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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:AP3S1-ARL14EPL (FusionGDB2 ID:HG1176TG644100)

Fusion Gene Summary for AP3S1-ARL14EPL

check button Fusion gene summary
Fusion gene informationFusion gene name: AP3S1-ARL14EPL
Fusion gene ID: hg1176tg644100
HgeneTgene
Gene symbol

AP3S1

ARL14EPL

Gene ID

1176

644100

Gene nameadaptor related protein complex 3 subunit sigma 1ADP ribosylation factor like GTPase 14 effector protein like
SynonymsCLAPS3|Sigma3A-
Cytomap('AP3S1')('ARL14EPL')

5q22.3-q23.1

5q23.1

Type of geneprotein-codingprotein-coding
DescriptionAP-3 complex subunit sigma-1adapter-related protein complex 3 subunit sigma-1adaptor related protein complex 3 sigma 1 subunitclathrin adaptor complex AP3, sigma-3A subunitclathrin-associated/assembly/adapter protein, small 3clathrin-associated/assemARL14 effector protein-likeADP-ribosylation factor-like 14 effector protein-like
Modification date2020032020200313
UniProtAcc

Q92572

P0DKL9

Ensembl transtripts involved in fusion geneENST00000316788, ENST00000505423, 
Fusion gene scores* DoF score9 X 5 X 6=2707 X 10 X 2=140
# samples 912
** MAII scorelog2(9/270*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/140*10)=-0.222392421336448
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AP3S1 [Title/Abstract] AND ARL14EPL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAP3S1(115177803)-ARL14EPL(115389711), # samples:1
Anticipated loss of major functional domain due to fusion event.AP3S1-ARL14EPL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
AP3S1-ARL14EPL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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

check buttonFusion gene breakpoints across AP3S1 (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 ARL14EPL (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
* 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
ChimerDB4PRADTCGA-HC-7818-01AAP3S1chr5

115177803

+ARL14EPLchr5

115389711

+


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Fusion Gene ORF analysis for AP3S1-ARL14EPL

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
In-frameENST00000316788ENST00000601302AP3S1chr5

115177803

+ARL14EPLchr5

115389711

+
intron-3CDSENST00000505423ENST00000601302AP3S1chr5

115177803

+ARL14EPLchr5

115389711

+

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)
ENST00000316788AP3S1chr5115177803+ENST00000601302ARL14EPLchr5115389711+2160626257988243

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
ENST00000316788ENST00000601302AP3S1chr5115177803+ARL14EPLchr5115389711+0.0068326790.99316734

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Fusion Genomic Features for AP3S1-ARL14EPL


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)
AP3S1chr5115177803+ARL14EPLchr5115389710+7.52E-070.9999993
AP3S1chr5115177803+ARL14EPLchr5115389710+7.52E-070.9999993

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 AP3S1-ARL14EPL


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/chr5:115177803/chr5:115389711)
- 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
AP3S1

Q92572

ARL14EPL

P0DKL9

FUNCTION: Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals.

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
TgeneARL14EPLchr5:115177803chr5:115389711ENST000006013020392_12632153.0Compositional biasNote=Cys-rich

- 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 AP3S1-ARL14EPL


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.
>5293_5293_1_AP3S1-ARL14EPL_AP3S1_chr5_115177803_ENST00000316788_ARL14EPL_chr5_115389711_ENST00000601302_length(transcript)=2160nt_BP=626nt
ATCCGTAAGTCCTTCCCCTCCAGCAGCAATTGAAGTAGGAAGCTGCAACACAGACTGCGGCTCCTCCGCCATCTTGCTTGGAGACACTCG
AGAGCGGAAGTAGCGACTGAGCGCGTGCAGTGGGCGTGCTTTTCTCCAGGGAGCGTCGCAAAGGAGGCGCCGGAGTAGGGGGACGCAATT
ACACAGTGAAACTTGGTGTTCCCGGCTAGTCATTCAAATCGAAGCTGTCGCAGACCTCTGAACGTTAGTAACGCAACATGTGTTTCTCCG
CGACTACAGACCTCGGGAGAGGAGCGGTGGGCAACGTGTCTGTGCTCGGTCGAATGCGCACACTCCAGTTAGGCCGCTGGCTCGGACCTA
GAAATGTTTCCGCTTTCCTTAGTGCCTGCCCCGCCCAGGCCCCGCCCCTTGGGCCCCGCCCGACGGCTCGGGAGCGCGCGCGGTCGCGTG
CGGGAGGGGGCGGGTGGGGAAGGATCGCAGGCGAGATTACGAGGCGAGGCTCGCGCGCCCGCCCCCGCCCTGGCCCCCAGTGCCCACCCG
GTCGGCCCGGCACAGCCATGATCAAGGCGATCCTAATCTTCAACAACCACGGGAAGCCGCGGCTCTCCAAGTTCTACCAGCCCTACCAAC
AAATAGAGCGGCAGTTAAAATGCTTGGCATTTCGAAACCCTGGACCACAGGTAGCAGACTTTAATCCTGAAACAAGGCAGCAGAAAAAGA
AAGCCCGGATGTCAAAGATGAATGAATATTTTTCTACCAAATACAAAATAATGAGGAAGTATGACAAAAGTGGCAGGCTCATCTGTAATG
ACGCTGATCTGTGTGATTGTCTAGAGAAGAACTGCCTGGGCTGCTTCTACCCATGCCCGAAGTGTAACTCCAACAAGTGTGGGCCCGAGT
GCCGCTGCAACCGACGGTGGGTTTACGATGCCATCGTCACTGAGTCAGGAGAGGTCATCAGCACGCTGCCGTTTAATGTTCCTGACTAGG
TGCTCTTGTATATGGACTGATTTGTTTCTTCTTCTTACACATTTAAGTTGACCTCTTTCTTTTGGGTGAATTTTAGGGCTTGGGGGAAAT
ATCGAAAAAACATACTGAAGACTCATGTTCTGTCAAGCCCCAGAACAATGTAGAATGGGCAATAATTCTGTAACCTTCTTAACTGTGTCA
ACAATTTTCAAGTCCCTTAACTTGCAACCAAAGAATGTAACAATGGAGGGATCAGCATTTCTCATCAGCACCCTCATCTCTACTCTGCCT
TCAAATTAAAACTCTCTTCCCTCTTTGCTGATATCTGAGAAAATGTAGCTTTAAGATTTTCAAAACTCTGTAGTTGAGAGCTTTTCTTAC
ATAGAACATAGAATCTTAAATTTATAATATCTAGTTGTCCTTAGAATCTTATACATCACTAGCTGTAAATCAGAATTGCCATTTGGATTT
TGAAGAAAAACTGTGACTTTGCACTGTATACCCATAGCCTCATTTTTTTATTGTTCATGTTTTAATAACATTAAAATGAAATTTAGTAAT
ACTTGGTAGTATTTTTAATCATTAAAATTTGTATTGTACTTGTAAAATTGAAAAGTTAGGAATTTATTATCCTAAAAGCCAGGAGTTTAC
ATATTTTTGATTTCAGAAGCAGTATTTCAGGATTTGTTTTTCATAGAGAGAAAACAAGTTATACAAAAATGATTTTCTGTATGTTTGCTA
ATTGAGTGTGTTGATAAGCAATTGACTAGATAAATGATGTAGTCTTTTCAACTTTGATACATCATCAGAGCTATAAAATATTGAATTCAG
CTTTCTTTGAATTCATTTTTTTATGACAGTCTTTTTTTTAACCCTAAGTCAATGGTTCTCATTCATGAGAATTGCCTAGAGAACTTGTCA
AAACATAGATTTTTGCAGCCCCACATTCAGAATCTGGGACAGGGCTCAACCATCTGTTCCACGTTCCCAGGTGATGTTGATGCTGCTGAT
GTGGGGACCACACTTTGAGAACCACTTCTCTAAATTATTTTAGATACATAATGTAAGGAAGTATTTAAACCTCATTGACTATGATACTGC
CACTGCACAAAGCTGGAAGTATTTAAATAAAGTAACGTAATAAAAATTTAAAAGTAAATAAAAGCATTTAAGTTTTAAAATAAATTTGAA

>5293_5293_1_AP3S1-ARL14EPL_AP3S1_chr5_115177803_ENST00000316788_ARL14EPL_chr5_115389711_ENST00000601302_length(amino acids)=243AA_BP=0
MCFSATTDLGRGAVGNVSVLGRMRTLQLGRWLGPRNVSAFLSACPAQAPPLGPRPTARERARSRAGGGGWGRIAGEITRRGSRARPRPGP
QCPPGRPGTAMIKAILIFNNHGKPRLSKFYQPYQQIERQLKCLAFRNPGPQVADFNPETRQQKKKARMSKMNEYFSTKYKIMRKYDKSGR

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

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Fusion Gene PPI Analysis for AP3S1-ARL14EPL


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 AP3S1-ARL14EPL


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 AP3S1-ARL14EPL


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAP3S1C0023893Liver Cirrhosis, Experimental1CTD_human