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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:PDE4B-ITGB3BP (FusionGDB2 ID:63701)

Fusion Gene Summary for PDE4B-ITGB3BP

check button Fusion gene summary
Fusion gene informationFusion gene name: PDE4B-ITGB3BP
Fusion gene ID: 63701
HgeneTgene
Gene symbol

PDE4B

ITGB3BP

Gene ID

5142

23421

Gene namephosphodiesterase 4Bintegrin subunit beta 3 binding protein
SynonymsDPDE4|PDEIVBCENP-R|CENPR|HSU37139|NRIF3|TAP20
Cytomap

1p31.3

1p31.3

Type of geneprotein-codingprotein-coding
DescriptioncAMP-specific 3',5'-cyclic phosphodiesterase 4Bdunce-like phosphodiesterase E4phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)centromere protein Rbeta 3 endonexinbeta3-endonexinintegrin beta 3 binding protein (beta3-endonexin)integrin beta-3-binding proteinnuclear receptor-interacting factor 3
Modification date2020031320200313
UniProtAcc.

Q13352

Ensembl transtripts involved in fusion geneENST00000423207, ENST00000329654, 
ENST00000371045, ENST00000371048, 
ENST00000371049, ENST00000480109, 
ENST00000461681, ENST00000271002, 
ENST00000283568, ENST00000371092, 
Fusion gene scores* DoF score8 X 9 X 3=21610 X 4 X 8=320
# samples 109
** MAII scorelog2(10/216*10)=-1.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PDE4B [Title/Abstract] AND ITGB3BP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPDE4B(66458825)-ITGB3BP(63974241), # samples:1
Anticipated loss of major functional domain due to fusion event.PDE4B-ITGB3BP seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PDE4B-ITGB3BP seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target 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

check buttonFusion gene breakpoints across PDE4B (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 ITGB3BP (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
ChimerDB4GBMTCGA-14-0817-01APDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-


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Fusion Gene ORF analysis for PDE4B-ITGB3BP

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-intronENST00000423207ENST00000461681PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
Frame-shiftENST00000423207ENST00000271002PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
In-frameENST00000423207ENST00000283568PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
In-frameENST00000423207ENST00000371092PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000329654ENST00000271002PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000329654ENST00000283568PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000329654ENST00000371092PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371045ENST00000271002PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371045ENST00000283568PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371045ENST00000371092PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371048ENST00000271002PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371048ENST00000283568PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371048ENST00000371092PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371049ENST00000271002PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371049ENST00000283568PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000371049ENST00000371092PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000480109ENST00000271002PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000480109ENST00000283568PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-3CDSENST00000480109ENST00000371092PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-intronENST00000329654ENST00000461681PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-intronENST00000371045ENST00000461681PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-intronENST00000371048ENST00000461681PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-intronENST00000371049ENST00000461681PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-
intron-intronENST00000480109ENST00000461681PDE4Bchr1

66458825

+ITGB3BPchr1

63974241

-

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)
ENST00000423207PDE4Bchr166458825+ENST00000371092ITGB3BPchr163974241-15827214851249254
ENST00000423207PDE4Bchr166458825+ENST00000283568ITGB3BPchr163974241-12297214851228248

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
ENST00000423207ENST00000371092PDE4Bchr166458825+ITGB3BPchr163974241-0.0092480480.990752
ENST00000423207ENST00000283568PDE4Bchr166458825+ITGB3BPchr163974241-0.0106821770.98931783

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Fusion Genomic Features for PDE4B-ITGB3BP


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

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.

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Fusion Protein Features for PDE4B-ITGB3BP


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/chr1:66458825/chr1:63974241)
- 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
.ITGB3BP

Q13352

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: Transcription coregulator that can have both coactivator and corepressor functions. Isoform 1, but not other isoforms, is involved in the coactivation of nuclear receptors for retinoid X (RXRs) and thyroid hormone (TRs) in a ligand-dependent fashion. In contrast, it does not coactivate nuclear receptors for retinoic acid, vitamin D, progesterone receptor, nor glucocorticoid. Acts as a coactivator for estrogen receptor alpha. Acts as a transcriptional corepressor via its interaction with the NFKB1 NF-kappa-B subunit, possibly by interfering with the transactivation domain of NFKB1. Induces apoptosis in breast cancer cells, but not in other cancer cells, via a caspase-2 mediated pathway that involves mitochondrial membrane permeabilization but does not require other caspases. May also act as an inhibitor of cyclin A-associated kinase. Also acts a component of the CENPA-CAD (nucleosome distal) complex, a complex recruited to centromeres which is involved in assembly of kinetochore proteins, mitotic progression and chromosome segregation. May be involved in incorporation of newly synthesized CENPA into centromeres via its interaction with the CENPA-NAC complex. {ECO:0000269|PubMed:11713274, ECO:0000269|PubMed:12244126, ECO:0000269|PubMed:15082778, ECO:0000269|PubMed:15254226, ECO:0000269|PubMed:16622420}.

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
TgeneITGB3BPchr1:66458825chr1:63974241ENST000002710020983_1131262.0Coiled coilOntology_term=ECO:0000255
TgeneITGB3BPchr1:66458825chr1:63974241ENST000002835680883_1131171.0Coiled coilOntology_term=ECO:0000255
TgeneITGB3BPchr1:66458825chr1:63974241ENST0000037109211083_11340283.3333333333333Coiled coilOntology_term=ECO:0000255
TgeneITGB3BPchr1:66458825chr1:63974241ENST00000271002099_131262.0MotifNote=LXXLL motif
TgeneITGB3BPchr1:66458825chr1:63974241ENST00000283568089_131171.0MotifNote=LXXLL motif
TgeneITGB3BPchr1:66458825chr1:63974241ENST000002710020920_501262.0RegionNote=DD1
TgeneITGB3BPchr1:66458825chr1:63974241ENST000002835680820_501171.0RegionNote=DD1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePDE4Bchr1:66458825chr1:63974241ENST00000329654+117330_6590737.0DomainPDEase
HgenePDE4Bchr1:66458825chr1:63974241ENST00000371045+110330_6590565.0DomainPDEase
HgenePDE4Bchr1:66458825chr1:63974241ENST00000371049+116330_6590737.0DomainPDEase
HgenePDE4Bchr1:66458825chr1:63974241ENST00000423207+115330_65978722.0DomainPDEase
HgenePDE4Bchr1:66458825chr1:63974241ENST00000480109+110330_6590504.0DomainPDEase
HgenePDE4Bchr1:66458825chr1:63974241ENST00000329654+117406_4100737.0Nucleotide bindingNote=cAMP
HgenePDE4Bchr1:66458825chr1:63974241ENST00000371045+110406_4100565.0Nucleotide bindingNote=cAMP
HgenePDE4Bchr1:66458825chr1:63974241ENST00000371049+116406_4100737.0Nucleotide bindingNote=cAMP
HgenePDE4Bchr1:66458825chr1:63974241ENST00000423207+115406_41078722.0Nucleotide bindingNote=cAMP
HgenePDE4Bchr1:66458825chr1:63974241ENST00000480109+110406_4100504.0Nucleotide bindingNote=cAMP
TgeneITGB3BPchr1:66458825chr1:63974241ENST000003710921109_1340283.3333333333333MotifNote=LXXLL motif
TgeneITGB3BPchr1:66458825chr1:63974241ENST0000037109211020_5040283.3333333333333RegionNote=DD1


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Fusion Gene Sequence for PDE4B-ITGB3BP


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.
>63701_63701_1_PDE4B-ITGB3BP_PDE4B_chr1_66458825_ENST00000423207_ITGB3BP_chr1_63974241_ENST00000283568_length(transcript)=1229nt_BP=721nt
CACATGCTGGACGGATTCTGGGTCTGCTCTTTGTGCAAACAAAACAAGTGACTAGGTTTTGCTTACTATCCATTAGTGAATGCAGCTTGT
TTAATAAGATTTTTTTTAAAAAAATGCATGTAAAGGATTTATCAAAAGCCTTTATGAATATTTCATGAGTTGATATATTCAGCTGAATGA
ATTCAGTGAGTGTCAGTGTGTAGCTTGCAGACAAACCTCATCCACAAGGAGGCTACTGACATTGGAAGCACTTTGGCGCATTTTCAGAGG
CAAAGCCAGCCTGATAAAGCTCCTTGTGACAGCCTGACTTGCTATTCTTCGAGTATGCTGCTCTTGCTCTAAGACGCTCATACATTGGAG
TCACAGCTTCGTAAATTAAACTGGAAATAGTTTGCAGACTTATCAGTCTTCTGACCTGCAGCAGTGTCTCTGCTATGTTTGAGATTTTTG
TTTTGGATGGTGAAAGCTAGCACTCCTTACAAGACATGACAGCAAAAGATTCTTCAAAGGAACTTACTGCTTCTGAACCTGAGGTTTGCA
TAAAGACTTTCAAGGAGCAAATGCATTTAGAACTTGAGCTTCCGAGATTACCAGGAAACAGACCTACATCTCCTAAAATTTCTCCACGCA
GTTCACCAAGGAACTCACCATGCTTTTTCAGAAAGTTGCTGGTGAATAAAAGCATTCGGCAGCGTCGTCGCTTCACTGTGGCTCATACAT
GTGTTAAAAGATCACTGAAGTTGGATGGTCTGTTAGAAGAAAATTCATTTGATCCTTCAAAAATCACAAGGAAGAAAAGTGTTATAACTT
ATTCTCCAACAACTGGAACTTGTCAAATGAGTCTATTTGCTTCTCCCACAAGTTCTGAAGAGCAAAAGCACAGAAATGGACTATCAAATG
AAAAGAGAAAAAAATTGAATCACCCCAGTTTAACTGAAAGCAAAGAATCTACAACAAAAGACAATGATGAATTCATGATGTTGCTATCAA
AAGTTGAGAAATTGTCAGAAGAAATCATGGAGATAATGCAAAATTTAAGTAGTATACAGGCTTTGGAGGGCAGTAGAGAGCTTGAAAATC
TCATTGGAATCTCCTGTGCATCACATTTCTTAAAAAGAGAAATGCAGAAAACCAAAGAACTAATGACAAAAGTGAATAAACAAAAACTGT

>63701_63701_1_PDE4B-ITGB3BP_PDE4B_chr1_66458825_ENST00000423207_ITGB3BP_chr1_63974241_ENST00000283568_length(amino acids)=248AA_BP=73
MTAKDSSKELTASEPEVCIKTFKEQMHLELELPRLPGNRPTSPKISPRSSPRNSPCFFRKLLVNKSIRQRRRFTVAHTCVKRSLKLDGLL
EENSFDPSKITRKKSVITYSPTTGTCQMSLFASPTSSEEQKHRNGLSNEKRKKLNHPSLTESKESTTKDNDEFMMLLSKVEKLSEEIMEI

--------------------------------------------------------------
>63701_63701_2_PDE4B-ITGB3BP_PDE4B_chr1_66458825_ENST00000423207_ITGB3BP_chr1_63974241_ENST00000371092_length(transcript)=1582nt_BP=721nt
CACATGCTGGACGGATTCTGGGTCTGCTCTTTGTGCAAACAAAACAAGTGACTAGGTTTTGCTTACTATCCATTAGTGAATGCAGCTTGT
TTAATAAGATTTTTTTTAAAAAAATGCATGTAAAGGATTTATCAAAAGCCTTTATGAATATTTCATGAGTTGATATATTCAGCTGAATGA
ATTCAGTGAGTGTCAGTGTGTAGCTTGCAGACAAACCTCATCCACAAGGAGGCTACTGACATTGGAAGCACTTTGGCGCATTTTCAGAGG
CAAAGCCAGCCTGATAAAGCTCCTTGTGACAGCCTGACTTGCTATTCTTCGAGTATGCTGCTCTTGCTCTAAGACGCTCATACATTGGAG
TCACAGCTTCGTAAATTAAACTGGAAATAGTTTGCAGACTTATCAGTCTTCTGACCTGCAGCAGTGTCTCTGCTATGTTTGAGATTTTTG
TTTTGGATGGTGAAAGCTAGCACTCCTTACAAGACATGACAGCAAAAGATTCTTCAAAGGAACTTACTGCTTCTGAACCTGAGGTTTGCA
TAAAGACTTTCAAGGAGCAAATGCATTTAGAACTTGAGCTTCCGAGATTACCAGGAAACAGACCTACATCTCCTAAAATTTCTCCACGCA
GTTCACCAAGGAACTCACCATGCTTTTTCAGAAAGTTGCTGGTGAATAAAAGCATTCGGCAGCGTCGTCGCTTCACTGTGGCTCATACAT
GTGTTAAAAGATCACTGAAGTTGGATGGTCTGTTAGAAGAAAATTCATTTGATCCTTCAAAAATCACAAGGAAGAAAAGTGTTATAACTT
ATTCTCCAACAACTGGAACTTGTCAAATGAGTCTATTTGCTTCTCCCACAAGTTCTGAAGAGCAAAAGCACAGAAATGGACTATCAAATG
AAAAGAGAAAAAAATTGAATCACCCCAGTTTAACTGAAAGCAAAGAATCTACAACAAAAGACAATGATGAATTCATGATGTTGCTATCAA
AAGTTGAGAAATTGTCAGAAGAAATCATGGAGATAATGCAAAATTTAAGTAGTATACAGGCTTTGGAGGGCAGTAGAGAGCTTGAAAATC
TCATTGGAATCTCCTGTGCATCACATTTCTTAAAAAGAGAAATGCAGAAAACCAAAGAACTAATGACAAAAGTGAATAAACAAAAACTGT
TTGAAAAGAGTACAGGACTTCCTCACAAAGCATCACGTCATCTTGACAGCTATGAATTCCTTAAAGCCATTTTAAACTGAGGCATTAAGA
AGAAATGCACTCACCATGAGCACCAACTTCTGCATCTGCCTGATCATATTTAAAGGAACAGAGAAATATTTGTAATTAATCTGCCCAGTA
AATACCAGCTCGTAGCAGTTGGCAGGTGCATGTCTAGATAAAATTTCTTGCAGCTAATTTAAACTTTCTACACGCACCAGTAGATAATCT
CAATGTAAATAATACATTTCTTCTTGGCTCTTTAATGTAAGCCAACATGGAGAGGAAGATCTTGACTTATATTCTGTACCACATACACTT

>63701_63701_2_PDE4B-ITGB3BP_PDE4B_chr1_66458825_ENST00000423207_ITGB3BP_chr1_63974241_ENST00000371092_length(amino acids)=254AA_BP=73
MTAKDSSKELTASEPEVCIKTFKEQMHLELELPRLPGNRPTSPKISPRSSPRNSPCFFRKLLVNKSIRQRRRFTVAHTCVKRSLKLDGLL
EENSFDPSKITRKKSVITYSPTTGTCQMSLFASPTSSEEQKHRNGLSNEKRKKLNHPSLTESKESTTKDNDEFMMLLSKVEKLSEEIMEI

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

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Fusion Gene PPI Analysis for PDE4B-ITGB3BP


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 PDE4B-ITGB3BP


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 PDE4B-ITGB3BP


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