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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:APP-LINC00159 (FusionGDB2 ID:5764)

Fusion Gene Summary for APP-LINC00159

check button Fusion gene summary
Fusion gene informationFusion gene name: APP-LINC00159
Fusion gene ID: 5764
HgeneTgene
Gene symbol

APP

LINC00159

Gene ID

351

100551499

Gene nameamyloid beta precursor proteinlong intergenic non-protein coding RNA 159
SynonymsAAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4C21orf44|NCRNA00159
Cytomap

21q21.3

21q22.11

Type of geneprotein-codingncRNA
Descriptionamyloid-beta precursor proteinalzheimer disease amyloid proteinamyloid beta (A4) precursor proteinamyloid beta A4 proteinamyloid precursor proteinbeta-amyloid peptidebeta-amyloid peptide(1-40)beta-amyloid peptide(1-42)beta-amyloid precursor protei-
Modification date2020032920200313
UniProtAcc

P05067

.
Ensembl transtripts involved in fusion geneENST00000346798, ENST00000354192, 
ENST00000348990, ENST00000357903, 
ENST00000358918, ENST00000359726, 
ENST00000448388, ENST00000440126, 
ENST00000439274, ENST00000474136, 
ENST00000411605, 
Fusion gene scores* DoF score31 X 25 X 12=93006 X 5 X 3=90
# samples 337
** MAII scorelog2(33/9300*10)=-4.81669278663694
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/90*10)=-0.362570079384708
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: APP [Title/Abstract] AND LINC00159 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPP(27277335)-LINC00159(33458608), # samples:1
APP(27277336)-LINC00159(33458608), # 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
HgeneAPP

GO:0001934

positive regulation of protein phosphorylation

11404397

HgeneAPP

GO:0008285

negative regulation of cell proliferation

22944668

HgeneAPP

GO:1905606

regulation of presynapse assembly

19726636


check buttonFusion gene breakpoints across APP (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across LINC00159 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4LIHCTCGA-RC-A6M3APPchr21

27277335

-LINC00159chr21

33458608

-
ChimerDB4LIHCTCGA-RC-A6M3-01AAPPchr21

27277336

-LINC00159chr21

33458608

-


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Fusion Gene ORF analysis for APP-LINC00159

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
Frame-shiftENST00000346798ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000354192ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000348990ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000357903ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
intron-3CDSENST00000358918ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000359726ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000448388ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000440126ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000439274ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
intron-3CDSENST00000474136ENST00000411605APPchr21

27277335

-LINC00159chr21

33458608

-
Frame-shiftENST00000346798ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
Frame-shiftENST00000354192ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
Frame-shiftENST00000348990ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
Frame-shiftENST00000357903ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
intron-3CDSENST00000358918ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
Frame-shiftENST00000359726ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
Frame-shiftENST00000448388ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
Frame-shiftENST00000440126ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
Frame-shiftENST00000439274ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-
intron-3CDSENST00000474136ENST00000411605APPchr21

27277336

-LINC00159chr21

33458608

-

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 APP-LINC00159


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for APP-LINC00159


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

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

P05067

.
FUNCTION: Functions as a cell surface receptor and performs physiological functions on the surface of neurons relevant to neurite growth, neuronal adhesion and axonogenesis. Interaction between APP molecules on neighboring cells promotes synaptogenesis (PubMed:25122912). Involved in cell mobility and transcription regulation through protein-protein interactions. Can promote transcription activation through binding to APBB1-KAT5 and inhibits Notch signaling through interaction with Numb. Couples to apoptosis-inducing pathways such as those mediated by G(O) and JIP. Inhibits G(o) alpha ATPase activity (By similarity). Acts as a kinesin I membrane receptor, mediating the axonal transport of beta-secretase and presenilin 1 (By similarity). By acting as a kinesin I membrane receptor, plays a role in axonal anterograde transport of cargo towards synapes in axons (PubMed:17062754, PubMed:23011729). Involved in copper homeostasis/oxidative stress through copper ion reduction. In vitro, copper-metallated APP induces neuronal death directly or is potentiated through Cu(2+)-mediated low-density lipoprotein oxidation. Can regulate neurite outgrowth through binding to components of the extracellular matrix such as heparin and collagen I and IV. The splice isoforms that contain the BPTI domain possess protease inhibitor activity. Induces a AGER-dependent pathway that involves activation of p38 MAPK, resulting in internalization of amyloid-beta peptide and leading to mitochondrial dysfunction in cultured cortical neurons. Provides Cu(2+) ions for GPC1 which are required for release of nitric oxide (NO) and subsequent degradation of the heparan sulfate chains on GPC1. {ECO:0000250, ECO:0000250|UniProtKB:P12023, ECO:0000269|PubMed:17062754, ECO:0000269|PubMed:23011729, ECO:0000269|PubMed:25122912}.; FUNCTION: Amyloid-beta peptides are lipophilic metal chelators with metal-reducing activity. Bind transient metals such as copper, zinc and iron. In vitro, can reduce Cu(2+) and Fe(3+) to Cu(+) and Fe(2+), respectively. Amyloid-beta protein 42 is a more effective reductant than amyloid-beta protein 40. Amyloid-beta peptides bind to lipoproteins and apolipoproteins E and J in the CSF and to HDL particles in plasma, inhibiting metal-catalyzed oxidation of lipoproteins. APP42-beta may activate mononuclear phagocytes in the brain and elicit inflammatory responses. Promotes both tau aggregation and TPK II-mediated phosphorylation. Interaction with overexpressed HADH2 leads to oxidative stress and neurotoxicity. Also binds GPC1 in lipid rafts.; FUNCTION: Appicans elicit adhesion of neural cells to the extracellular matrix and may regulate neurite outgrowth in the brain. {ECO:0000250}.; FUNCTION: The gamma-CTF peptides as well as the caspase-cleaved peptides, including C31, are potent enhancers of neuronal apoptosis.; FUNCTION: N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 APP-LINC00159


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 APP-LINC00159


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 APP-LINC00159


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneAPPP05067DB03754TromethamineInhibitorSmall moleculeApproved
HgeneAPPP05067DB03754TromethamineInhibitorSmall moleculeApproved
HgeneAPPP05067DB03754TromethamineInhibitorSmall moleculeApproved
HgeneAPPP05067DB06782DimercaprolSmall moleculeApproved
HgeneAPPP05067DB06782DimercaprolSmall moleculeApproved
HgeneAPPP05067DB06782DimercaprolSmall moleculeApproved
HgeneAPPP05067DB09148Florbetaben (18F)BinderSmall moleculeApproved
HgeneAPPP05067DB09148Florbetaben (18F)BinderSmall moleculeApproved
HgeneAPPP05067DB09148Florbetaben (18F)BinderSmall moleculeApproved
HgeneAPPP05067DB14548Zinc sulfate, unspecified formLigandSmall moleculeApproved|Experimental
HgeneAPPP05067DB14548Zinc sulfate, unspecified formLigandSmall moleculeApproved|Experimental
HgeneAPPP05067DB14548Zinc sulfate, unspecified formLigandSmall moleculeApproved|Experimental
HgeneAPPP05067DB00746DeferoxamineSmall moleculeApproved|Investigational
HgeneAPPP05067DB00746DeferoxamineSmall moleculeApproved|Investigational
HgeneAPPP05067DB00746DeferoxamineSmall moleculeApproved|Investigational
HgeneAPPP05067DB01370AluminiumSmall moleculeApproved|Investigational
HgeneAPPP05067DB01370AluminiumSmall moleculeApproved|Investigational
HgeneAPPP05067DB01370AluminiumSmall moleculeApproved|Investigational
HgeneAPPP05067DB01593ZincCofactorSmall moleculeApproved|Investigational
HgeneAPPP05067DB01593ZincCofactorSmall moleculeApproved|Investigational
HgeneAPPP05067DB01593ZincCofactorSmall moleculeApproved|Investigational
HgeneAPPP05067DB09130CopperAggregation inhibitorSmall moleculeApproved|Investigational
HgeneAPPP05067DB09130CopperAggregation inhibitorSmall moleculeApproved|Investigational
HgeneAPPP05067DB09130CopperAggregation inhibitorSmall moleculeApproved|Investigational
HgeneAPPP05067DB09149Florbetapir (18F)BinderSmall moleculeApproved|Investigational
HgeneAPPP05067DB09149Florbetapir (18F)BinderSmall moleculeApproved|Investigational
HgeneAPPP05067DB09149Florbetapir (18F)BinderSmall moleculeApproved|Investigational
HgeneAPPP05067DB09151Flutemetamol (18F)BinderSmall moleculeApproved|Investigational
HgeneAPPP05067DB09151Flutemetamol (18F)BinderSmall moleculeApproved|Investigational
HgeneAPPP05067DB09151Flutemetamol (18F)BinderSmall moleculeApproved|Investigational
HgeneAPPP05067DB14487Zinc acetateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14487Zinc acetateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14487Zinc acetateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14517Aluminium phosphateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14517Aluminium phosphateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14517Aluminium phosphateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14518Aluminum acetateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14518Aluminum acetateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14518Aluminum acetateSmall moleculeApproved|Investigational
HgeneAPPP05067DB14533Zinc chlorideLigandSmall moleculeApproved|Investigational
HgeneAPPP05067DB14533Zinc chlorideLigandSmall moleculeApproved|Investigational
HgeneAPPP05067DB14533Zinc chlorideLigandSmall moleculeApproved|Investigational

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Related Diseases for APP-LINC00159


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAPPC0002395Alzheimer's Disease63CTD_human;UNIPROT
HgeneAPPC0011265Presenile dementia35CTD_human
HgeneAPPC0276496Familial Alzheimer Disease (FAD)35CTD_human
HgeneAPPC0494463Alzheimer Disease, Late Onset35CTD_human
HgeneAPPC0546126Acute Confusional Senile Dementia35CTD_human
HgeneAPPC0750900Alzheimer's Disease, Focal Onset35CTD_human
HgeneAPPC0750901Alzheimer Disease, Early Onset35CTD_human
HgeneAPPC0025261Memory Disorders16CTD_human
HgeneAPPC0233794Memory impairment16CTD_human
HgeneAPPC0751292Age-Related Memory Disorders16CTD_human
HgeneAPPC0751293Memory Disorder, Semantic16CTD_human
HgeneAPPC0751294Memory Disorder, Spatial16CTD_human
HgeneAPPC0751295Memory Loss16CTD_human
HgeneAPPC0027746Nerve Degeneration11CTD_human
HgeneAPPC0023186Learning Disorders8CTD_human
HgeneAPPC0751262Adult Learning Disorders8CTD_human
HgeneAPPC0751263Learning Disturbance8CTD_human
HgeneAPPC0751265Learning Disabilities8CTD_human
HgeneAPPC1330966Developmental Academic Disorder8CTD_human
HgeneAPPC2751536CEREBRAL AMYLOID ANGIOPATHY, APP-RELATED7CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneAPPC0009241Cognition Disorders5CTD_human
HgeneAPPC0011570Mental Depression5PSYGENET
HgeneAPPC0011581Depressive disorder5PSYGENET
HgeneAPPC0234544Todd Paralysis5CTD_human
HgeneAPPC0522224Paralysed5CTD_human
HgeneAPPC0497327Dementia3CTD_human;GENOMICS_ENGLAND
HgeneAPPC2931672Cerebral hemorrhage with amyloidosis, hereditary, Dutch type3CTD_human;ORPHANET
HgeneAPPC0270715Degenerative Diseases, Central Nervous System2CTD_human
HgeneAPPC0333463Senile Plaques2CTD_human
HgeneAPPC0524851Neurodegenerative Disorders2CTD_human
HgeneAPPC0600467Neurogenic Inflammation2CTD_human
HgeneAPPC0751733Degenerative Diseases, Spinal Cord2CTD_human
HgeneAPPC2751494CEREBRAL AMYLOID ANGIOPATHY, APP-RELATED, ARCTIC VARIANT2CTD_human
HgeneAPPC2936349Plaque, Amyloid2CTD_human
HgeneAPPC3888307CEREBRAL AMYLOID ANGIOPATHY, APP-RELATED, FLEMISH VARIANT2CTD_human
HgeneAPPC3888308CEREBRAL AMYLOID ANGIOPATHY, APP-RELATED, ITALIAN VARIANT2CTD_human
HgeneAPPC3888309CEREBRAL AMYLOID ANGIOPATHY, APP-RELATED, IOWA VARIANT2CTD_human
HgeneAPPC0002622Amnesia1CTD_human
HgeneAPPC0002726Amyloidosis1CTD_human
HgeneAPPC0003469Anxiety Disorders1CTD_human
HgeneAPPC0005586Bipolar Disorder1PSYGENET
HgeneAPPC0006111Brain Diseases1CTD_human
HgeneAPPC0011573Endogenous depression1PSYGENET
HgeneAPPC0016667Fragile X Syndrome1CTD_human
HgeneAPPC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneAPPC0027540Necrosis1CTD_human
HgeneAPPC0033141Cardiomyopathies, Primary1CTD_human
HgeneAPPC0036529Myocardial Diseases, Secondary1CTD_human
HgeneAPPC0036572Seizures1GENOMICS_ENGLAND
HgeneAPPC0037928Spinal Cord Diseases1CTD_human
HgeneAPPC0038002Splenomegaly1CTD_human
HgeneAPPC0038454Cerebrovascular accident1GENOMICS_ENGLAND
HgeneAPPC0043094Weight Gain1CTD_human
HgeneAPPC0085220Cerebral Amyloid Angiopathy1CTD_human
HgeneAPPC0085584Encephalopathies1CTD_human
HgeneAPPC0231341Premature aging syndrome1CTD_human
HgeneAPPC0233750Hysterical amnesia1CTD_human
HgeneAPPC0233796Temporary Amnesia1CTD_human
HgeneAPPC0234985Mental deterioration1CTD_human
HgeneAPPC0236795Dissociative Amnesia1CTD_human
HgeneAPPC0262497Global Amnesia1CTD_human
HgeneAPPC0270612Leukoencephalopathy1GENOMICS_ENGLAND
HgeneAPPC0338582Sporadic Cerebral Amyloid Angiopathy1CTD_human
HgeneAPPC0338630Senile Paranoid Dementia1CTD_human
HgeneAPPC0338656Impaired cognition1CTD_human
HgeneAPPC0376280Anxiety States, Neurotic1CTD_human
HgeneAPPC0553692Brain hemorrhage1GENOMICS_ENGLAND
HgeneAPPC0750906Tactile Amnesia1CTD_human
HgeneAPPC0750907Amnestic State1CTD_human
HgeneAPPC0751071Familial Dementia1CTD_human
HgeneAPPC0751156FRAXA Syndrome1CTD_human
HgeneAPPC0751157FRAXE Syndrome1CTD_human
HgeneAPPC0878544Cardiomyopathies1CTD_human
HgeneAPPC0948008Ischemic stroke1GENOMICS_ENGLAND
HgeneAPPC1270972Mild cognitive disorder1CTD_human
HgeneAPPC1279420Anxiety neurosis (finding)1CTD_human