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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:ATG5-PDSS2 (FusionGDB2 ID:HG9474TG57107)

Fusion Gene Summary for ATG5-PDSS2

check button Fusion gene summary
Fusion gene informationFusion gene name: ATG5-PDSS2
Fusion gene ID: hg9474tg57107
HgeneTgene
Gene symbol

ATG5

PDSS2

Gene ID

9474

57107

Gene nameautophagy related 5decaprenyl diphosphate synthase subunit 2
SynonymsAPG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5C6orf210|COQ10D3|COQ1B|DLP1|bA59I9.3|hDLP1
Cytomap('ATG5')('PDSS2')

6q21

6q21

Type of geneprotein-codingprotein-coding
Descriptionautophagy protein 5APG5 autophagy 5-likeATG5 autophagy related 5 homologapoptosis-specific proteindecaprenyl-diphosphate synthase subunit 2all-trans-decaprenyl-diphosphate synthase subunit 2decaprenyl pyrophosphate synthase subunit 2decaprenyl pyrophosphate synthetase subunit 2prenyl (decaprenyl) diphosphate synthase, subunit 2subunit 2 of decapr
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000360666, ENST00000343245, 
ENST00000369070, ENST00000369076, 
ENST00000475645, 
ENST00000475645, 
ENST00000360666, ENST00000343245, 
ENST00000369070, ENST00000369076, 
Fusion gene scores* DoF score25 X 16 X 9=36009 X 7 X 6=378
# samples 2910
** MAII scorelog2(29/3600*10)=-3.6338721012021
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/378*10)=-1.91838623444635
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATG5 [Title/Abstract] AND PDSS2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATG5(106649847)-PDSS2(107475981), # samples:3
Anticipated loss of major functional domain due to fusion event.ATG5-PDSS2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
ATG5-PDSS2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PDSS2-ATG5 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PDSS2-ATG5 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor 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
TgenePDSS2

GO:0006744

ubiquinone biosynthetic process

16262699

TgenePDSS2

GO:0008299

isoprenoid biosynthetic process

16262699


check buttonFusion gene breakpoints across ATG5 (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 PDSS2 (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
ChimerDB4GBMTCGA-06-1804-01AATG5chr6

106649847

-PDSS2chr6

107475981

-


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Fusion Gene ORF analysis for ATG5-PDSS2

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-3CDSENST00000360666ENST00000369037ATG5chr6

106649847

-PDSS2chr6

107475981

-
3UTR-3CDSENST00000360666ENST00000453874ATG5chr6

106649847

-PDSS2chr6

107475981

-
3UTR-intronENST00000360666ENST00000369031ATG5chr6

106649847

-PDSS2chr6

107475981

-
5CDS-intronENST00000343245ENST00000369031ATG5chr6

106649847

-PDSS2chr6

107475981

-
5CDS-intronENST00000369070ENST00000369031ATG5chr6

106649847

-PDSS2chr6

107475981

-
5CDS-intronENST00000369076ENST00000369031ATG5chr6

106649847

-PDSS2chr6

107475981

-
5UTR-3CDSENST00000475645ENST00000369037ATG5chr6

106649847

-PDSS2chr6

107475981

-
5UTR-3CDSENST00000475645ENST00000453874ATG5chr6

106649847

-PDSS2chr6

107475981

-
5UTR-intronENST00000475645ENST00000369031ATG5chr6

106649847

-PDSS2chr6

107475981

-
Frame-shiftENST00000343245ENST00000369037ATG5chr6

106649847

-PDSS2chr6

107475981

-
Frame-shiftENST00000343245ENST00000453874ATG5chr6

106649847

-PDSS2chr6

107475981

-
Frame-shiftENST00000369070ENST00000369037ATG5chr6

106649847

-PDSS2chr6

107475981

-
Frame-shiftENST00000369076ENST00000369037ATG5chr6

106649847

-PDSS2chr6

107475981

-
In-frameENST00000369070ENST00000453874ATG5chr6

106649847

-PDSS2chr6

107475981

-
In-frameENST00000369076ENST00000453874ATG5chr6

106649847

-PDSS2chr6

107475981

-

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)
ENST00000369070ATG5chr6106649847-ENST00000453874PDSS2chr6107475981-1219887406933175
ENST00000369076ATG5chr6106649847-ENST00000453874PDSS2chr6107475981-134710153241061245

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
ENST00000369070ENST00000453874ATG5chr6106649847-PDSS2chr6107475981-0.0021476690.9978523
ENST00000369076ENST00000453874ATG5chr6106649847-PDSS2chr6107475981-0.0013013110.9986987

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Fusion Genomic Features for ATG5-PDSS2


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.
genomic feature

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Fusion Protein Features for ATG5-PDSS2


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/chr6:106649847/chr6:107475981)
- 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 ATG5-PDSS2


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.
>7598_7598_1_ATG5-PDSS2_ATG5_chr6_106649847_ENST00000369070_PDSS2_chr6_107475981_ENST00000453874_length(transcript)=1219nt_BP=887nt
CTGGACTTGTGGTGCGCTGCCAGGGCTCCGCAGCGTTGCCGGTTGTATTCGCTGGATACCAGAGGGCGGAAGTGCAGCAGGGTTCAGCTC
CGACCTCCGCGCCGGTGCTTTTTGCGGCTGCGCGGGCTTCCTGGAGTCCTGCTACCGCGTCCCCGCAGGACAGTGTGTCAGGCGGGCAGC
TTGCCCCGCCGCCCCACCGGAGCGCGGAATCTGGGCGTCCCCACCAGTGCGGGGAGCCGGAAGGAGGAGCCATAGCTTGGAGTAGGTTTG
GCTTTGGTTGAAATAAGAATTTAGCCTGTATGTACTGCTTTAACTCCTGGAAGAATGACAGATGACAAAGATGTGCTTCGAGATGTGTGG
TTTGGACGAATTCCAACTTGTTTCACGCTATATCAGGATGAGATAACTGAAAGGGAAGCAGAACCATACTATGCATTATCCAATTGGTTT
GCTATTTGATCTTCTTGCATCAAGTTCAGCTCTTCCTTGGAACATCACAGTACATTTTAAGAGTTTTCCAGAAAAAGACCTTCTGCACTG
TCCATCTAAGGATGCAATTGAAGCTCATTTTATGTCATGTATGAAAGAAGCTGATGCTTTAAAACATAAAAGTCAAGTAATCAATGAAAT
GCAGAAAAAAGATCACAAGCAACTCTGGATGGGATTGCAAAATGACAGATTTGACCAGTTTTGGGCCATCAATCGGAAACTCATGGAATA
TCCTGCAGAAGAAAATGGATTTCGTTATATCCCCTTTAGAATATATCAGACAACGACTGAAAGACCTTTCATTCAGAAGCTGTTTCGTCC
TGTGGCTGCAGATGGACAGTTGCACACACTAGGAGATCTCCTCAAAGAAGTTTGTCCTTCTGCTATTGATCCTGAAGTTGCGAGAAAGAA
TCAAAGCTGGCAAAGGTGTGACTTCAGCTATTGACCTGTGTCGTTACCATGGAAACAAGGCACTGGAGGCCCTGGAGAGCTTTCCTCCCT
CGGAGGCCAGATCTGCTTTAGAAAACATTGTGTTTGCTGTGACCAGATTTTCATGACATCAAATTAAAAAGACACTATTGTTAGTTAGCT
GAAAATCCTAGGGAATGAGGTTGATTGGGAGCGCTTTCACGATGCGTTAATGACTTTTAAAACATATGCATTTTTCCTTCCTTTTATCAC

>7598_7598_1_ATG5-PDSS2_ATG5_chr6_106649847_ENST00000369070_PDSS2_chr6_107475981_ENST00000453874_length(amino acids)=175AA_BP=160
MKGKQNHTMHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND

--------------------------------------------------------------
>7598_7598_2_ATG5-PDSS2_ATG5_chr6_106649847_ENST00000369076_PDSS2_chr6_107475981_ENST00000453874_length(transcript)=1347nt_BP=1015nt
CTGGACTTGTGGTGCGCTGCCAGGGCTCCGCAGCGTTGCCGGTTGTATTCGCTGGATACCAGAGGGCGGAAGTGCAGCAGGGTTCAGCTC
CGACCTCCGCGCCGGTGCTTTTTGCGGCTGCGCGGGCTTCCTGGAGTCCTGCTACCGCGTCCCCGCAGGACAGTGTGTCAGGCGGGCAGC
TTGCCCCGCCGCCCCACCGGAGCGCGGAATCTGGGCGTCCCCACCAGTGCGGGGAGCCGGAAGGAGGAGCCATAGCTTGGAGTAGGTTTG
GCTTTGGTTGAAATAAGAATTTAGCCTGTATGTACTGCTTTAACTCCTGGAAGAATGACAGATGACAAAGATGTGCTTCGAGATGTGTGG
TTTGGACGAATTCCAACTTGTTTCACGCTATATCAGGATGAGATAACTGAAAGGGAAGCAGAACCATACTATTTGCTTTTGCCAAGAGTA
AGTTATTTGACGTTGGTAACTGACAAAGTGAAAAAGCACTTTCAGAAGGTTATGAGACAAGAAGACATTAGTGAGATATGGTTTGAATAT
GAAGGCACACCACTGAAATGGCATTATCCAATTGGTTTGCTATTTGATCTTCTTGCATCAAGTTCAGCTCTTCCTTGGAACATCACAGTA
CATTTTAAGAGTTTTCCAGAAAAAGACCTTCTGCACTGTCCATCTAAGGATGCAATTGAAGCTCATTTTATGTCATGTATGAAAGAAGCT
GATGCTTTAAAACATAAAAGTCAAGTAATCAATGAAATGCAGAAAAAAGATCACAAGCAACTCTGGATGGGATTGCAAAATGACAGATTT
GACCAGTTTTGGGCCATCAATCGGAAACTCATGGAATATCCTGCAGAAGAAAATGGATTTCGTTATATCCCCTTTAGAATATATCAGACA
ACGACTGAAAGACCTTTCATTCAGAAGCTGTTTCGTCCTGTGGCTGCAGATGGACAGTTGCACACACTAGGAGATCTCCTCAAAGAAGTT
TGTCCTTCTGCTATTGATCCTGAAGTTGCGAGAAAGAATCAAAGCTGGCAAAGGTGTGACTTCAGCTATTGACCTGTGTCGTTACCATGG
AAACAAGGCACTGGAGGCCCTGGAGAGCTTTCCTCCCTCGGAGGCCAGATCTGCTTTAGAAAACATTGTGTTTGCTGTGACCAGATTTTC
ATGACATCAAATTAAAAAGACACTATTGTTAGTTAGCTGAAAATCCTAGGGAATGAGGTTGATTGGGAGCGCTTTCACGATGCGTTAATG

>7598_7598_2_ATG5-PDSS2_ATG5_chr6_106649847_ENST00000369076_PDSS2_chr6_107475981_ENST00000453874_length(amino acids)=245AA_BP=230
MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLL
ASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEEN

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Fusion Gene PPI Analysis for ATG5-PDSS2


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 ATG5-PDSS2


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 ATG5-PDSS2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATG5C0002871Anemia1CTD_human
HgeneATG5C0019193Hepatitis, Toxic1CTD_human
HgeneATG5C0019209Hepatomegaly1CTD_human
HgeneATG5C0023380Lethargy1CTD_human
HgeneATG5C0024312Lymphopenia1CTD_human
HgeneATG5C0027540Necrosis1CTD_human
HgeneATG5C0860207Drug-Induced Liver Disease1CTD_human
HgeneATG5C0919267ovarian neoplasm1CTD_human
HgeneATG5C1140680Malignant neoplasm of ovary1CTD_human
HgeneATG5C1262477Weight decreased1CTD_human
HgeneATG5C1262760Hepatitis, Drug-Induced1CTD_human
HgeneATG5C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneATG5C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneATG5C4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneATG5C4539808SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 251UNIPROT
TgeneC3553358COENZYME Q10 DEFICIENCY, PRIMARY, 33CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0023264Leigh Disease1GENOMICS_ENGLAND