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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:GDNF-AS1-GDNF (FusionGDB2 ID:HG100861519TG2668)

Fusion Gene Summary for GDNF-AS1-GDNF

check button Fusion gene summary
Fusion gene informationFusion gene name: GDNF-AS1-GDNF
Fusion gene ID: hg100861519tg2668
HgeneTgene
Gene symbol

GDNF-AS1

GDNF

Gene ID

100861519

2668

Gene nameGDNF antisense RNA 1glial cell derived neurotrophic factor
SynonymsGDNFOSATF|ATF1|ATF2|HFB1-GDNF|HSCR3
Cytomap('GDNF-AS1')('GDNF')

5p13.2

5p13.2

Type of genencRNAprotein-coding
DescriptionGDNF antisense RNA 1 (head to head)GDNF opposite strandglial cell line-derived neurotrophic factorastrocyte-derived trophic factor
Modification date2020031320200314
UniProtAcc.

P39905

Ensembl transtripts involved in fusion geneENST00000514532, 
Fusion gene scores* DoF score1 X 1 X 1=11 X 1 X 1=1
# samples 11
** MAII scorelog2(1/1*10)=3.32192809488736log2(1/1*10)=3.32192809488736
Context

PubMed: GDNF-AS1 [Title/Abstract] AND GDNF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGDNF-AS1(37812357)-GDNF(37812359), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneGDNF

GO:0001755

neural crest cell migration

15242795

TgeneGDNF

GO:0008284

positive regulation of cell proliferation

22897442

TgeneGDNF

GO:0031175

neuron projection development

15242795

TgeneGDNF

GO:0032770

positive regulation of monooxygenase activity

12358785

TgeneGDNF

GO:0043524

negative regulation of neuron apoptotic process

8493557

TgeneGDNF

GO:0045944

positive regulation of transcription by RNA polymerase II

12358785

TgeneGDNF

GO:0048255

mRNA stabilization

12358785

TgeneGDNF

GO:0051584

regulation of dopamine uptake involved in synaptic transmission

8493557

TgeneGDNF

GO:0072107

positive regulation of ureteric bud formation

8657307

TgeneGDNF

GO:0090190

positive regulation of branching involved in ureteric bud morphogenesis

8657307|17229286

TgeneGDNF

GO:2001240

negative regulation of extrinsic apoptotic signaling pathway in absence of ligand

10921886



check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand


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Fusion Gene ORF analysis for GDNF-AS1-GDNF

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for GDNF-AS1-GDNF


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for GDNF-AS1-GDNF


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:37812357/:37812359)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.GDNF

P39905

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Neurotrophic factor that enhances survival and morphological differentiation of dopaminergic neurons and increases their high-affinity dopamine uptake. {ECO:0000269|PubMed:8493557}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for GDNF-AS1-GDNF


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for GDNF-AS1-GDNF


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for GDNF-AS1-GDNF


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneGDNFP39905DB09301Chondroitin sulfateSmall moleculeApproved|Investigational|Nutraceutical

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Related Diseases for GDNF-AS1-GDNF


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3150974HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 35GENOMICS_ENGLAND;UNIPROT
TgeneC0036341Schizophrenia4PSYGENET
TgeneC0041696Unipolar Depression4PSYGENET
TgeneC1269683Major Depressive Disorder4PSYGENET
TgeneC0005586Bipolar Disorder2PSYGENET
TgeneC0009171Cocaine Abuse2CTD_human
TgeneC0019569Hirschsprung Disease2CTD_human
TgeneC0030567Parkinson Disease2CTD_human
TgeneC0038220Status Epilepticus2CTD_human
TgeneC0085758Aganglionosis, Colonic2CTD_human
TgeneC0236736Cocaine-Related Disorders2CTD_human
TgeneC0242422Parkinsonian Disorders2CTD_human
TgeneC0242423Ramsay Hunt Paralysis Syndrome2CTD_human
TgeneC0270823Petit mal status2CTD_human
TgeneC0311335Grand Mal Status Epilepticus2CTD_human
TgeneC0393734Complex Partial Status Epilepticus2CTD_human
TgeneC0600427Cocaine Dependence2CTD_human
TgeneC0751522Status Epilepticus, Subclinical2CTD_human
TgeneC0751523Non-Convulsive Status Epilepticus2CTD_human
TgeneC0751524Simple Partial Status Epilepticus2CTD_human
TgeneC0752097Autosomal Dominant Juvenile Parkinson Disease2CTD_human
TgeneC0752098Autosomal Dominant Parkinsonism2CTD_human
TgeneC0752100Autosomal Recessive Parkinsonism2CTD_human
TgeneC0752101Parkinsonism, Experimental2CTD_human
TgeneC0752104Familial Juvenile Parkinsonism2CTD_human
TgeneC0752105Parkinsonism, Juvenile2CTD_human
TgeneC1257840Aganglionosis, Rectosigmoid Colon2CTD_human
TgeneC1868675PARKINSON DISEASE 2, AUTOSOMAL RECESSIVE JUVENILE2CTD_human
TgeneC3661523Congenital Intestinal Aganglionosis2CTD_human
TgeneC0013386Dyskinesia, Drug-Induced1CTD_human
TgeneC0014474Ependymoma1CTD_human
TgeneC0017636Glioblastoma1CTD_human
TgeneC0017638Glioma1CTD_human
TgeneC0020179Huntington Disease1CTD_human
TgeneC0020429Hyperalgesia1CTD_human
TgeneC0027854Neurologic Manifestations1CTD_human
TgeneC0028945oligodendroglioma1CTD_human
TgeneC0030569Secondary Parkinson Disease1CTD_human
TgeneC0031511Pheochromocytoma1CTD_human;UNIPROT
TgeneC0035304Retinal Degeneration1CTD_human
TgeneC0205769Myxopapillary ependymoma1CTD_human
TgeneC0235031Neurologic Symptoms1CTD_human
TgeneC0236733Amphetamine-Related Disorders1CTD_human
TgeneC0236804Amphetamine Addiction1CTD_human
TgeneC0236807Amphetamine Abuse1CTD_human
TgeneC0259783mixed gliomas1CTD_human
TgeneC0270715Degenerative Diseases, Central Nervous System1CTD_human
TgeneC0279070Adult Oligodendroglioma1CTD_human
TgeneC0280475Childhood Oligodendroglioma1CTD_human
TgeneC0280788Anaplastic Ependymoma1CTD_human
TgeneC0280793Mixed Oligodendroglioma-Astrocytoma1CTD_human
TgeneC0334578Papillary ependymoma1CTD_human
TgeneC0334588Giant Cell Glioblastoma1CTD_human
TgeneC0334590Anaplastic Oligodendroglioma1CTD_human
TgeneC0344461Oligodendroblastoma1CTD_human
TgeneC0393574Huntington Disease, Late Onset1CTD_human
TgeneC0422837Neurological observations1CTD_human
TgeneC0458247Allodynia1CTD_human
TgeneC0521654Neurologic Deficits1CTD_human
TgeneC0524851Neurodegenerative Disorders1CTD_human
TgeneC0555198Malignant Glioma1CTD_human
TgeneC0683357Excessive drinking1PSYGENET
TgeneC0746857Focal Neurologic Deficits1CTD_human
TgeneC0751088Dyskinesia, Medication-Induced1CTD_human
TgeneC0751207Akinetic-Rigid Variant of Huntington Disease1CTD_human
TgeneC0751208Juvenile Huntington Disease1CTD_human
TgeneC0751211Hyperalgesia, Primary1CTD_human
TgeneC0751212Hyperalgesia, Secondary1CTD_human
TgeneC0751213Tactile Allodynia1CTD_human
TgeneC0751214Hyperalgesia, Thermal1CTD_human
TgeneC0751377Neurologic Dysfunction1CTD_human
TgeneC0751378Neurologic Signs1CTD_human
TgeneC0751395Mixed Oligodendroglioma-Ependymoma1CTD_human
TgeneC0751396Well Differentiated Oligodendroglioma1CTD_human
TgeneC0751414Parkinson Disease, Secondary Vascular1CTD_human
TgeneC0751415Atherosclerotic Parkinsonism1CTD_human
TgeneC0751733Degenerative Diseases, Spinal Cord1CTD_human
TgeneC1257877Pheochromocytoma, Extra-Adrenal1CTD_human
TgeneC1275808Congenital central hypoventilation1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC1384403Cellular Ependymoma1CTD_human
TgeneC1621958Glioblastoma Multiforme1CTD_human
TgeneC1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome1CLINGEN
TgeneC1859049CCHS WITH HIRSCHSPRUNG DISEASE1CTD_human
TgeneC2936719Mechanical Allodynia1CTD_human