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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:HNRNPA1-BEST3 (FusionGDB2 ID:37036)

Fusion Gene Summary for HNRNPA1-BEST3

check button Fusion gene summary
Fusion gene informationFusion gene name: HNRNPA1-BEST3
Fusion gene ID: 37036
HgeneTgene
Gene symbol

HNRNPA1

BEST3

Gene ID

3178

144453

Gene nameheterogeneous nuclear ribonucleoprotein A1bestrophin 3
SynonymsALS19|ALS20|HNRPA1|HNRPA1L3|IBMPFD3|UP 1|hnRNP A1|hnRNP-A1VMD2L3
Cytomap

12q13.13

12q15

Type of geneprotein-codingprotein-coding
Descriptionheterogeneous nuclear ribonucleoprotein A1epididymis secretory sperm binding proteinhelix-destabilizing proteinheterogeneous nuclear ribonucleoprotein A1B proteinheterogeneous nuclear ribonucleoprotein B2 proteinheterogeneous nuclear ribonucleoproteibestrophin-3vitelliform macular dystrophy 2-like 3vitelliform macular dystrophy 2-like protein 3
Modification date2020031520200313
UniProtAcc

P09651

Q8N1M1

Ensembl transtripts involved in fusion geneENST00000330752, ENST00000340913, 
ENST00000546500, ENST00000547276, 
ENST00000551803, 		ENST00000266661, 
ENST00000330891, ENST00000331471, 
ENST00000393365, ENST00000476098, 
ENST00000488961, ENST00000533674, 
ENST00000551160, ENST00000553096, 
Fusion gene scores* DoF score8 X 8 X 7=44810 X 6 X 5=300
# samples 811
** MAII scorelog2(8/448*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/300*10)=-1.44745897697122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HNRNPA1 [Title/Abstract] AND BEST3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHNRNPA1(54674858)-BEST3(70065944), # 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
HgeneHNRNPA1

GO:0032212

positive regulation of telomere maintenance via telomerase

23935072

HgeneHNRNPA1

GO:0051168

nuclear export

8521471

HgeneHNRNPA1

GO:0051170

import into nucleus

8521471

HgeneHNRNPA1

GO:1903936

cellular response to sodium arsenite

27694260


check buttonFusion gene breakpoints across HNRNPA1 (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 BEST3 (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/ACR748314HNRNPA1chr12

54674858

+BEST3chr12

70065944

-


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Fusion Gene ORF analysis for HNRNPA1-BEST3

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-intronENST00000330752ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000330752ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000340913ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000546500ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000547276ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000266661HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000330891HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000331471HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000393365HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000476098HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000488961HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000533674HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000551160HNRNPA1chr12

54674858

+BEST3chr12

70065944

-
intron-intronENST00000551803ENST00000553096HNRNPA1chr12

54674858

+BEST3chr12

70065944

-

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 HNRNPA1-BEST3


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 HNRNPA1-BEST3


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/:54674858/:70065944)
- 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
HNRNPA1

P09651

BEST3

Q8N1M1

FUNCTION: Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection (PubMed:17371836). May bind to specific miRNA hairpins (PubMed:28431233). Binds to the IRES and thereby inhibits the translation of the apoptosis protease activating factor APAF1 (PubMed:31498791). {ECO:0000269|PubMed:17371836, ECO:0000269|PubMed:28431233, ECO:0000269|PubMed:31498791}.; FUNCTION: (Microbial infection) May play a role in HCV RNA replication. {ECO:0000269|PubMed:17229681}.; FUNCTION: (Microbial infection) Cleavage by Enterovirus 71 protease 3C results in increased translation of apoptosis protease activating factor APAF1, leading to apoptosis. {ECO:0000269|PubMed:17229681}.FUNCTION: Forms calcium-sensitive chloride channels. Permeable to bicarbonate. {ECO:0000269|PubMed:12907679}.

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 HNRNPA1-BEST3


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 HNRNPA1-BEST3


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 HNRNPA1-BEST3


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 HNRNPA1-BEST3


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