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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:NRP1-AMOTL1 (FusionGDB2 ID:60339)

Fusion Gene Summary for NRP1-AMOTL1

check button Fusion gene summary
Fusion gene informationFusion gene name: NRP1-AMOTL1
Fusion gene ID: 60339
HgeneTgene
Gene symbol

NRP1

AMOTL1

Gene ID

8829

154810

Gene nameneuropilin 1angiomotin like 1
SynonymsBDCA4|CD304|NP1|NRP|VEGF165RJEAP
Cytomap

10p11.22

11q21

Type of geneprotein-codingprotein-coding
Descriptionneuropilin-1transmembrane receptorvascular endothelial cell growth factor 165 receptorangiomotin-like protein 1junction-enriched and associated protein
Modification date2020032220200313
UniProtAcc

O14786

Q8IY63

Ensembl transtripts involved in fusion geneENST00000265371, ENST00000374816, 
ENST00000374821, ENST00000374822, 
ENST00000374823, ENST00000374867, 
ENST00000374875, ENST00000395995, 
ENST00000432372, 		ENST00000317829, 
ENST00000317837, ENST00000433060, 
ENST00000539727, 
Fusion gene scores* DoF score13 X 9 X 6=7025 X 6 X 2=60
# samples 146
** MAII scorelog2(14/702*10)=-2.32604420335959
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/60*10)=0
Context

PubMed: NRP1 [Title/Abstract] AND AMOTL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNRP1(33500749)-AMOTL1(94537912), # 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
HgeneNRP1

GO:0051894

positive regulation of focal adhesion assembly

24863063


check buttonFusion gene breakpoints across NRP1 (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 AMOTL1 (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
ChiTaRS5.0N/AFN146101NRP1chr10

33500749

+AMOTL1chr11

94537912

+


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Fusion Gene ORF analysis for NRP1-AMOTL1

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
intron-intronENST00000265371ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000265371ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000265371ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000265371ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374816ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374816ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374816ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374816ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374821ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374821ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374821ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374821ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374822ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374822ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374822ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374822ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374823ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374823ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374823ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374823ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374867ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374867ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374867ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374867ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374875ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374875ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374875ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000374875ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000395995ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000395995ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000395995ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000395995ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000432372ENST00000317829NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000432372ENST00000317837NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000432372ENST00000433060NRP1chr10

33500749

+AMOTL1chr11

94537912

+
intron-intronENST00000432372ENST00000539727NRP1chr10

33500749

+AMOTL1chr11

94537912

+

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 NRP1-AMOTL1


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 NRP1-AMOTL1


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/:33500749/:94537912)
- 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
NRP1

O14786

AMOTL1

Q8IY63

FUNCTION: Cell-surface receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system. Mediates the chemorepulsant activity of semaphorins (PubMed:9288753, PubMed:9529250, PubMed:10688880). Recognizes a C-end rule (CendR) motif R/KXXR/K on its ligands which causes cellular internalization and vascular leakage (PubMed:19805273). It binds to semaphorin 3A, the PLGF-2 isoform of PGF, the VEGF165 isoform of VEGFA and VEGFB (PubMed:9288753, PubMed:9529250, PubMed:10688880, PubMed:19805273). Coexpression with KDR results in increased VEGF165 binding to KDR as well as increased chemotaxis. Regulates VEGF-induced angiogenesis. Binding to VEGFA initiates a signaling pathway needed for motor neuron axon guidance and cell body migration, including for the caudal migration of facial motor neurons from rhombomere 4 to rhombomere 6 during embryonic development (By similarity). Regulates mitochondrial iron transport via interaction with ABCB8/MITOSUR (PubMed:30623799). {ECO:0000250|UniProtKB:P97333, ECO:0000269|PubMed:10688880, ECO:0000269|PubMed:19805273, ECO:0000269|PubMed:30623799, ECO:0000269|PubMed:9288753, ECO:0000269|PubMed:9529250}.; FUNCTION: [Isoform 2]: Binds VEGF-165 and may inhibit its binding to cells (PubMed:10748121, PubMed:26503042). May induce apoptosis by sequestering VEGF-165 (PubMed:10748121). May bind as well various members of the semaphorin family. Its expression has an averse effect on blood vessel number and integrity. {ECO:0000269|PubMed:10748121, ECO:0000269|PubMed:26503042}.; FUNCTION: (Microbial infection) Acts as a host factor for human coronavirus SARS-CoV-2 infection. Recognizes and binds to CendR motif RRAR on SARS-CoV-2 spike protein S1 which enhances SARS-CoV-2 infection. {ECO:0000269|PubMed:33082293, ECO:0000269|PubMed:33082294}.FUNCTION: Inhibits the Wnt/beta-catenin signaling pathway, probably by recruiting CTNNB1 to recycling endosomes and hence preventing its translocation to the nucleus. {ECO:0000269|PubMed:22362771}.

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 NRP1-AMOTL1


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 NRP1-AMOTL1


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 NRP1-AMOTL1


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 NRP1-AMOTL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource