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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:ARNT-PRPF3 (FusionGDB2 ID:HG405TG9129)

Fusion Gene Summary for ARNT-PRPF3

check button Fusion gene summary
Fusion gene informationFusion gene name: ARNT-PRPF3
Fusion gene ID: hg405tg9129
HgeneTgene
Gene symbol

ARNT

PRPF3

Gene ID

405

9129

Gene namearyl hydrocarbon receptor nuclear translocatorpre-mRNA processing factor 3
SynonymsHIF-1-beta|HIF-1beta|HIF1-beta|HIF1B|HIF1BETA|TANGO|bHLHe2HPRP3|HPRP3P|PRP3|Prp3p|RP18|SNRNP90
Cytomap('ARNT')('PRPF3')

1q21.3

1q21.2

Type of geneprotein-codingprotein-coding
Descriptionaryl hydrocarbon receptor nuclear translocatorclass E basic helix-loop-helix protein 2dioxin receptor, nuclear translocatorhypoxia-inducible factor 1, beta subunitU4/U6 small nuclear ribonucleoprotein Prp3PRP3 pre-mRNA processing factor 3 homologU4/U6 snRNP 90 kDa proteinU4/U6-associated RNA splicing factorpre-mRNA-splicing factor 3
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000354396, ENST00000358595, 
ENST00000505755, ENST00000515192, 
ENST00000468970, 
Fusion gene scores* DoF score18 X 16 X 9=25927 X 5 X 6=210
# samples 187
** MAII scorelog2(18/2592*10)=-3.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARNT [Title/Abstract] AND PRPF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARNT(150830824)-PRPF3(150321632), # samples:1
Anticipated loss of major functional domain due to fusion event.ARNT-PRPF3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
ARNT-PRPF3 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
ARNT-PRPF3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneARNT

GO:0001666

response to hypoxia

8756616

HgeneARNT

GO:0010575

positive regulation of vascular endothelial growth factor production

8756616

HgeneARNT

GO:0043619

regulation of transcription from RNA polymerase II promoter in response to oxidative stress

8089148

HgeneARNT

GO:0045893

positive regulation of transcription, DNA-templated

8089148

HgeneARNT

GO:0046886

positive regulation of hormone biosynthetic process

1448077

TgenePRPF3

GO:0000244

spliceosomal tri-snRNP complex assembly

20595234

TgenePRPF3

GO:0000398

mRNA splicing, via spliceosome

28781166



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
ChimerDB4Non-Cancer5357NARNTchr1

150830824

-PRPF3chr1

150321632

+


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Fusion Gene ORF analysis for ARNT-PRPF3

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
5CDS-3UTRENST00000354396ENST00000467329ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-3UTRENST00000358595ENST00000467329ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-3UTRENST00000505755ENST00000467329ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-3UTRENST00000515192ENST00000467329ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000354396ENST00000414970ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000354396ENST00000543398ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000358595ENST00000414970ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000358595ENST00000543398ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000505755ENST00000414970ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000505755ENST00000543398ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000515192ENST00000414970ARNTchr1

150830824

-PRPF3chr1

150321632

+
5CDS-intronENST00000515192ENST00000543398ARNTchr1

150830824

-PRPF3chr1

150321632

+
Frame-shiftENST00000354396ENST00000324862ARNTchr1

150830824

-PRPF3chr1

150321632

+
Frame-shiftENST00000358595ENST00000324862ARNTchr1

150830824

-PRPF3chr1

150321632

+
Frame-shiftENST00000505755ENST00000324862ARNTchr1

150830824

-PRPF3chr1

150321632

+
Frame-shiftENST00000515192ENST00000324862ARNTchr1

150830824

-PRPF3chr1

150321632

+
intron-3CDSENST00000468970ENST00000324862ARNTchr1

150830824

-PRPF3chr1

150321632

+
intron-3UTRENST00000468970ENST00000467329ARNTchr1

150830824

-PRPF3chr1

150321632

+
intron-intronENST00000468970ENST00000414970ARNTchr1

150830824

-PRPF3chr1

150321632

+
intron-intronENST00000468970ENST00000543398ARNTchr1

150830824

-PRPF3chr1

150321632

+

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 ARNT-PRPF3


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)
ARNTchr1150830824-PRPF3chr1150321632+5.05E-091
ARNTchr1150830824-PRPF3chr1150321632+5.05E-091


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.
genomic feature of top 1%

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Fusion Protein Features for ARNT-PRPF3


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/:150830824/:150321632)
- 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
..
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: 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}.

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 ARNT-PRPF3


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 ARNT-PRPF3


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 ARNT-PRPF3


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 ARNT-PRPF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneARNTC0000786Spontaneous abortion1CTD_human
HgeneARNTC0000822Abortion, Tubal1CTD_human
HgeneARNTC0009402Colorectal Carcinoma1CTD_human
HgeneARNTC0009404Colorectal Neoplasms1CTD_human
HgeneARNTC0014175Endometriosis1CTD_human
HgeneARNTC0019193Hepatitis, Toxic1CTD_human
HgeneARNTC0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
HgeneARNTC0023453L2 Acute Lymphoblastic Leukemia1CTD_human
HgeneARNTC0023890Liver Cirrhosis1CTD_human
HgeneARNTC0025202melanoma1CTD_human
HgeneARNTC0027659Neoplasms, Experimental1CTD_human
HgeneARNTC0239946Fibrosis, Liver1CTD_human
HgeneARNTC0269102Endometrioma1CTD_human
HgeneARNTC0860207Drug-Induced Liver Disease1CTD_human
HgeneARNTC1262760Hepatitis, Drug-Induced1CTD_human
HgeneARNTC1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
HgeneARNTC3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneARNTC3830362Early Pregnancy Loss1CTD_human
HgeneARNTC4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneARNTC4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneARNTC4552766Miscarriage1CTD_human
TgeneC1832378Retinitis Pigmentosa 183CTD_human;GENOMICS_ENGLAND;UNIPROT