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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:CYFIP1-UBR4 (FusionGDB2 ID:20973)

Fusion Gene Summary for CYFIP1-UBR4

check button Fusion gene summary
Fusion gene informationFusion gene name: CYFIP1-UBR4
Fusion gene ID: 20973
HgeneTgene
Gene symbol

CYFIP1

UBR4

Gene ID

23191

23352

Gene namecytoplasmic FMR1 interacting protein 1ubiquitin protein ligase E3 component n-recognin 4
SynonymsP140SRA-1|SHYC|SRA-1|SRA1RBAF600|ZUBR1|p600
Cytomap

15q11.2

1p36.13

Type of geneprotein-codingprotein-coding
Descriptioncytoplasmic FMR1-interacting protein 1cytoplasmic FMRP interacting protein 1selective hybridizing clonespecifically Rac1-associated protein 1E3 ubiquitin-protein ligase UBR4N-recognin-4RING-type E3 ubiquitin transferase UBR4retinoblastoma-associated factor 600-like proteinretinoblastoma-associated factor of 600 kDazinc finger UBR1-type protein 1
Modification date2020031320200313
UniProtAcc

Q7L576

.
Ensembl transtripts involved in fusion geneENST00000313077, ENST00000560848, 
ENST00000435939, 		ENST00000375217, 
ENST00000375226, ENST00000375267, 
ENST00000375254, ENST00000375225, 
ENST00000429347, ENST00000375224, 
ENST00000543981, ENST00000467272, 
ENST00000375218, 
Fusion gene scores* DoF score7 X 9 X 4=25214 X 16 X 7=1568
# samples 616
** MAII scorelog2(6/252*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1568*10)=-3.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CYFIP1 [Title/Abstract] AND UBR4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCYFIP1(22929835)-UBR4(19423732), # samples:1
Anticipated loss of major functional domain due to fusion event.CYFIP1-UBR4 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CYFIP1-UBR4 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
TgeneUBR4

GO:0006511

ubiquitin-dependent protein catabolic process

23932781


check buttonFusion gene breakpoints across CYFIP1 (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 UBR4 (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
ChiTaRS5.0N/ABF748810CYFIP1chr15

22929835

+UBR4chr1

19423732

+


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Fusion Gene ORF analysis for CYFIP1-UBR4

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
Frame-shiftENST00000313077ENST00000375217CYFIP1chr15

22929835

+UBR4chr1

19423732

+
Frame-shiftENST00000313077ENST00000375226CYFIP1chr15

22929835

+UBR4chr1

19423732

+
Frame-shiftENST00000313077ENST00000375267CYFIP1chr15

22929835

+UBR4chr1

19423732

+
Frame-shiftENST00000313077ENST00000375254CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000313077ENST00000375225CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000313077ENST00000429347CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000313077ENST00000375224CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000313077ENST00000543981CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-5UTRENST00000313077ENST00000467272CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000313077ENST00000375218CYFIP1chr15

22929835

+UBR4chr1

19423732

+
Frame-shiftENST00000560848ENST00000375217CYFIP1chr15

22929835

+UBR4chr1

19423732

+
Frame-shiftENST00000560848ENST00000375226CYFIP1chr15

22929835

+UBR4chr1

19423732

+
Frame-shiftENST00000560848ENST00000375267CYFIP1chr15

22929835

+UBR4chr1

19423732

+
Frame-shiftENST00000560848ENST00000375254CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000560848ENST00000375225CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000560848ENST00000429347CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000560848ENST00000375224CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000560848ENST00000543981CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-5UTRENST00000560848ENST00000467272CYFIP1chr15

22929835

+UBR4chr1

19423732

+
5CDS-intronENST00000560848ENST00000375218CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-3CDSENST00000435939ENST00000375217CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-3CDSENST00000435939ENST00000375226CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-3CDSENST00000435939ENST00000375267CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-3CDSENST00000435939ENST00000375254CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-intronENST00000435939ENST00000375225CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-intronENST00000435939ENST00000429347CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-intronENST00000435939ENST00000375224CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-intronENST00000435939ENST00000543981CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-5UTRENST00000435939ENST00000467272CYFIP1chr15

22929835

+UBR4chr1

19423732

+
intron-intronENST00000435939ENST00000375218CYFIP1chr15

22929835

+UBR4chr1

19423732

+

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 CYFIP1-UBR4


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 CYFIP1-UBR4


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CYFIP1

Q7L576

.
FUNCTION: Component of the CYFIP1-EIF4E-FMR1 complex which binds to the mRNA cap and mediates translational repression. In the CYFIP1-EIF4E-FMR1 complex this subunit is an adapter between EIF4E and FMR1. Promotes the translation repression activity of FMR1 in brain probably by mediating its association with EIF4E and mRNA (By similarity). Regulates formation of membrane ruffles and lamellipodia. Plays a role in axon outgrowth. Binds to F-actin but not to RNA. Part of the WAVE complex that regulates actin filament reorganization via its interaction with the Arp2/3 complex. Actin remodeling activity is regulated by RAC1. Regulator of epithelial morphogenesis. As component of the WAVE1 complex, required for BDNF-NTRK2 endocytic trafficking and signaling from early endosomes (By similarity). May act as an invasion suppressor in cancers. {ECO:0000250|UniProtKB:Q7TMB8, ECO:0000269|PubMed:16260607, ECO:0000269|PubMed:19524508, ECO:0000269|PubMed:21107423, ECO:0000269|PubMed:9417078}.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.

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 CYFIP1-UBR4


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 CYFIP1-UBR4


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 CYFIP1-UBR4


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 CYFIP1-UBR4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCYFIP1C0036341Schizophrenia1PSYGENET
TgeneUBR4C1720189Episodic Ataxia1GENOMICS_ENGLAND
TgeneUBR4C4015108Episodic ataxia with slurred speech1GENOMICS_ENGLAND