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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:ARPP19-AATF (FusionGDB2 ID:6826)

Fusion Gene Summary for ARPP19-AATF

check button Fusion gene summary
Fusion gene informationFusion gene name: ARPP19-AATF
Fusion gene ID: 6826
HgeneTgene
Gene symbol

ARPP19

AATF

Gene ID

10776

26574

Gene namecAMP regulated phosphoprotein 19apoptosis antagonizing transcription factor
SynonymsARPP-16|ARPP-19|ARPP16|ENSALBFR2|CHE-1|CHE1|DED
Cytomap

15q21.2

17q12

Type of geneprotein-codingprotein-coding
DescriptioncAMP-regulated phosphoprotein 19cAMP-regulated phosphoprotein 19kDacyclic AMP phosphoprotein, 19 kDprotein AATFrb-binding protein Che-1
Modification date2020031320200313
UniProtAcc.

Q9NY61

Ensembl transtripts involved in fusion geneENST00000249822, ENST00000561971, 
ENST00000564163, ENST00000566423, 
ENST00000567669, ENST00000569281, 
ENST00000569723, ENST00000561650, 
ENST00000563277, ENST00000563566, 
ENST00000565288, ENST00000568196, 
ENST00000590321, ENST00000225402, 
Fusion gene scores* DoF score2 X 2 X 3=1226 X 13 X 11=3718
# samples 328
** MAII scorelog2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(28/3718*10)=-3.73102803797452
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARPP19 [Title/Abstract] AND AATF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARPP19(52861044)-AATF(35376303), # 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
HgeneARPP19

GO:0045722

positive regulation of gluconeogenesis

9653196

TgeneAATF

GO:0032929

negative regulation of superoxide anion generation

15207272

TgeneAATF

GO:0045944

positive regulation of transcription by RNA polymerase II

18049476

TgeneAATF

GO:2000378

negative regulation of reactive oxygen species metabolic process

15207272


check buttonFusion gene breakpoints across ARPP19 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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

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
ChimerDB4STADTCGA-KB-A93JARPP19chr15

52861044

-AATFchr17

35376303

+


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Fusion Gene ORF analysis for ARPP19-AATF

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-intronENST00000249822ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
5CDS-intronENST00000561971ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
5CDS-intronENST00000564163ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
5CDS-intronENST00000566423ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
5CDS-intronENST00000567669ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
5CDS-intronENST00000569281ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
5CDS-intronENST00000569723ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
Frame-shiftENST00000561971ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
Frame-shiftENST00000567669ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
Frame-shiftENST00000569281ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
In-frameENST00000249822ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
In-frameENST00000564163ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
In-frameENST00000566423ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
In-frameENST00000569723ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-3CDSENST00000561650ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-3CDSENST00000563277ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-3CDSENST00000563566ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-3CDSENST00000565288ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-3CDSENST00000568196ENST00000225402ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-intronENST00000561650ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-intronENST00000563277ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-intronENST00000563566ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-intronENST00000565288ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+
intron-intronENST00000568196ENST00000590321ARPP19chr15

52861044

-AATFchr17

35376303

+

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)
ENST00000566423ARPP19chr1552861044-ENST00000225402AATFchr1735376303+671179134463109
ENST00000249822ARPP19chr1552861044-ENST00000225402AATFchr1735376303+809317182601139
ENST00000569723ARPP19chr1552861044-ENST00000225402AATFchr1735376303+5869449378109
ENST00000564163ARPP19chr1552861044-ENST00000225402AATFchr1735376303+66016833452139

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
ENST00000566423ENST00000225402ARPP19chr1552861044-AATFchr1735376303+0.0198693670.9801307
ENST00000249822ENST00000225402ARPP19chr1552861044-AATFchr1735376303+0.0230684190.97693163
ENST00000569723ENST00000225402ARPP19chr1552861044-AATFchr1735376303+0.0161951280.9838049
ENST00000564163ENST00000225402ARPP19chr1552861044-AATFchr1735376303+0.0198875480.98011243

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Fusion Genomic Features for ARPP19-AATF


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)
ARPP19chr1552861044-AATFchr1735376303+5.78E-101
ARPP19chr1552861044-AATFchr1735376303+5.78E-101

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.
genomic feature

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 ARPP19-AATF


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/chr15:52861044/chr17:35376303)
- 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
.AATF

Q9NY61

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 function as a general inhibitor of the histone deacetylase HDAC1. Binding to the pocket region of RB1 may displace HDAC1 from RB1/E2F complexes, leading to activation of E2F target genes and cell cycle progression. Conversely, displacement of HDAC1 from SP1 bound to the CDKN1A promoter leads to increased expression of this CDK inhibitor and blocks cell cycle progression. Also antagonizes PAWR mediated induction of aberrant amyloid peptide production in Alzheimer disease (presenile and senile dementia), although the molecular basis for this phenomenon has not been described to date. {ECO:0000269|PubMed:12450794, ECO:0000269|PubMed:12847090, ECO:0000269|PubMed:14627703, ECO:0000269|PubMed:15207272}.

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
TgeneAATFchr15:52861044chr17:35376303ENST0000022540271296_195466561.0Compositional biasNote=Glu-rich
TgeneAATFchr15:52861044chr17:35376303ENST00000225402712273_315466561.0RegionNote=POLR2J binding
TgeneAATFchr15:52861044chr17:35376303ENST00000225402712316_372466561.0RegionNote=RB1 binding
TgeneAATFchr15:52861044chr17:35376303ENST00000225402712373_472466561.0RegionNote=RB1 and SP1 binding


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Fusion Gene Sequence for ARPP19-AATF


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.
>6826_6826_1_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000249822_AATF_chr17_35376303_ENST00000225402_length(transcript)=809nt_BP=317nt
GGAAAAAAGGAAGTGTTTGGACGACAGCGAGCGGGAGAAGCGGGGTCAAGTAGGTAGGGGTGCGGTGCGGGAGGGGCAGGCGGGCTCCGG
CGTGCGAGGGCCTTGGCCAGCGGAGCGTTTCGCGGCTCCGTGTCGTCATAAGGCGGCGGCCATTTTCGCGGGCGGAGGCGGCCCGGCGGG
CCCTGGGAGAGCTGGGACGGGCGGCGGCCGGGTGGCCTCGGCCACCCGCTAATTGCATCTTTTCCCGGCGTCTCGTCTGCAGAGGGAGCA
CTATGTCTGCGGAAGTCCCCGAGGCAGCCTCCGCGGAGGAGCAGAAGCTCCTTCGAGAACTCATAGAACGGAAGACCAGCTCCTTGGATC
CCAACGATCAGGTGGCCATGGGAAGGCAGTGGCTTGCAATCCAGAAGTTACGAAGCAAAATCCACAAAAAAGTAGATAGGAAAGCCAGCA
AAGGCAGGAAACTTCGGTTTCATGTCCTTAGCAAGCTACTGAGTTTCATGGCACCTATTGACCATACTACAATGAATGATGATGCCAGGA
CAGAACTGTACCGCTCTCTTTTTGGCCAGCTCCACCCTCCCGACGAAGGCCACGGGGATTGACATCGCCCACCTCCGACACCCAGTGGGC
GCCTTGGCTGGTGCGGCTGCTGGTCCAGATGGAGGAAACCAGTGACTTTATGGGGCTGAGCTAGTAGGGAAGCCCCTGGAAAGATGCTGC

>6826_6826_1_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000249822_AATF_chr17_35376303_ENST00000225402_length(amino acids)=139AA_BP=45
MGELGRAAAGWPRPPANCIFSRRLVCRGSTMSAEVPEAASAEEQKLLRELIERKTSSLDPNDQVAMGRQWLAIQKLRSKIHKKVDRKASK

--------------------------------------------------------------
>6826_6826_2_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000564163_AATF_chr17_35376303_ENST00000225402_length(transcript)=660nt_BP=168nt
CCATTTTCGCGGGCGGAGGCGGCCCGGCGGGCCCTGGGAGAGCTGGGACGGGCGGCGGCCGGGTGGCCTCGGCCACCCGCTAATTGCATC
TTTTCCCGGCGTCTCGTCTGCAGAGGGAGCACTATGTCTGCGGAAGTCCCCGAGGCAGCCTCCGCGGAGGAGCAGAAGCTCCTTCGAGAA
CTCATAGAACGGAAGACCAGCTCCTTGGATCCCAACGATCAGGTGGCCATGGGAAGGCAGTGGCTTGCAATCCAGAAGTTACGAAGCAAA
ATCCACAAAAAAGTAGATAGGAAAGCCAGCAAAGGCAGGAAACTTCGGTTTCATGTCCTTAGCAAGCTACTGAGTTTCATGGCACCTATT
GACCATACTACAATGAATGATGATGCCAGGACAGAACTGTACCGCTCTCTTTTTGGCCAGCTCCACCCTCCCGACGAAGGCCACGGGGAT
TGACATCGCCCACCTCCGACACCCAGTGGGCGCCTTGGCTGGTGCGGCTGCTGGTCCAGATGGAGGAAACCAGTGACTTTATGGGGCTGA
GCTAGTAGGGAAGCCCCTGGAAAGATGCTGCGTTCCGAACCTGTGCCTAATACACGCAAGGGCGCTGTCCCGCCCAACCCCGCCTTTAAA

>6826_6826_2_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000564163_AATF_chr17_35376303_ENST00000225402_length(amino acids)=139AA_BP=45
MGELGRAAAGWPRPPANCIFSRRLVCRGSTMSAEVPEAASAEEQKLLRELIERKTSSLDPNDQVAMGRQWLAIQKLRSKIHKKVDRKASK

--------------------------------------------------------------
>6826_6826_3_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000566423_AATF_chr17_35376303_ENST00000225402_length(transcript)=671nt_BP=179nt
AGAAACTACAATTCCCAGGAAGCACTCGGCAGCCACAAACGGATGTGAGGTGAGGCAGGAGCGGCGACCTTTGAAGGAAAAAAGGAAGTG
TTTGGACGACAGCGAGCGGGAGAAGCGGGGTCAAAGGGAGCACTATGTCTGCGGAAGTCCCCGAGGCAGCCTCCGCGGAGGAGCAGAAGC
TCCTTCGAGAACTCATAGAACGGAAGACCAGCTCCTTGGATCCCAACGATCAGGTGGCCATGGGAAGGCAGTGGCTTGCAATCCAGAAGT
TACGAAGCAAAATCCACAAAAAAGTAGATAGGAAAGCCAGCAAAGGCAGGAAACTTCGGTTTCATGTCCTTAGCAAGCTACTGAGTTTCA
TGGCACCTATTGACCATACTACAATGAATGATGATGCCAGGACAGAACTGTACCGCTCTCTTTTTGGCCAGCTCCACCCTCCCGACGAAG
GCCACGGGGATTGACATCGCCCACCTCCGACACCCAGTGGGCGCCTTGGCTGGTGCGGCTGCTGGTCCAGATGGAGGAAACCAGTGACTT
TATGGGGCTGAGCTAGTAGGGAAGCCCCTGGAAAGATGCTGCGTTCCGAACCTGTGCCTAATACACGCAAGGGCGCTGTCCCGCCCAACC

>6826_6826_3_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000566423_AATF_chr17_35376303_ENST00000225402_length(amino acids)=109AA_BP=15
MSAEVPEAASAEEQKLLRELIERKTSSLDPNDQVAMGRQWLAIQKLRSKIHKKVDRKASKGRKLRFHVLSKLLSFMAPIDHTTMNDDART

--------------------------------------------------------------
>6826_6826_4_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000569723_AATF_chr17_35376303_ENST00000225402_length(transcript)=586nt_BP=94nt
AAGTGTTTGGACGACAGCGAGCGGGAGAAGCGGGGTCAAAGGGAGCACTATGTCTGCGGAAGTCCCCGAGGCAGCCTCCGCGGAGGAGCA
GAAGCTCCTTCGAGAACTCATAGAACGGAAGACCAGCTCCTTGGATCCCAACGATCAGGTGGCCATGGGAAGGCAGTGGCTTGCAATCCA
GAAGTTACGAAGCAAAATCCACAAAAAAGTAGATAGGAAAGCCAGCAAAGGCAGGAAACTTCGGTTTCATGTCCTTAGCAAGCTACTGAG
TTTCATGGCACCTATTGACCATACTACAATGAATGATGATGCCAGGACAGAACTGTACCGCTCTCTTTTTGGCCAGCTCCACCCTCCCGA
CGAAGGCCACGGGGATTGACATCGCCCACCTCCGACACCCAGTGGGCGCCTTGGCTGGTGCGGCTGCTGGTCCAGATGGAGGAAACCAGT
GACTTTATGGGGCTGAGCTAGTAGGGAAGCCCCTGGAAAGATGCTGCGTTCCGAACCTGTGCCTAATACACGCAAGGGCGCTGTCCCGCC

>6826_6826_4_ARPP19-AATF_ARPP19_chr15_52861044_ENST00000569723_AATF_chr17_35376303_ENST00000225402_length(amino acids)=109AA_BP=15
MSAEVPEAASAEEQKLLRELIERKTSSLDPNDQVAMGRQWLAIQKLRSKIHKKVDRKASKGRKLRFHVLSKLLSFMAPIDHTTMNDDART

--------------------------------------------------------------

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Fusion Gene PPI Analysis for ARPP19-AATF


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 ARPP19-AATF


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 ARPP19-AATF


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