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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:GFAP-APOBEC3A (FusionGDB2 ID:HG2670TG200315)

Fusion Gene Summary for GFAP-APOBEC3A

check button Fusion gene summary
Fusion gene informationFusion gene name: GFAP-APOBEC3A
Fusion gene ID: hg2670tg200315
HgeneTgene
Gene symbol

GFAP

APOBEC3A

Gene ID

2670

200315

Gene nameglial fibrillary acidic proteinapolipoprotein B mRNA editing enzyme catalytic subunit 3A
SynonymsALXDRDA3A|ARP3|PHRBN|bK150C2.1
Cytomap('GFAP')('APOBEC3A')

17q21.31

22q13.1

Type of geneprotein-codingprotein-coding
Descriptionglial fibrillary acidic proteinDNA dC->dU-editing enzyme APOBEC-3Aapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3Aphorbolin-1probable DNA dC->dU-editing enzyme APOBEC-3A
Modification date2020032720200329
UniProtAcc

P14136

P31941

Ensembl transtripts involved in fusion geneENST00000253408, ENST00000435360, 
ENST00000586793, ENST00000588735, 
ENST00000591327, 
Fusion gene scores* DoF score28 X 17 X 2=95210 X 10 X 2=200
# samples 2911
** MAII scorelog2(29/952*10)=-1.71490867329301
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/200*10)=-0.862496476250065
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GFAP [Title/Abstract] AND APOBEC3A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGFAP(42982999)-APOBEC3A(39366201), # 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
HgeneGFAP

GO:0045109

intermediate filament organization

15732097

TgeneAPOBEC3A

GO:0010529

negative regulation of transposition

16527742|20062055|21123384

TgeneAPOBEC3A

GO:0044355

clearance of foreign intracellular DNA

20062055

TgeneAPOBEC3A

GO:0045071

negative regulation of viral genome replication

16527742

TgeneAPOBEC3A

GO:0045087

innate immune response

21123384

TgeneAPOBEC3A

GO:0051607

defense response to virus

21123384|22457529

TgeneAPOBEC3A

GO:0070383

DNA cytosine deamination

16527742|21123384

TgeneAPOBEC3A

GO:0071466

cellular response to xenobiotic stimulus

20062055

TgeneAPOBEC3A

GO:0080111

DNA demethylation

21496894



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 GFAP-APOBEC3A

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 GFAP-APOBEC3A


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 GFAP-APOBEC3A


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/:42982999/:39366201)
- 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
GFAP

P14136

APOBEC3A

P31941

FUNCTION: GFAP, a class-III intermediate filament, is a cell-specific marker that, during the development of the central nervous system, distinguishes astrocytes from other glial cells.FUNCTION: DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno-associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation. {ECO:0000269|PubMed:10469298, ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:19461882, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:20615867, ECO:0000269|PubMed:21123384, ECO:0000269|PubMed:21368204, ECO:0000269|PubMed:21460793, ECO:0000269|PubMed:21496894, ECO:0000269|PubMed:22457529, ECO:0000269|PubMed:22896697}.

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 GFAP-APOBEC3A


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 GFAP-APOBEC3A


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 GFAP-APOBEC3A


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

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Related Diseases for GFAP-APOBEC3A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGFAPC0270726Alexander Disease30CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneGFAPC0011570Mental Depression3PSYGENET
HgeneGFAPC0011581Depressive disorder3PSYGENET
HgeneGFAPC0027765nervous system disorder3CTD_human
HgeneGFAPC0005586Bipolar Disorder2PSYGENET
HgeneGFAPC0036341Schizophrenia2PSYGENET
HgeneGFAPC0041696Unipolar Depression2PSYGENET
HgeneGFAPC1269683Major Depressive Disorder2PSYGENET
HgeneGFAPC0001973Alcoholic Intoxication, Chronic1PSYGENET
HgeneGFAPC0002736Amyotrophic Lateral Sclerosis1CTD_human
HgeneGFAPC0014544Epilepsy1CTD_human
HgeneGFAPC0017639Gliosis1CTD_human
HgeneGFAPC0020429Hyperalgesia1CTD_human
HgeneGFAPC0027873Neuromyelitis Optica1CTD_human
HgeneGFAPC0030567Parkinson Disease1CTD_human
HgeneGFAPC0036572Seizures1GENOMICS_ENGLAND
HgeneGFAPC0037917Spina Bifida Cystica1CTD_human
HgeneGFAPC0040997Trigeminal Neuralgia1CTD_human
HgeneGFAPC0086237Epilepsy, Cryptogenic1CTD_human
HgeneGFAPC0236018Aura1CTD_human
HgeneGFAPC0393554Amyotrophic Lateral Sclerosis With Dementia1CTD_human
HgeneGFAPC0393786Trigeminal Neuralgia, Idiopathic1CTD_human
HgeneGFAPC0393787Secondary Trigeminal Neuralgia1CTD_human
HgeneGFAPC0458247Allodynia1CTD_human
HgeneGFAPC0543859Amyotrophic Lateral Sclerosis, Guam Form1CTD_human
HgeneGFAPC0751111Awakening Epilepsy1CTD_human
HgeneGFAPC0751211Hyperalgesia, Primary1CTD_human
HgeneGFAPC0751212Hyperalgesia, Secondary1CTD_human
HgeneGFAPC0751213Tactile Allodynia1CTD_human
HgeneGFAPC0751214Hyperalgesia, Thermal1CTD_human
HgeneGFAPC0752347Lewy Body Disease1CTD_human
HgeneGFAPC0917813Spina Bifida, Open1CTD_human
HgeneGFAPC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
HgeneGFAPC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
HgeneGFAPC2931673Ceroid lipofuscinosis, neuronal 1, infantile1CTD_human
HgeneGFAPC2936719Mechanical Allodynia1CTD_human
HgeneGFAPC3887640Astrocytosis1CTD_human
HgeneGFAPC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human
HgeneGFAPC4721453Peripheral Nervous System Diseases1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0006826Malignant Neoplasms1CTD_human
TgeneC0027651Neoplasms1CTD_human
TgeneC0033975Psychotic Disorders1PSYGENET
TgeneC0086692Benign Neoplasm1CTD_human
TgeneC0087031Juvenile-Onset Still Disease1CTD_human
TgeneC0349204Nonorganic psychosis1PSYGENET
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC3495559Juvenile arthritis1CTD_human
TgeneC3714758Juvenile psoriatic arthritis1CTD_human
TgeneC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
TgeneC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human