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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 PHGDH |
Gene summary |
Gene information | Gene symbol | PHGDH | Gene ID | 26227 |
Gene name | phosphoglycerate dehydrogenase | |
Synonyms | 3-PGDH|3PGDH|HEL-S-113|NLS|NLS1|PDG|PGAD|PGD|PGDH|PHGDHD|SERA | |
Cytomap | 1p12 | |
Type of gene | protein-coding | |
Description | D-3-phosphoglycerate dehydrogenase2-oxoglutarate reductase3-phosphoglycerate dehydrogenaseepididymis secretory protein Li 113malate dehydrogenase | |
Modification date | 20200320 | |
UniProtAcc | A0A286YER3, A0A286YEZ0, A0A286YF22, A0A286YF34, A0A286YF78, A0A286YFA2, | |
Context | - 32130882(Impairment of Glycolysis-Derived l-Serine Production in Astrocytes Contributes to Cognitive Deficits in Alzheimer's Disease) |
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 PHGDH |
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. |
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 |
PCC | UP | ENST00000482968.1 | PHGDH-205:retained_intron:PHGDH | 5.016415e+00 | 8.081165e-01 | 3.953574e-05 | 3.278414e-03 |
STG | UP | ENST00000369407.3 | PHGDH-201:retained_intron:PHGDH | 9.333254e+00 | 9.761000e-01 | 1.646142e-03 | 4.942043e-02 |
PG | UP | ENST00000482968.1 | PHGDH-205:retained_intron:PHGDH | 9.725375e+00 | 8.364955e-01 | 2.036096e-05 | 8.484269e-04 |
CB | UP | ENST00000641570.1 | PHGDH-220:nonsense_mediated_decay:PHGDH | 2.588107e+00 | 8.867970e-01 | 4.340439e-03 | 1.752088e-02 |
TC | UP | ENST00000641371.1 | PHGDH-215:nonsense_mediated_decay:PHGDH | 6.685052e+01 | 8.122203e-01 | 9.519185e-08 | 5.853469e-06 |
TC | UP | ENST00000496756.2 | PHGDH-207:retained_intron:PHGDH | 2.676625e+02 | 9.825221e-01 | 2.139287e-05 | 4.713922e-04 |
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 PHGDH |
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_106131 | chr1 | 119737114:119737266:119742807:119743044:119743886:119744011 | 119742807:119743044 |
exon_skip_108856 | chr1 | 119737219:119737266:119740386:119740518:119742807:119743044 | 119740386:119740518 |
exon_skip_139195 | chr1 | 119724319:119724469:119724785:119724875:119726851:119726899 | 119724785:119724875 |
exon_skip_149234 | chr1 | 119737219:119737266:119742807:119743044:119743886:119744011 | 119742807:119743044 |
exon_skip_153963 | chr1 | 119723376:119723441:119724319:119724469:119726851:119726905 | 119724319:119724469 |
exon_skip_183895 | chr1 | 119724319:119724469:119724785:119724957:119726851:119726899 | 119724785:119724957 |
exon_skip_187511 | chr1 | 119734634:119734766:119735295:119735443:119737114:119737154 | 119735295:119735443 |
exon_skip_193704 | chr1 | 119721276:119721321:119723376:119723441:119726851:119726899 | 119723376:119723441 |
exon_skip_213090 | chr1 | 119721170:119721321:119723376:119723441:119726851:119726905 | 119723376:119723441 |
exon_skip_215741 | chr1 | 119737226:119737266:119740386:119740518:119742807:119743044 | 119740386:119740518 |
exon_skip_227177 | chr1 | 119737114:119737266:119740386:119740518:119742807:119743044 | 119740386:119740518 |
exon_skip_231866 | chr1 | 119740398:119740518:119741767:119741876:119742807:119743044 | 119741767:119741876 |
exon_skip_261761 | chr1 | 119723376:119723441:119724319:119724469:119724785:119724875 | 119724319:119724469 |
exon_skip_271926 | chr1 | 119724319:119724469:119724785:119724875:119726851:119726905 | 119724785:119724875 |
exon_skip_273217 | chr1 | 119724319:119724469:119724785:119724957:119726851:119726905 | 119724785:119724957 |
exon_skip_28015 | chr1 | 119740386:119740518:119742807:119743044:119743886:119744011 | 119742807:119743044 |
exon_skip_280377 | chr1 | 119737226:119737266:119742807:119743044:119743886:119744011 | 119742807:119743044 |
exon_skip_3172 | chr1 | 119740386:119740518:119741767:119741897:119742807:119743044 | 119741767:119741897 |
exon_skip_39967 | chr1 | 119740398:119740518:119741767:119741897:119742807:119743044 | 119741767:119741897 |
exon_skip_58170 | chr1 | 119740386:119740518:119741767:119743044:119743886:119744011 | 119741767:119743044 |
exon_skip_75520 | chr1 | 119723376:119723441:119724785:119724875:119726851:119726899 | 119724785:119724875 |
exon_skip_76953 | chr1 | 119740386:119740518:119741767:119741876:119742807:119743044 | 119741767:119741876 |
exon_skip_85336 | chr1 | 119741767:119741897:119742807:119743044:119743886:119744011 | 119742807:119743044 |
exon_skip_88214 | chr1 | 119723376:119723441:119724319:119724469:119726851:119726899 | 119724319:119724469 |
exon_skip_90190 | chr1 | 119723376:119723441:119726851:119726905:119727004:119727063 | 119726851:119726905 |
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 PHGDH |
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 |
ENST00000641023 | 119726851 | 119726905 | Frame-shift |
ENST00000641597 | 119726851 | 119726905 | Frame-shift |
ENST00000641023 | 119735295 | 119735443 | Frame-shift |
ENST00000641597 | 119735295 | 119735443 | Frame-shift |
ENST00000641023 | 119741767 | 119741897 | Frame-shift |
ENST00000641597 | 119741767 | 119741897 | Frame-shift |
ENST00000641023 | 119723376 | 119723441 | In-frame |
ENST00000641597 | 119723376 | 119723441 | 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 |
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 |
ENST00000641023 | 119726851 | 119726905 | Frame-shift |
ENST00000641597 | 119726851 | 119726905 | Frame-shift |
ENST00000641023 | 119735295 | 119735443 | Frame-shift |
ENST00000641597 | 119735295 | 119735443 | Frame-shift |
ENST00000641023 | 119741767 | 119741897 | Frame-shift |
ENST00000641597 | 119741767 | 119741897 | Frame-shift |
ENST00000641023 | 119742807 | 119743044 | Frame-shift |
ENST00000641597 | 119742807 | 119743044 | Frame-shift |
ENST00000641023 | 119723376 | 119723441 | In-frame |
ENST00000641597 | 119723376 | 119723441 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PHGDH |
p-ENSG00000092621_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 |
ENST00000641023 | 2113 | 533 | 119723376 | 119723441 | 600 | 664 | 97 | 118 |
ENST00000641597 | 2602 | 533 | 119723376 | 119723441 | 1125 | 1189 | 97 | 118 |
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 |
ENST00000641023 | 2113 | 533 | 119723376 | 119723441 | 600 | 664 | 97 | 118 |
ENST00000641597 | 2602 | 533 | 119723376 | 119723441 | 1125 | 1189 | 97 | 118 |
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 |
O43175 | 97 | 118 | 2 | 533 | Chain | ID=PRO_0000076012;Note=D-3-phosphoglycerate dehydrogenase |
O43175 | 97 | 118 | 2 | 533 | Chain | ID=PRO_0000076012;Note=D-3-phosphoglycerate dehydrogenase |
O43175 | 97 | 118 | 103 | 119 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5NZO |
O43175 | 97 | 118 | 103 | 119 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5NZO |
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 |
O43175 | 97 | 118 | 2 | 533 | Chain | ID=PRO_0000076012;Note=D-3-phosphoglycerate dehydrogenase |
O43175 | 97 | 118 | 2 | 533 | Chain | ID=PRO_0000076012;Note=D-3-phosphoglycerate dehydrogenase |
O43175 | 97 | 118 | 103 | 119 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5NZO |
O43175 | 97 | 118 | 103 | 119 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5NZO |
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3'-UTR located exon skipping events that lost miRNA binding sites in PHGDH |
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 PHGDH |
- 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 PHGDH |
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 PHGDH |
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 PHGDH |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PHGDH |
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 PHGDH |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |