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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 SCG3 |
 Gene summary |
| Gene information | Gene symbol | SCG3 | Gene ID | 29106 |
| Gene name | secretogranin III | |
| Synonyms | SGIII | |
| Cytomap | 15q21.2 | |
| Type of gene | protein-coding | |
| Description | secretogranin-3 | |
| Modification date | 20200313 | |
| UniProtAcc | H0YKC2, Q8WXD2, | |
| 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 SCG3 |
| 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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ENSG00000104112
| 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 |
| 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 SCG3 |
| 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_112477 | chr15 | 51683219:51683434:51688260:51688402:51689219:51689368 | 51688260:51688402 |
| exon_skip_113455 | chr15 | 51681532:51681837:51683079:51683124:51683219:51683230 | 51683079:51683124 |
| exon_skip_118044 | chr15 | 51701107:51701244:51713333:51713413:51719408:51720071 | 51713333:51713413 |
| exon_skip_142485 | chr15 | 51683423:51683434:51688260:51688402:51689219:51689368 | 51688260:51688402 |
| exon_skip_144898 | chr15 | 51681532:51681837:51682517:51682569:51683079:51683123 | 51682517:51682569 |
| exon_skip_162241 | chr15 | 51683079:51683124:51683219:51683434:51688260:51688402 | 51683219:51683434 |
| exon_skip_175693 | chr15 | 51701107:51701244:51713333:51713413:51719408:51719713 | 51713333:51713413 |
| exon_skip_198001 | chr15 | 51695875:51695991:51699319:51699402:51701107:51701244 | 51699319:51699402 |
| exon_skip_201970 | chr15 | 51683285:51683434:51688260:51688402:51689219:51689368 | 51688260:51688402 |
| exon_skip_206390 | chr15 | 51695875:51695991:51699319:51699402:51701107:51701126 | 51699319:51699402 |
| exon_skip_217794 | chr15 | 51683098:51683124:51683219:51683434:51688260:51688402 | 51683219:51683434 |
| exon_skip_220325 | chr15 | 51681532:51681837:51682517:51682569:51683079:51683124 | 51682517:51682569 |
| exon_skip_237069 | chr15 | 51681532:51681837:51683079:51683124:51683219:51683434 | 51683079:51683124 |
| exon_skip_28011 | chr15 | 51683220:51683434:51688260:51688402:51689219:51689368 | 51688260:51688402 |
| exon_skip_69528 | chr15 | 51681532:51681837:51682517:51682569:51683079:51683122 | 51682517:51682569 |
| exon_skip_88205 | chr15 | 51683310:51683434:51688260:51688402:51689219:51689368 | 51688260:51688402 |
| 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 SCG3 |
| 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 |
| ENST00000220478 | 51682517 | 51682569 | Frame-shift |
| ENST00000220478 | 51688260 | 51688402 | Frame-shift |
| ENST00000220478 | 51683219 | 51683434 | In-frame |
| ENST00000220478 | 51699319 | 51699402 | In-frame |
| ENST00000220478 | 51713333 | 51713413 | 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 |
| ENST00000220478 | 51682517 | 51682569 | Frame-shift |
| ENST00000220478 | 51688260 | 51688402 | Frame-shift |
| ENST00000220478 | 51683219 | 51683434 | In-frame |
| ENST00000220478 | 51699319 | 51699402 | 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 |
| ENST00000220478 | 51682517 | 51682569 | Frame-shift |
| ENST00000220478 | 51688260 | 51688402 | Frame-shift |
| ENST00000220478 | 51683219 | 51683434 | In-frame |
| ENST00000220478 | 51699319 | 51699402 | In-frame |
| ENST00000220478 | 51713333 | 51713413 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SCG3 |
p-ENSG00000104112_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 |
| ENST00000220478 | 3332 | 468 | 51683219 | 51683434 | 586 | 800 | 61 | 132 |
| ENST00000220478 | 3332 | 468 | 51699319 | 51699402 | 1390 | 1472 | 329 | 356 |
| ENST00000220478 | 3332 | 468 | 51713333 | 51713413 | 1612 | 1691 | 403 | 429 |
| 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 |
| ENST00000220478 | 3332 | 468 | 51683219 | 51683434 | 586 | 800 | 61 | 132 |
| ENST00000220478 | 3332 | 468 | 51699319 | 51699402 | 1390 | 1472 | 329 | 356 |
| 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 |
| ENST00000220478 | 3332 | 468 | 51683219 | 51683434 | 586 | 800 | 61 | 132 |
| ENST00000220478 | 3332 | 468 | 51699319 | 51699402 | 1390 | 1472 | 329 | 356 |
| ENST00000220478 | 3332 | 468 | 51713333 | 51713413 | 1612 | 1691 | 403 | 429 |
| 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 |
| Q8WXD2 | 61 | 132 | 1 | 232 | Alternative sequence | ID=VSP_042876;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8WXD2 | 61 | 132 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-3 |
| Q8WXD2 | 61 | 132 | 125 | 125 | Natural variant | ID=VAR_013827;Note=S->N;Dbxref=dbSNP:rs2305710 |
| Q8WXD2 | 61 | 132 | 79 | 79 | Sequence conflict | Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8WXD2 | 329 | 356 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-3 |
| Q8WXD2 | 403 | 429 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-3 |
| Q8WXD2 | 403 | 429 | 421 | 421 | Sequence conflict | Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q8WXD2 | 61 | 132 | 1 | 232 | Alternative sequence | ID=VSP_042876;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8WXD2 | 61 | 132 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-3 |
| Q8WXD2 | 61 | 132 | 125 | 125 | Natural variant | ID=VAR_013827;Note=S->N;Dbxref=dbSNP:rs2305710 |
| Q8WXD2 | 61 | 132 | 79 | 79 | Sequence conflict | Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8WXD2 | 329 | 356 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-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 |
| Q8WXD2 | 61 | 132 | 1 | 232 | Alternative sequence | ID=VSP_042876;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q8WXD2 | 61 | 132 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-3 |
| Q8WXD2 | 61 | 132 | 125 | 125 | Natural variant | ID=VAR_013827;Note=S->N;Dbxref=dbSNP:rs2305710 |
| Q8WXD2 | 61 | 132 | 79 | 79 | Sequence conflict | Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q8WXD2 | 329 | 356 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-3 |
| Q8WXD2 | 403 | 429 | 20 | 468 | Chain | ID=PRO_0000005461;Note=Secretogranin-3 |
| Q8WXD2 | 403 | 429 | 421 | 421 | Sequence conflict | Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SCG3 |
| 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 SCG3 |
| - 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 SCG3 |
| 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 SCG3 |
| 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 SCG3 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| TC | KHDRBS2 | exon_skip_69528 | 4.316046e-01 | 1.210894e-08 |
| TC | HNRNPDL | exon_skip_69528 | 4.314945e-01 | 1.222417e-08 |
| TC | NUP42 | exon_skip_69528 | 4.059896e-01 | 1.002100e-07 |
| TC | ZCRB1 | exon_skip_69528 | 4.106017e-01 | 6.938393e-08 |
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RelatedDrugs for SCG3 |
| 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 SCG3 |
| 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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