272:49193463:49194166:49194361:49198968:49199033 | 49194166:49194361 |
| exon_skip_86979 | chrX | 49189253:49189282:49191433:49191763:49193272:49193331 | 49191433:49191763 |
| exon_skip_94609 | chrX | 49194311:49194361:49198968:49199033:49200151:49200176 | 49198968:49199033 |
| exon_skip_95476 | chrX | 49194311:49194361:49197715:49197839:49198968:49199033 | 49197715:49197839 |
| 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 SYP |
| 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 |
| ENST00000263233 | 49191433 | 49191763 | 5CDS-5UTR |
| ENST00000263233 | 49194166 | 49194361 | Frame-shift |
| ENST00000479808 | 49194166 | 49194361 | Frame-shift |
| ENST00000263233 | 49197715 | 49197839 | Frame-shift |
| ENST00000479808 | 49197715 | 49197839 | 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 |
| ENST00000263233 | 49197715 | 49197839 | Frame-shift |
| ENST00000479808 | 49197715 | 49197839 | 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 |
| ENST00000263233 | 49191433 | 49191763 | 5CDS-5UTR |
| ENST00000263233 | 49194166 | 49194361 | Frame-shift |
| ENST00000479808 | 49194166 | 49194361 | Frame-shift |
| ENST00000263233 | 49197715 | 49197839 | Frame-shift |
| ENST00000479808 | 49197715 | 49197839 | Frame-shift |
| ENST00000479808 | 49198968 | 49199033 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SYP |
p-ENSG00000102003_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 |
| ENST00000479808 | 1867 | 313 | 49198968 | 49199033 | 50 | 114 | 12 | 33 |
| 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 |
| P08247 | 12 | 33 | 1 | 118 | Alternative sequence | ID=VSP_056897;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P08247 | 12 | 33 | 1 | 313 | Chain | ID=PRO_0000179161;Note=Synaptophysin |
| P08247 | 12 | 33 | 21 | 227 | Domain | Note=MARVEL;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00581 |
| P08247 | 12 | 33 | 1 | 25 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P08247 | 12 | 33 | 26 | 49 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SYP |
| 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 SYP |
| - 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 SYP |
| 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 SYP |
| 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 SYP |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | DAZAP1 | exon_skip_88796 | -4.809985e-01 | 1.386051e-10 |
| CB | TARDBP | exon_skip_88796 | -4.637882e-01 | 7.421079e-10 |
| CB | ELAVL1 | exon_skip_88796 | -4.105001e-01 | 7.694394e-08 |
| CB | RBM6 | exon_skip_88796 | -4.599320e-01 | 1.067253e-09 |
| CB | SAMD4A | exon_skip_88796 | -5.250282e-01 | 1.207663e-12 |
| CB | CNOT4 | exon_skip_88796 | -4.677290e-01 | 5.095249e-10 |
| CB | FXR2 | exon_skip_88796 | -4.323791e-01 | 1.260086e-08 |
| CB | PCBP1 | exon_skip_88796 | -4.242926e-01 | 2.496595e-08 |
| CB | PCBP4 | exon_skip_88796 | 6.563895e-01 | 5.862296e-21 |
| CB | FUBP1 | exon_skip_88796 | -4.487331e-01 | 2.989325e-09 |
| CB | KHSRP | exon_skip_88796 | -4.148301e-01 | 5.433376e-08 |
| CB | HNRNPA2B1 | exon_skip_88796 | -4.407110e-01 | 6.112190e-09 |
| CB | HNRNPC | exon_skip_88796 | -4.689059e-01 | 4.549817e-10 |
| CB | NUP42 | exon_skip_88796 | 4.623543e-01 | 8.499141e-10 |
| CB | SRSF4 | exon_skip_88796 | -5.251745e-01 | 1.187408e-12 |
| CB | HNRNPF | exon_skip_88796 | -4.082195e-01 | 9.223690e-08 |
| CB | RBM4 | exon_skip_88796 | -7.027121e-01 | 5.530436e-25 |
| CB | RBM4 | exon_skip_95476 | -7.740430e-01 | 5.590226e-33 |
| CB | RBM6 | exon_skip_94609 | -4.612449e-01 | 1.541297e-09 |
| CB | PCBP1 | exon_skip_94609 | -4.005143e-01 | 2.419559e-07 |
| CB | NUP42 | exon_skip_94609 | 4.973176e-01 | 4.619400e-11 |
| DLPFC | ESRP1 | exon_skip_133066 | -4.152013e-01 | 4.771777e-12 |
| DLPFC | RBM4 | exon_skip_133066 | -4.189187e-01 | 2.942733e-12 |
| IFG | RBM24 | exon_skip_70267 | 4.607982e-01 | 2.043849e-02 |
| IFG | SRSF2 | exon_skip_3067 | 4.235232e-01 | 4.951662e-02 |
| TC | HNRNPH2 | exon_skip_95476 | 4.224898e-01 | 2.621158e-08 |
| TC | NOVA1 | exon_skip_95476 | 4.644142e-01 | 6.174370e-10 |
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RelatedDrugs for SYP |
| 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 SYP |
| 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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