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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:ARNTL2-PPFIBP1 (FusionGDB2 ID:HG56938TG8496)

Fusion Gene Summary for ARNTL2-PPFIBP1

check button Fusion gene summary
Fusion gene informationFusion gene name: ARNTL2-PPFIBP1
Fusion gene ID: hg56938tg8496
HgeneTgene
Gene symbol

ARNTL2

PPFIBP1

Gene ID

56938

8496

Gene namearyl hydrocarbon receptor nuclear translocator like 2PPFIA binding protein 1
SynonymsBMAL2|CLIF|MOP9|PASD9|bHLHe6L2|SGT2|hSGT2|hSgt2p
Cytomap('ARNTL2')('PPFIBP1')

12p11.23

12p11.23-p11.22

Type of geneprotein-codingprotein-coding
Descriptionaryl hydrocarbon receptor nuclear translocator-like protein 2CYCLE-like factorPAS domain-containing protein 9basic-helix-loop-helix-PAS protein MOP9brain and muscle ARNT-like 2class E basic helix-loop-helix protein 6member of PAS protein 9transcripliprin-beta-1PTPRF interacting protein, binding protein 1 (liprin beta 1)PTPRF-interacting protein-binding protein 1liprin related proteinprotein-tyrosine phosphatase receptor-type f polypeptide-interacting protein-binding protein 1
Modification date2020031320200313
UniProtAcc.

Q86W92

Ensembl transtripts involved in fusion geneENST00000539558, ENST00000261178, 
ENST00000266503, ENST00000311001, 
ENST00000395901, ENST00000542388, 
ENST00000544915, ENST00000546179, 
ENST00000261178, ENST00000266503, 
ENST00000311001, ENST00000395901, 
ENST00000544915, ENST00000546179, 
ENST00000539558, ENST00000542388, 
Fusion gene scores* DoF score4 X 3 X 4=489 X 11 X 6=594
# samples 413
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/594*10)=-2.19195130777231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARNTL2 [Title/Abstract] AND PPFIBP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARNTL2(27521345)-PPFIBP1(27731085), # samples:2
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
HgeneARNTL2

GO:0006357

regulation of transcription by RNA polymerase II

12055078

HgeneARNTL2

GO:0007623

circadian rhythm

10864977

HgeneARNTL2

GO:0045893

positive regulation of transcription, DNA-templated

12738229

HgeneARNTL2

GO:0045944

positive regulation of transcription by RNA polymerase II

15147242



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
ChimerDB4LIHCTCGA-K7-AAU7-01AARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+


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Fusion Gene ORF analysis for ARNTL2-PPFIBP1

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
3UTR-3UTRENST00000539558ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
3UTR-5UTRENST00000539558ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
3UTR-5UTRENST00000539558ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
3UTR-5UTRENST00000539558ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
3UTR-5UTRENST00000539558ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
3UTR-5UTRENST00000539558ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
3UTR-5UTRENST00000539558ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-3UTRENST00000261178ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-3UTRENST00000266503ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-3UTRENST00000311001ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-3UTRENST00000395901ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-3UTRENST00000542388ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-3UTRENST00000544915ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-3UTRENST00000546179ENST00000541633ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000261178ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000261178ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000261178ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000261178ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000261178ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000261178ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000266503ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000266503ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000266503ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000266503ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000266503ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000266503ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000311001ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000311001ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000311001ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000311001ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000311001ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000311001ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000395901ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000395901ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000395901ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000395901ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000395901ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000395901ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000542388ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000542388ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000542388ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000542388ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000542388ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000542388ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000544915ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000544915ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000544915ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000544915ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000544915ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000544915ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000546179ENST00000228425ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000546179ENST00000318304ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000546179ENST00000535047ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000546179ENST00000537927ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000546179ENST00000542629ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+
5CDS-5UTRENST00000546179ENST00000545334ARNTL2chr12

27521345

+PPFIBP1chr12

27731085

+

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 ARNTL2-PPFIBP1


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)
ARNTL2chr1227521345+PPFIBP1chr1227731084+0.0008647210.9991353
ARNTL2chr1227521345+PPFIBP1chr1227731084+0.0008647210.9991353


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 ARNTL2-PPFIBP1


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/:27521345/:27731085)
- 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
.PPFIBP1

Q86W92

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: May regulate the disassembly of focal adhesions. Did not bind receptor-like tyrosine phosphatases type 2A. {ECO:0000269|PubMed:9624153}.

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 ARNTL2-PPFIBP1


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 ARNTL2-PPFIBP1


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 ARNTL2-PPFIBP1


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 ARNTL2-PPFIBP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneARNTL2C0005586Bipolar Disorder2PSYGENET
HgeneARNTL2C0085762Alcohol abuse2PSYGENET
TgeneC0085269Plasma Cell Granuloma, Pulmonary1CTD_human