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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for GDPD3 |
 Gene summary |
| Gene information | Gene symbol | GDPD3 | Gene ID | 79153 |
| Gene name | glycerophosphodiester phosphodiesterase domain containing 3 | |
| Synonyms | GDE7 | |
| Cytomap | 16p11.2 | |
| Type of gene | protein-coding | |
| Description | lysophospholipase D GDPD3glycerophosphodiester phosphodiesterase 7glycerophosphodiester phosphodiesterase domain-containing protein 3 | |
| Modification date | 20180519 | |
| UniProtAcc | Q7L5L3 | |
| Context | PubMed: GDPD3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| 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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Exon skipping events across known transcript of Ensembl for GDPD3 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for GDPD3 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for GDPD3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_143822 | 16 | 30116164:30116330:30119441:30119585:30119693:30119753 | 30119441:30119585 | ENSG00000102886.10 | ENST00000566434.1 |
| exon_skip_143824 | 16 | 30116164:30116330:30119533:30119585:30119693:30119753 | 30119533:30119585 | ENSG00000102886.10 | ENST00000360688.3,ENST00000406256.3 |
| exon_skip_143827 | 16 | 30116164:30116330:30119693:30119753:30122708:30122711 | 30119693:30119753 | ENSG00000102886.10 | ENST00000566613.1 |
| exon_skip_143829 | 16 | 30119693:30119753:30122708:30122842:30123452:30123538 | 30122708:30122842 | ENSG00000102886.10 | ENST00000360688.3,ENST00000406256.3 |
| exon_skip_143835 | 16 | 30123843:30123889:30123978:30124114:30124342:30124385 | 30123978:30124114 | ENSG00000102886.10 | ENST00000406256.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for GDPD3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_143822 | 16 | 30116164:30116330:30119441:30119585:30119693:30119753 | 30119441:30119585 | ENSG00000102886.10 | ENST00000566434.1 |
| exon_skip_143824 | 16 | 30116164:30116330:30119533:30119585:30119693:30119753 | 30119533:30119585 | ENSG00000102886.10 | ENST00000360688.3,ENST00000406256.3 |
| exon_skip_143827 | 16 | 30116164:30116330:30119693:30119753:30122708:30122711 | 30119693:30119753 | ENSG00000102886.10 | ENST00000566613.1 |
| exon_skip_143829 | 16 | 30119693:30119753:30122708:30122842:30123452:30123538 | 30122708:30122842 | ENSG00000102886.10 | ENST00000360688.3,ENST00000406256.3 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for GDPD3 |
| Open reading frame (ORF) of individual exon skipping events in TCGA 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 GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
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Infer the effects of exon skipping event on protein functional features for GDPD3 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 GTEx 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 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 GTEx. |
| 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 |
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SNVs in the skipped exons for GDPD3 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_143822 | 30119442 | 30119585 | 30119553 | 30119553 | Frame_Shift_Del | A | - | p.L267fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_143824 | 30119534 | 30119585 | 30119553 | 30119553 | Frame_Shift_Del | A | - | p.L267fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_143827 | 30119694 | 30119753 | 30119696 | 30119696 | Frame_Shift_Del | T | - | p.K255fs |
| SKCM | TCGA-EE-A29C-06 | exon_skip_143827 | 30119694 | 30119753 | 30119700 | 30119700 | Frame_Shift_Del | G | - | p.S254fs |
| LGG | TCGA-CS-5397-01 | exon_skip_143827 | 30119694 | 30119753 | 30119725 | 30119725 | Frame_Shift_Del | G | - | p.L246fs |
| BLCA | TCGA-KQ-A41N-01 | exon_skip_143822 | 30119442 | 30119585 | 30119560 | 30119560 | Nonsense_Mutation | G | A | p.R265* |
| BLCA | TCGA-KQ-A41N-01 | exon_skip_143824 | 30119534 | 30119585 | 30119560 | 30119560 | Nonsense_Mutation | G | A | p.R265* |
| HNSC | TCGA-CN-4730-01 | exon_skip_143829 | 30122709 | 30122842 | 30122798 | 30122798 | Nonsense_Mutation | C | T | p.W206* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| HS863T_FIBROBLAST | 30122709 | 30122842 | 30122713 | 30122715 | In_Frame_Del | TGA | - | p.I234del |
| JEG3_PLACENTA | 30119694 | 30119753 | 30119700 | 30119700 | Missense_Mutation | G | A | p.S254L |
| WM35_SKIN | 30123979 | 30124114 | 30124023 | 30124023 | Missense_Mutation | G | T | p.R92S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GDPD3 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GDPD3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GDPD3 |
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RelatedDrugs for GDPD3 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for GDPD3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| GDPD3 | C0023794 | Lipoidosis | 3 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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