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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:RCC1-ITGB3BP (FusionGDB2 ID:73207)

Fusion Gene Summary for RCC1-ITGB3BP

check button Fusion gene summary
Fusion gene informationFusion gene name: RCC1-ITGB3BP
Fusion gene ID: 73207
HgeneTgene
Gene symbol

RCC1

ITGB3BP

Gene ID

1104

23421

Gene nameregulator of chromosome condensation 1integrin subunit beta 3 binding protein
SynonymsCHC1|RCC1-I|SNHG3-RCC1CENP-R|CENPR|HSU37139|NRIF3|TAP20
Cytomap

1p35.3

1p31.3

Type of geneprotein-codingprotein-coding
Descriptionregulator of chromosome condensationSNHG3-RCC1 readthroughcell cycle regulatory proteinguanine nucleotide-releasing proteincentromere protein Rbeta 3 endonexinbeta3-endonexinintegrin beta 3 binding protein (beta3-endonexin)integrin beta-3-binding proteinnuclear receptor-interacting factor 3
Modification date2020031320200313
UniProtAcc

RCCD1

Q13352

Ensembl transtripts involved in fusion geneENST00000373833, ENST00000398958, 
ENST00000373831, ENST00000373832, 
ENST00000429051, 		ENST00000271002, 
ENST00000283568, ENST00000371092, 
ENST00000461681, 
Fusion gene scores* DoF score139 X 16 X 21=4670410 X 4 X 8=320
# samples 1369
** MAII scorelog2(136/46704*10)=-5.10186755936457
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: RCC1 [Title/Abstract] AND ITGB3BP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRCC1(28834672)-ITGB3BP(63920639), # samples:4
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
HgeneRCC1

GO:0007052

mitotic spindle organization

15014043

HgeneRCC1

GO:0007088

regulation of mitotic nuclear division

15014043


check buttonFusion gene breakpoints across RCC1 (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 ITGB3BP (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
ChimerDB4CESCTCGA-LP-A5U2-01ARCC1chr1

28834672

-ITGB3BPchr1

63920639

-
ChimerDB4CESCTCGA-LP-A5U2-01ARCC1chr1

28834672

+ITGB3BPchr1

63920639

-
ChimerDB4OVTCGA-24-0970RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
ChimerDB4OVTCGA-61-2095RCC1chr1

28834672

+ITGB3BPchr1

63920639

-


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Fusion Gene ORF analysis for RCC1-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
5UTR-3CDSENST00000373833ENST00000271002RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
5UTR-3CDSENST00000373833ENST00000283568RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
5UTR-3CDSENST00000373833ENST00000371092RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
5UTR-3CDSENST00000398958ENST00000271002RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
5UTR-3CDSENST00000398958ENST00000283568RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
5UTR-3CDSENST00000398958ENST00000371092RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
5UTR-5UTRENST00000373833ENST00000461681RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
5UTR-5UTRENST00000398958ENST00000461681RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000373831ENST00000271002RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000373831ENST00000283568RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000373831ENST00000371092RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000373832ENST00000271002RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000373832ENST00000283568RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000373832ENST00000371092RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000429051ENST00000271002RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000429051ENST00000283568RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-3CDSENST00000429051ENST00000371092RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-5UTRENST00000373831ENST00000461681RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-5UTRENST00000373832ENST00000461681RCC1chr1

28834672

+ITGB3BPchr1

63920639

-
intron-5UTRENST00000429051ENST00000461681RCC1chr1

28834672

+ITGB3BPchr1

63920639

-

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 RCC1-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.

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 RCC1-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/:28834672/:63920639)
- 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
RCC1

RCCD1

ITGB3BP

Q13352

376FUNCTION: 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

- 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 RCC1-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.

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Fusion Gene PPI Analysis for RCC1-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 RCC1-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 RCC1-ITGB3BP


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