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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PDSS2-ATG5

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PDSS2-ATG5
FusionPDB ID: 64077
FusionGDB2.0 ID: 64077
HgeneTgene
Gene symbol

PDSS2

ATG5

Gene ID

57107

9474

Gene namedecaprenyl diphosphate synthase subunit 2autophagy related 5
SynonymsC6orf210|COQ10D3|COQ1B|DLP1|bA59I9.3|hDLP1APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5
Cytomap

6q21

6q21

Type of geneprotein-codingprotein-coding
Descriptiondecaprenyl-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 decaprautophagy protein 5APG5 autophagy 5-likeATG5 autophagy related 5 homologapoptosis-specific protein
Modification date2020031320200313
UniProtAcc.

Q9H1Y0

Ensembl transtripts involved in fusion geneENST idsENST00000369031, ENST00000369037, 
ENST00000453874, 
ENST00000475645, 
ENST00000360666, ENST00000343245, 
ENST00000369070, ENST00000369076, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 8 X 6=52815 X 12 X 7=1260
# samples 1315
** MAII scorelog2(13/528*10)=-2.02202630633
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(15/1260*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

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

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATG5(106649847)-PDSS2(107475981), # samples:3
PDSS2(107780194)-ATG5(106649964), # samples:1
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
HgenePDSS2

GO:0006744

ubiquinone biosynthetic process

16262699

HgenePDSS2

GO:0008299

isoprenoid biosynthetic process

16262699


check buttonFusion gene breakpoints across PDSS2 (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 ATG5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-CancerTCGA-BR-6564-11APDSS2chr6

107780194

-ATG5chr6

106649964

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000369037PDSS2chr6107780194-ENST00000343245ATG5chr6106649964-2893574130828232
ENST00000369037PDSS2chr6107780194-ENST00000369070ATG5chr6106649964-2893574130828232
ENST00000369037PDSS2chr6107780194-ENST00000369076ATG5chr6106649964-2893574130828232
ENST00000453874PDSS2chr6107780194-ENST00000343245ATG5chr6106649964-2886567123821232
ENST00000453874PDSS2chr6107780194-ENST00000369070ATG5chr6106649964-2886567123821232
ENST00000453874PDSS2chr6107780194-ENST00000369076ATG5chr6106649964-2886567123821232
ENST00000369031PDSS2chr6107780194-ENST00000343245ATG5chr6106649964-2894575131829232
ENST00000369031PDSS2chr6107780194-ENST00000369070ATG5chr6106649964-2894575131829232
ENST00000369031PDSS2chr6107780194-ENST00000369076ATG5chr6106649964-2894575131829232

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
ENST00000369037ENST00000343245PDSS2chr6107780194-ATG5chr6106649964-0.71386190.28613815
ENST00000369037ENST00000369070PDSS2chr6107780194-ATG5chr6106649964-0.71386190.28613815
ENST00000369037ENST00000369076PDSS2chr6107780194-ATG5chr6106649964-0.71386190.28613815
ENST00000453874ENST00000343245PDSS2chr6107780194-ATG5chr6106649964-0.810617570.18938239
ENST00000453874ENST00000369070PDSS2chr6107780194-ATG5chr6106649964-0.810617570.18938239
ENST00000453874ENST00000369076PDSS2chr6107780194-ATG5chr6106649964-0.810617570.18938239
ENST00000369031ENST00000343245PDSS2chr6107780194-ATG5chr6106649964-0.62736650.37263355
ENST00000369031ENST00000369070PDSS2chr6107780194-ATG5chr6106649964-0.62736650.37263355
ENST00000369031ENST00000369076PDSS2chr6107780194-ATG5chr6106649964-0.62736650.37263355

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>64077_64077_1_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000369031_ATG5_chr6_106649964_ENST00000343245_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_2_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000369031_ATG5_chr6_106649964_ENST00000369070_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_3_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000369031_ATG5_chr6_106649964_ENST00000369076_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_4_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000369037_ATG5_chr6_106649964_ENST00000343245_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_5_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000369037_ATG5_chr6_106649964_ENST00000369070_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_6_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000369037_ATG5_chr6_106649964_ENST00000369076_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_7_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000453874_ATG5_chr6_106649964_ENST00000343245_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_8_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000453874_ATG5_chr6_106649964_ENST00000369070_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

>64077_64077_9_PDSS2-ATG5_PDSS2_chr6_107780194_ENST00000453874_ATG5_chr6_106649964_ENST00000369076_length(amino acids)=232AA_BP=148
MVTAPGSHLTLRVKNCRFLLVTVSSSSAPGLFPAALLDTPRSQTLPDSNHELSAAAVALATLSWSLGFPASPVVVPVPRHHLLGGLLAWS
VLQVPGPLESGSVRGGEDRGVPHVLHEPSLPAERRAQQHRYAGAEAGGHSAPSAYHSQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVC

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

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Fusion Protein Functional Features


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
.ATG5

Q9H1Y0

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Involved in autophagic vesicle formation. Conjugation with ATG12, through a ubiquitin-like conjugating system involving ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme, is essential for its function. The ATG12-ATG5 conjugate acts as an E3-like enzyme which is required for lipidation of ATG8 family proteins and their association to the vesicle membranes. Involved in mitochondrial quality control after oxidative damage, and in subsequent cellular longevity. Plays a critical role in multiple aspects of lymphocyte development and is essential for both B and T lymphocyte survival and proliferation. Required for optimal processing and presentation of antigens for MHC II. Involved in the maintenance of axon morphology and membrane structures, as well as in normal adipocyte differentiation. Promotes primary ciliogenesis through removal of OFD1 from centriolar satellites and degradation of IFT20 via the autophagic pathway. {ECO:0000250|UniProtKB:Q99J83, ECO:0000269|PubMed:12207896, ECO:0000269|PubMed:20580051, ECO:0000269|PubMed:22170153, ECO:0000269|PubMed:26812546}.; FUNCTION: May play an important role in the apoptotic process, possibly within the modified cytoskeleton. Its expression is a relatively late event in the apoptotic process, occurring downstream of caspase activity. Plays a crucial role in IFN-gamma-induced autophagic cell death by interacting with FADD. {ECO:0000269|PubMed:15778222, ECO:0000269|PubMed:7796880}.; FUNCTION: (Microbial infection) May act as a proviral factor. In association with ATG12, negatively regulates the innate antiviral immune response by impairing the type I IFN production pathway upon vesicular stomatitis virus (VSV) infection (PubMed:17709747). Required for the translation of incoming hepatitis C virus (HCV) RNA and, thereby, for initiation of HCV replication, but not required once infection is established (PubMed:19666601). {ECO:0000269|PubMed:17709747, ECO:0000269|PubMed:19666601}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PDSS2
ATG5


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to PDSS2-ATG5


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to PDSS2-ATG5


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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