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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 GDNF |
 Gene summary |
| Gene information | Gene symbol | GDNF | Gene ID | 2668 |
| Gene name | glial cell derived neurotrophic factor | |
| Synonyms | ATF|ATF1|ATF2|HFB1-GDNF|HSCR3 | |
| Cytomap | 5p13.2 | |
| Type of gene | protein-coding | |
| Description | glial cell line-derived neurotrophic factorastrocyte-derived trophic factor | |
| Modification date | 20180519 | |
| UniProtAcc | P39905 | |
| Context | PubMed: GDNF [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 |
| GDNF | GO:0001755 | neural crest cell migration | 15242795 |
| GDNF | GO:0008284 | positive regulation of cell proliferation | 22897442 |
| GDNF | GO:0031175 | neuron projection development | 15242795 |
| GDNF | GO:0032770 | positive regulation of monooxygenase activity | 12358785 |
| GDNF | GO:0043524 | negative regulation of neuron apoptotic process | 8493557 |
| GDNF | GO:0045944 | positive regulation of transcription by RNA polymerase II | 12358785 |
| GDNF | GO:0048255 | mRNA stabilization | 12358785 |
| GDNF | GO:0051584 | regulation of dopamine uptake involved in synaptic transmission | 8493557 |
| GDNF | GO:0072107 | positive regulation of ureteric bud formation | 8657307 |
| GDNF | GO:0090190 | positive regulation of branching involved in ureteric bud morphogenesis | 8657307|17229286 |
| GDNF | GO:2001240 | negative regulation of extrinsic apoptotic signaling pathway in absence of ligand | 10921886 |
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Exon skipping events across known transcript of Ensembl for GDNF 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 GDNF |
| 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 GDNF |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_441640 | 5 | 37816127:37816237:37834825:37834924:37839608:37839782 | 37834825:37834924 | ENSG00000168621.10 | ENST00000515058.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for GDNF |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_441640 | 5 | 37816127:37816237:37834825:37834924:37839608:37839782 | 37834825:37834924 | ENSG00000168621.10 | ENST00000515058.1 |
| 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 GDNF |
| 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 GDNF |
| 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 GDNF |
| - 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-5C-A9VH-01 | exon_skip_441640 | 37834826 | 37834924 | 37834855 | 37834855 | Frame_Shift_Del | T | - | p.H32fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_441640 | 37834826 | 37834924 | 37834886 | 37834886 | Frame_Shift_Del | C | - | p.D5fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_441640 | 37834826 | 37834924 | 37834886 | 37834886 | Frame_Shift_Del | C | - | p.D5fs |
| KIRP | TCGA-B9-A44B-01 | exon_skip_441640 | 37834826 | 37834924 | 37834925 | 37834925 | Splice_Site | C | A | . |
| - 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 |
| SKGT2_STOMACH | 37834826 | 37834924 | 37834838 | 37834838 | Missense_Mutation | G | A | p.P21S |
| CAMA1_BREAST | 37834826 | 37834924 | 37834838 | 37834838 | Missense_Mutation | G | A | p.P21S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GDNF |
| 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 GDNF |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GDNF |
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RelatedDrugs for GDNF |
| 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 |
| P39905 | DB09301 | Chondroitin sulfate | Glial cell line-derived neurotrophic factor | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for GDNF |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| GDNF | C0036341 | Schizophrenia | 4 | PSYGENET |
| GDNF | C0041696 | Unipolar Depression | 4 | PSYGENET |
| GDNF | C1269683 | Major Depressive Disorder | 4 | PSYGENET |
| GDNF | C0005586 | Bipolar Disorder | 2 | PSYGENET |
| GDNF | C0019569 | Hirschsprung Disease | 2 | CTD_human;HPO;ORPHANET |
| GDNF | C0030567 | Parkinson Disease | 2 | CTD_human |
| GDNF | C0038220 | Status Epilepticus | 2 | CTD_human |
| GDNF | C0236736 | Cocaine-Related Disorders | 2 | CTD_human |
| GDNF | C0242422 | Parkinsonian Disorders | 2 | CTD_human |
| GDNF | C3150974 | HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 3 | 2 | UNIPROT |
| GDNF | C0013386 | Dyskinesia, Drug-Induced | 1 | CTD_human |
| GDNF | C0014474 | Ependymoma | 1 | CTD_human |
| GDNF | C0017636 | Glioblastoma | 1 | CTD_human |
| GDNF | C0017638 | Glioma | 1 | CTD_human |
| GDNF | C0020179 | Huntington Disease | 1 | CTD_human |
| GDNF | C0020429 | Hyperalgesia | 1 | CTD_human |
| GDNF | C0027854 | Neurologic Manifestations | 1 | CTD_human |
| GDNF | C0028945 | oligodendroglioma | 1 | CTD_human |
| GDNF | C0030569 | Secondary Parkinson Disease | 1 | CTD_human |
| GDNF | C0031511 | Pheochromocytoma | 1 | CTD_human |
| GDNF | C0035304 | Retinal Degeneration | 1 | CTD_human |
| GDNF | C0236733 | Amphetamine-Related Disorders | 1 | CTD_human |
| GDNF | C0524851 | Neurodegenerative Disorders | 1 | CTD_human |
| GDNF | C0683357 | excessive drinking | 1 | PSYGENET |
| GDNF | C1275808 | Congenital central hypoventilation | 1 | CTD_human;ORPHANET |
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