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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 GNPDA1 |
 Gene summary |
| Gene information | Gene symbol | GNPDA1 | Gene ID | 10007 |
| Gene name | glucosamine-6-phosphate deaminase 1 | |
| Synonyms | GNP1|GNPDA|GNPI|GPI|HLN | |
| Cytomap | 5q31.3 | |
| Type of gene | protein-coding | |
| Description | glucosamine-6-phosphate isomerase 1GNPDA 1glcN6P deaminase 1oscillin | |
| 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 |
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Gene structures and expression levels for GNPDA1 |
| 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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ENSG00000113552
| 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 GNPDA1 |
| 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_142276 | chr5 | 142011949:142012041:142012288:142012339:142012995:142013027 | 142012288:142012339 |
| exon_skip_1439 | chr5 | 142011949:142012041:142012288:142012377:142012995:142013027 | 142012288:142012377 |
| exon_skip_158708 | chr5 | 142006144:142006326:142007799:142007900:142011912:142012041 | 142007799:142007900 |
| exon_skip_270514 | chr5 | 142011949:142012041:142012288:142012377:142012669:142012973 | 142012288:142012377 |
| exon_skip_280975 | chr5 | 142011949:142012041:142012288:142012339:142012669:142012996 | 142012288:142012339 |
| exon_skip_284258 | chr5 | 142011949:142012041:142012288:142012339:142012669:142012973 | 142012288:142012339 |
| 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 GNPDA1 |
| 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 |
| ENST00000500692 | 142012288 | 142012339 | 3UTR-3UTR |
| ENST00000503794 | 142012288 | 142012377 | 3UTR-3UTR |
| ENST00000311337 | 142007799 | 142007900 | In-frame |
| ENST00000500692 | 142007799 | 142007900 | In-frame |
| ENST00000503794 | 142007799 | 142007900 | In-frame |
| ENST00000508177 | 142007799 | 142007900 | 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 |
| ENST00000500692 | 142012288 | 142012339 | 3UTR-3UTR |
| ENST00000503794 | 142012288 | 142012377 | 3UTR-3UTR |
| ENST00000311337 | 142007799 | 142007900 | In-frame |
| ENST00000500692 | 142007799 | 142007900 | In-frame |
| ENST00000503794 | 142007799 | 142007900 | In-frame |
| ENST00000508177 | 142007799 | 142007900 | 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 |
| ENST00000503794 | 142012288 | 142012377 | 3UTR-3UTR |
| ENST00000311337 | 142007799 | 142007900 | In-frame |
| ENST00000500692 | 142007799 | 142007900 | In-frame |
| ENST00000503794 | 142007799 | 142007900 | In-frame |
| ENST00000508177 | 142007799 | 142007900 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GNPDA1 |
p-ENSG00000113552_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 |
| ENST00000311337 | 2290 | 289 | 142007799 | 142007900 | 168 | 268 | 41 | 75 |
| ENST00000500692 | 2336 | 289 | 142007799 | 142007900 | 219 | 319 | 41 | 75 |
| ENST00000503794 | 2639 | 289 | 142007799 | 142007900 | 526 | 626 | 41 | 75 |
| ENST00000508177 | 2997 | 289 | 142007799 | 142007900 | 884 | 984 | 41 | 75 |
| 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 |
| ENST00000311337 | 2290 | 289 | 142007799 | 142007900 | 168 | 268 | 41 | 75 |
| ENST00000500692 | 2336 | 289 | 142007799 | 142007900 | 219 | 319 | 41 | 75 |
| ENST00000503794 | 2639 | 289 | 142007799 | 142007900 | 526 | 626 | 41 | 75 |
| ENST00000508177 | 2997 | 289 | 142007799 | 142007900 | 884 | 984 | 41 | 75 |
| 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 |
| ENST00000311337 | 2290 | 289 | 142007799 | 142007900 | 168 | 268 | 41 | 75 |
| ENST00000500692 | 2336 | 289 | 142007799 | 142007900 | 219 | 319 | 41 | 75 |
| ENST00000503794 | 2639 | 289 | 142007799 | 142007900 | 526 | 626 | 41 | 75 |
| ENST00000508177 | 2997 | 289 | 142007799 | 142007900 | 884 | 984 | 41 | 75 |
| 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 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| 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 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| 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 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 72 | 72 | Active site | Note=Proton acceptor%3B for enolization step;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 69 | 145 | Alternative sequence | ID=VSP_057011;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 66 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 1 | 289 | Chain | ID=PRO_0000160122;Note=Glucosamine-6-phosphate isomerase 1 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 43 | 57 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NE7 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P46926 | 41 | 75 | 64 | 64 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
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3'-UTR located exon skipping events that lost miRNA binding sites in GNPDA1 |
| 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 | ENST00000503794 | 142012288 | 142012377 | hsa-miR-4433b-5p | chr5:142012352-142012359 | 8mer-1a | chr5:142012343-142012362 | 148.00 | -9.15 |
| MSBB | ENST00000503794 | 142012288 | 142012377 | hsa-miR-4433b-5p | chr5:142012352-142012359 | 8mer-1a | chr5:142012343-142012362 | 148.00 | -9.15 |
| ROSMAP | ENST00000503794 | 142012288 | 142012377 | hsa-miR-4433b-5p | chr5:142012352-142012359 | 8mer-1a | chr5:142012343-142012362 | 148.00 | -9.15 |
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SNVs in the skipped exons for GNPDA1 |
| - 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 GNPDA1 |
| 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 GNPDA1 |
| 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 GNPDA1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for GNPDA1 |
| 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 GNPDA1 |
| 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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