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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:PDE4D-INTS10 (FusionGDB2 ID:63728)

Fusion Gene Summary for PDE4D-INTS10

check button Fusion gene summary
Fusion gene informationFusion gene name: PDE4D-INTS10
Fusion gene ID: 63728
HgeneTgene
Gene symbol

PDE4D

INTS10

Gene ID

5144

55174

Gene namephosphodiesterase 4Dintegrator complex subunit 10
SynonymsACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1C8orf35|INT10
Cytomap

5q11.2-q12.1

8p21.3

Type of geneprotein-codingprotein-coding
DescriptioncAMP-specific 3',5'-cyclic phosphodiesterase 4DcAMP-specific phosphodiesterase PDE4D6phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila)testicular tissue protein Li 136integrator complex subunit 10
Modification date2020031320200313
UniProtAcc.

Q9NVR2

Ensembl transtripts involved in fusion geneENST00000502484, ENST00000546160, 
ENST00000317118, ENST00000340635, 
ENST00000358923, ENST00000360047, 
ENST00000405755, ENST00000502575, 
ENST00000503258, ENST00000503947, 
ENST00000507116, 		ENST00000521758, 
ENST00000397977, 
Fusion gene scores* DoF score40 X 32 X 12=153608 X 6 X 7=336
# samples 568
** MAII scorelog2(56/15360*10)=-4.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/336*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PDE4D [Title/Abstract] AND INTS10 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPDE4D(59284315)-INTS10(19677084), # samples:1
Anticipated loss of major functional domain due to fusion event.PDE4D-INTS10 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PDE4D-INTS10 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PDE4D-INTS10 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneINTS10

GO:0016180

snRNA processing

16239144


check buttonFusion gene breakpoints across PDE4D (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 INTS10 (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
ChimerDB4PRADTCGA-J4-A83K-01APDE4Dchr5

59284315

-INTS10chr8

19677084

+


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Fusion Gene ORF analysis for PDE4D-INTS10

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-3UTRENST00000502484ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
5CDS-3UTRENST00000546160ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
Frame-shiftENST00000502484ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
In-frameENST00000546160ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000317118ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000340635ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000358923ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000360047ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000405755ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000502575ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000503258ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000503947ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3CDSENST00000507116ENST00000397977PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000317118ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000340635ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000358923ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000360047ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000405755ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000502575ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000503258ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000503947ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+
intron-3UTRENST00000507116ENST00000521758PDE4Dchr5

59284315

-INTS10chr8

19677084

+

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)
ENST00000546160PDE4Dchr559284315-ENST00000397977INTS10chr819677084+248127202207735

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
ENST00000546160ENST00000397977PDE4Dchr559284315-INTS10chr819677084+0.000614170.99938583

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Fusion Genomic Features for PDE4D-INTS10


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)
PDE4Dchr559284314-INTS10chr819677083+1.61E-050.9999839
PDE4Dchr559284314-INTS10chr819677083+1.61E-050.9999839

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 PDE4D-INTS10


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/chr5:59284315/chr8:19677084)
- 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
.INTS10

Q9NVR2

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: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). May be not involved in the recruitment of cytoplasmic dynein to the nuclear envelope by different components of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.

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
HgenePDE4Dchr5:59284315chr8:19677084ENST00000502484-31742_8890749.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000546160-21642_8890749.0Compositional biasNote=Pro-rich
TgeneINTS10chr5:59284315chr8:19677084ENST00000397977117132_13665711.0Compositional biasNote=Poly-Leu

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePDE4Dchr5:59284315chr8:19677084ENST00000317118-11042_880519.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000340635-11542_880810.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000358923-11142_880508.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000360047-11542_880674.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000405755-11542_880688.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000502575-1642_880220.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000503258-11542_880680.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000507116-11542_880746.0Compositional biasNote=Pro-rich
HgenePDE4Dchr5:59284315chr8:19677084ENST00000317118-110386_7150519.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000340635-115386_7150810.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000358923-111386_7150508.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000360047-115386_7150674.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000405755-115386_7150688.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000502484-317386_71590749.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000502575-16386_7150220.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000503258-115386_7150680.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000507116-115386_7150746.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000546160-216386_71590749.0DomainPDEase
HgenePDE4Dchr5:59284315chr8:19677084ENST00000317118-110462_4660519.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000340635-115462_4660810.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000358923-111462_4660508.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000360047-115462_4660674.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000405755-115462_4660688.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000502484-317462_46690749.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000502575-16462_4660220.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000503258-115462_4660680.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000507116-115462_4660746.0Nucleotide bindingcAMP
HgenePDE4Dchr5:59284315chr8:19677084ENST00000546160-216462_46690749.0Nucleotide bindingcAMP


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Fusion Gene Sequence for PDE4D-INTS10


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.
>63728_63728_1_PDE4D-INTS10_PDE4D_chr5_59284315_ENST00000546160_INTS10_chr8_19677084_ENST00000397977_length(transcript)=2481nt_BP=272nt
ATGAAAAGAAATACCTGTGATTTGCTTTCTCGGAGCAAAAGTGCCTCTGAGGAAACACTACATTCCAGTAATGAAGAGGAAGACCCTTTC
CGCGGAATGGAACCCTATCTTGTCCGGAGACTTTCATGTCGCAATATTCAGCTTCCCCCTCTCGCCTTCAGACAGTTGGAACAAGCTGAC
TTGAAAAGTGAATCAGAGAACATTCAACGACCAACCAGCCTCCCCCTGAAGATTCTGCCGCTGATTGCTATCACTTCTGCAGAATCCAGT
GGGTTTGTGAATTTCCCAGACCAGCCGGTGGTGTGGAGAGAAATCAGCATTATTACATCAGCATTAAGGAACGATTCACAGGACAAACAA
ACCCAATTTTTAAGAAGTTTATTTGAAACTCTTCCTGGTCGGGTCCAGTGTGAAATGTTACTAAAGGTCACGGAACAATGCTTCAACACG
TTAGAACGATCAGAAATGTTGCTTCTACTTTTGAGGCGCTTCCCTGAAACGGTGGTGCAGCATGGGGTTGGCCTTGGGGAGGCACTATTA
GAGGCTGAAACTATTGAAGAACAAGAATCTCCAGTGAACTGCTTTAGAAAATTATTTGTTTGTGATGTCCTTCCTCTAATAATTAACAAC
CATGATGTTCGATTACCTGCCAATTTATTGTATAAGTACTTGAACAAAGCAGCTGAATTTTATATCAATTATGTCACTAGGTCTACTCAA
ATAGAAAATCAGCATCAAGGCGCCCAGGATACATCTGATTTAATGTCACCTAGCAAACGTAGCTCTCAGAAGTACATAATAGAAGGGCTG
ACGGAAAAATCATCCCAGATCGTGGACCCTTGGGAGAGGTTGTTTAAGATTTTGAATGTTGTTGGAATGAGATGTGAATGGCAGATGGAT
AAAGGAAGACGAAGCTATGGAGATATTTTGCATAGAATGAAGGATCTCTGCAGATACATGAACAACTTTGATAGTGAAGCACATGCAAAA
TATAAAAACCAAGTGGTGTATTCCACCATGCTGGTCTTCTTTAAGAATGCATTCCAGTATGTCAACAGCATACAGCCATCTCTCTTCCAA
GGTCCTAATGCCCCGAGCCAAGTTCCACTGGTTCTTCTTGAAGATGTATCGAATGTGTATGGTGATGTAGAAATTGATCGTAATAAACAC
ATCCATAAAAAGAGGAAACTAGCTGAAGGAAGAGAAAAAACCATGAGTTCAGACGATGAAGACTGTTCGGCGAAAGGAAGAAATCGTCAC
ATTGTAGTCAATAAAGCCGAACTTGCTAACTCCACTGAAGTGTTAGAAAGCTTTAAATTGGCCAGGGAGAGCTGGGAGTTGCTCTATTCC
CTAGAATTCCTTGACAAAGAATTTACAAGGATTTGCTTGGCCTGGAAGACGGATACTTGGCTTTGGTTAAGAATCTTCCTCACTGATATG
ATCATCTATCAGGGTCAATATAAAAAGGCGATAGCCAGCCTGCATCACTTAGCAGCTCTCCAGGGATCCATTTCTCAGCCACAGATCACA
GGGCAGGGGACCCTGGAGCATCAGAGGGCGCTCATCCAGCTGGCGACGTGCCACTTTGCGCTAGGGGAGTACAGAATGACATGTGAAAAA
GTCCTTGATTTGATGTGCTACATGGTACTCCCCATTCAAGATGGAGGCAAATCCCAGGAGGAACCCTCGAAAGTAAAGCCCAAATTTAGA
AAAGGTTCGGATCTGAAGCTCCTGCCTTGTACCAGCAAGGCTATCATGCCATACTGCCTCCATTTAATGTTAGCCTGTTTTAAGCTTAGA
GCTTTCACAGACAACAGAGACGACATGGCATTGGGGCATGTGATTGTGTTGCTTCAGCAAGAGTGGCCACGGGGCGAGAATCTTTTCCTG
AAAGCTGTCAATAAAATTTGCCAACAAGGAAATTTCCAATATGAGAATTTTTTCAATTACGTTACAAATATTGATATGCTGGAGGAATTT
GCCTACTTGAGAACTCAGGAAGGTGGGAAAATTCATCTGGAATTACTACCCAATCAAGGAATGCTGATCAAGCACCACACTGTAACTCGA
GGCATCACCAAAGGCGTGAAGGAGGACTTTCGCCTGGCCATGGAGCGCCAGGTCTCCCGCTGTGGAGAGAATCTGATGGTGGTTCTGCAC
AGGTTCTGCATTAATGAGAAGATCTTGCTCCTTCAGACTCTGACCTGAGTGGAGACCTTTCCACCAGACACAGCTCGGGCCTGTGTAATT
GTAGGAGAAGACACTCAGCAGTGATTGCCATGGCACAGAGCCGTGGTCATTGTTGCTGTTACAAAGAAGAAAACCATCTGAGTTCTAACT
CCTTGGTTGCTTAAAAGTAGTTCCCAAGAGTCTGAGAAGCTATTTCTATTTTTAAGAGTCATTTTTTGTAATTTTTGTAAAACAAAAGTA

>63728_63728_1_PDE4D-INTS10_PDE4D_chr5_59284315_ENST00000546160_INTS10_chr8_19677084_ENST00000397977_length(amino acids)=735AA_BP=91
MKRNTCDLLSRSKSASEETLHSSNEEEDPFRGMEPYLVRRLSCRNIQLPPLAFRQLEQADLKSESENIQRPTSLPLKILPLIAITSAESS
GFVNFPDQPVVWREISIITSALRNDSQDKQTQFLRSLFETLPGRVQCEMLLKVTEQCFNTLERSEMLLLLLRRFPETVVQHGVGLGEALL
EAETIEEQESPVNCFRKLFVCDVLPLIINNHDVRLPANLLYKYLNKAAEFYINYVTRSTQIENQHQGAQDTSDLMSPSKRSSQKYIIEGL
TEKSSQIVDPWERLFKILNVVGMRCEWQMDKGRRSYGDILHRMKDLCRYMNNFDSEAHAKYKNQVVYSTMLVFFKNAFQYVNSIQPSLFQ
GPNAPSQVPLVLLEDVSNVYGDVEIDRNKHIHKKRKLAEGREKTMSSDDEDCSAKGRNRHIVVNKAELANSTEVLESFKLARESWELLYS
LEFLDKEFTRICLAWKTDTWLWLRIFLTDMIIYQGQYKKAIASLHHLAALQGSISQPQITGQGTLEHQRALIQLATCHFALGEYRMTCEK
VLDLMCYMVLPIQDGGKSQEEPSKVKPKFRKGSDLKLLPCTSKAIMPYCLHLMLACFKLRAFTDNRDDMALGHVIVLLQQEWPRGENLFL
KAVNKICQQGNFQYENFFNYVTNIDMLEEFAYLRTQEGGKIHLELLPNQGMLIKHHTVTRGITKGVKEDFRLAMERQVSRCGENLMVVLH

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

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Fusion Gene PPI Analysis for PDE4D-INTS10


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 PDE4D-INTS10


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 PDE4D-INTS10


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