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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:ITGB1BP1-CPSF3 (FusionGDB2 ID:40503)

Fusion Gene Summary for ITGB1BP1-CPSF3

check button Fusion gene summary
Fusion gene informationFusion gene name: ITGB1BP1-CPSF3
Fusion gene ID: 40503
HgeneTgene
Gene symbol

ITGB1BP1

CPSF3

Gene ID

9270

51692

Gene nameintegrin subunit beta 1 binding protein 1cleavage and polyadenylation specific factor 3
SynonymsICAP-1A|ICAP-1B|ICAP-1alpha|ICAP1|ICAP1A|ICAP1BCPSF-73|CPSF73
Cytomap

2p25.1

2p25.1

Type of geneprotein-codingprotein-coding
Descriptionintegrin beta-1-binding protein 1bodeninintegrin cytoplasmic domain-associated protein 1integrin cytoplasmic domain-associated protein 1-alphaintegrin cytoplasmic domain-associated protein 1-betacleavage and polyadenylation specificity factor subunit 3cleavage and polyadenylation specific factor 3, 73kDamRNA 3'-end-processing endonuclease CPSF-73
Modification date2020031320200313
UniProtAcc

O14713

Q9UKF6

Ensembl transtripts involved in fusion geneENST00000238091, ENST00000355346, 
ENST00000456913, ENST00000488451, 
ENST00000490426, ENST00000359712, 
ENST00000360635, 		ENST00000238112, 
ENST00000460593, ENST00000489403, 
Fusion gene scores* DoF score3 X 4 X 5=606 X 13 X 7=546
# samples 512
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/546*10)=-2.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ITGB1BP1 [Title/Abstract] AND CPSF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointITGB1BP1(9563501)-CPSF3(9563850), # samples:1
ITGB1BP1(9563502)-CPSF3(9568892), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneITGB1BP1

GO:0002043

blood vessel endothelial cell proliferation involved in sprouting angiogenesis

20616313

HgeneITGB1BP1

GO:0006469

negative regulation of protein kinase activity

20616313

HgeneITGB1BP1

GO:0007160

cell-matrix adhesion

9281591

HgeneITGB1BP1

GO:0007229

integrin-mediated signaling pathway

11919189|15703214

HgeneITGB1BP1

GO:0008284

positive regulation of cell proliferation

15703214

HgeneITGB1BP1

GO:0008285

negative regulation of cell proliferation

20616313

HgeneITGB1BP1

GO:0010595

positive regulation of endothelial cell migration

20616313

HgeneITGB1BP1

GO:0032091

negative regulation of protein binding

12473654

HgeneITGB1BP1

GO:0032148

activation of protein kinase B activity

20616313

HgeneITGB1BP1

GO:0035148

tube formation

20616313

HgeneITGB1BP1

GO:0035924

cellular response to vascular endothelial growth factor stimulus

20616313

HgeneITGB1BP1

GO:0043087

regulation of GTPase activity

11807099

HgeneITGB1BP1

GO:0044344

cellular response to fibroblast growth factor stimulus

20616313

HgeneITGB1BP1

GO:0045747

positive regulation of Notch signaling pathway

20616313

HgeneITGB1BP1

GO:0045944

positive regulation of transcription by RNA polymerase II

15703214|20616313

HgeneITGB1BP1

GO:0051895

negative regulation of focal adhesion assembly

12473654

HgeneITGB1BP1

GO:0051897

positive regulation of protein kinase B signaling

20616313

HgeneITGB1BP1

GO:0070373

negative regulation of ERK1 and ERK2 cascade

20616313

HgeneITGB1BP1

GO:0072659

protein localization to plasma membrane

17916086

HgeneITGB1BP1

GO:0090051

negative regulation of cell migration involved in sprouting angiogenesis

20616313

HgeneITGB1BP1

GO:0090315

negative regulation of protein targeting to membrane

11807099

HgeneITGB1BP1

GO:0097746

regulation of blood vessel diameter

20616313

HgeneITGB1BP1

GO:1900025

negative regulation of substrate adhesion-dependent cell spreading

11807099

TgeneCPSF3

GO:0006398

mRNA 3'-end processing by stem-loop binding and cleavage

18688255


check buttonFusion gene breakpoints across ITGB1BP1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CPSF3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4LUADTCGA-05-4397-01AITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
ChiTaRS5.0N/ADB012789ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+


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Fusion Gene ORF analysis for ITGB1BP1-CPSF3

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
5UTR-3CDSENST00000238091ENST00000238112ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-3CDSENST00000355346ENST00000238112ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-3CDSENST00000456913ENST00000238112ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-3CDSENST00000488451ENST00000238112ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-3CDSENST00000490426ENST00000238112ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-5UTRENST00000238091ENST00000238112ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-5UTRENST00000238091ENST00000460593ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-5UTRENST00000355346ENST00000238112ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-5UTRENST00000355346ENST00000460593ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-5UTRENST00000456913ENST00000238112ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-5UTRENST00000456913ENST00000460593ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-5UTRENST00000488451ENST00000238112ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-5UTRENST00000488451ENST00000460593ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-5UTRENST00000490426ENST00000238112ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-5UTRENST00000490426ENST00000460593ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-intronENST00000238091ENST00000460593ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000238091ENST00000489403ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000238091ENST00000489403ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-intronENST00000355346ENST00000460593ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000355346ENST00000489403ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000355346ENST00000489403ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-intronENST00000456913ENST00000460593ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000456913ENST00000489403ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000456913ENST00000489403ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-intronENST00000488451ENST00000460593ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000488451ENST00000489403ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000488451ENST00000489403ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
5UTR-intronENST00000490426ENST00000460593ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000490426ENST00000489403ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
5UTR-intronENST00000490426ENST00000489403ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
intron-3CDSENST00000359712ENST00000238112ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
intron-3CDSENST00000360635ENST00000238112ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
intron-5UTRENST00000359712ENST00000238112ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
intron-5UTRENST00000359712ENST00000460593ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
intron-5UTRENST00000360635ENST00000238112ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
intron-5UTRENST00000360635ENST00000460593ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
intron-intronENST00000359712ENST00000460593ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
intron-intronENST00000359712ENST00000489403ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
intron-intronENST00000359712ENST00000489403ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+
intron-intronENST00000360635ENST00000460593ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
intron-intronENST00000360635ENST00000489403ITGB1BP1chr2

9563501

-CPSF3chr2

9563850

+
intron-intronENST00000360635ENST00000489403ITGB1BP1chr2

9563502

-CPSF3chr2

9568892

+

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)

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

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Fusion Genomic Features for ITGB1BP1-CPSF3


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)
ITGB1BP1chr29563501-CPSF3chr29568893+4.14E-050.9999585
ITGB1BP1chr29563501-CPSF3chr29568893+4.14E-050.9999585

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.

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 ITGB1BP1-CPSF3


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/:9563501/:9563850)
- 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
ITGB1BP1

O14713

CPSF3

Q9UKF6

FUNCTION: Key regulator of the integrin-mediated cell-matrix interaction signaling by binding to the ITGB1 cytoplasmic tail and preventing the activation of integrin alpha-5/beta-1 (heterodimer of ITGA5 and ITGB1) by talin or FERMT1. Plays a role in cell proliferation, differentiation, spreading, adhesion and migration in the context of mineralization and bone development and angiogenesis. Stimulates cellular proliferation in a fibronectin-dependent manner. Involved in the regulation of beta-1 integrin-containing focal adhesion (FA) site dynamics by controlling its assembly rate during cell adhesion; inhibits beta-1 integrin clustering within FA by directly competing with talin TLN1, and hence stimulates osteoblast spreading and migration in a fibronectin- and/or collagen-dependent manner. Acts as a guanine nucleotide dissociation inhibitor (GDI) by regulating Rho family GTPases during integrin-mediated cell matrix adhesion; reduces the level of active GTP-bound form of both CDC42 and RAC1 GTPases upon cell adhesion to fibronectin. Stimulates the release of active CDC42 from the membranes to maintain it in an inactive cytoplasmic pool. Participates in the translocation of the Rho-associated protein kinase ROCK1 to membrane ruffles at cell leading edges of the cell membrane, leading to an increase of myoblast cell migration on laminin. Plays a role in bone mineralization at a late stage of osteoblast differentiation; modulates the dynamic formation of focal adhesions into fibrillar adhesions, which are adhesive structures responsible for fibronectin deposition and fibrillogenesis. Plays a role in blood vessel development; acts as a negative regulator of angiogenesis by attenuating endothelial cell proliferation and migration, lumen formation and sprouting angiogenesis by promoting AKT phosphorylation and inhibiting ERK1/2 phosphorylation through activation of the Notch signaling pathway. Promotes transcriptional activity of the MYC promoter. {ECO:0000269|PubMed:11741838, ECO:0000269|PubMed:11807099, ECO:0000269|PubMed:11919189, ECO:0000269|PubMed:12473654, ECO:0000269|PubMed:15703214, ECO:0000269|PubMed:17916086, ECO:0000269|PubMed:20616313, ECO:0000269|PubMed:21768292, ECO:0000269|Ref.19}.FUNCTION: Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Has endonuclease activity, and functions as mRNA 3'-end-processing endonuclease. Also involved in the histone 3'-end pre-mRNA processing. U7 snRNP-dependent protein that induces both the 3'-endoribonucleolytic cleavage of histone pre-mRNAs and acts as a 5' to 3' exonuclease for degrading the subsequent downstream cleavage product (DCP) of mature histone mRNAs. Cleavage occurs after the 5'-ACCCA-3' sequence in the histone pre-mRNA leaving a 3'hydroxyl group on the upstream fragment containing the stem loop (SL) and 5' phosphate on the downstream cleavage product (DCP) starting with CU nucleotides. The U7-dependent 5' to 3' exonuclease activity is processive and degrades the DCP RNA substrate even after complete removal of the U7-binding site. Binds to the downstream cleavage product (DCP) of histone pre-mRNAs and the cleaved DCP RNA substrate in a U7 snRNP dependent manner. Required for the selective processing of microRNAs (miRNAs) during embryonic stem cell differentiation via its interaction with ISY1 (By similarity). Required for the biogenesis of all miRNAs from the pri-miR-17-92 primary transcript except miR-92a (By similarity). Only required for the biogenesis of miR-290 and miR-96 from the pri-miR-290-295 and pri-miR-96-183 primary transcripts, respectively (By similarity). {ECO:0000250|UniProtKB:Q9QXK7, ECO:0000269|PubMed:14749727, ECO:0000269|PubMed:15037765, ECO:0000269|PubMed:17128255, ECO:0000269|PubMed:18688255}.

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 ITGB1BP1-CPSF3


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.

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Fusion Gene PPI Analysis for ITGB1BP1-CPSF3


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 ITGB1BP1-CPSF3


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 ITGB1BP1-CPSF3


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