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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:RFWD2-FBXO28

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RFWD2-FBXO28
	FusionPDB ID: 73670
	FusionGDB2.0 ID: 73670
		Hgene	Tgene
	Gene symbol	RFWD2	FBXO28
	Gene ID	64326	23219
	Gene name	COP1 E3 ubiquitin ligase	F-box protein 28
	Synonyms	CFAP78\|FAP78\|RFWD2\|RNF200	CENP-30\|Fbx28
	Cytomap	1q25.1-q25.2	1q42.11
	Type of gene	protein-coding	protein-coding
	Description	E3 ubiquitin-protein ligase COP1E3 ubiquitin-protein ligase RFWD2RING finger protein 200RING-type E3 ubiquitin transferase RFWD2constitutive photomorphogenesis protein 1 homologconstitutive photomorphogenic protein 1putative ubiquitin ligase COP1ri	F-box only protein 28centromere protein 30
	Modification date	20200313	20200313
	UniProtAcc	.	Q9NVF7
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000308769, ENST00000367669,	ENST00000366862, ENST00000424254,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	17 X 15 X 10=2550	2 X 4 X 2=16
	# samples	20	3
	** MAII score	log2(20/2550*10)=-3.6724253419715 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/16*10)=0.906890595608518 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: RFWD2 [Title/Abstract] AND FBXO28 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RFWD2(176118141)-FBXO28(224318173), # samples:1
Anticipated loss of major functional domain due to fusion event.	RFWD2-FBXO28 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. RFWD2-FBXO28 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. RFWD2-FBXO28 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. RFWD2-FBXO28 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RFWD2	GO:0010212	response to ionizing radiation	19805145

Fusion gene breakpoints across RFWD2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across FBXO28 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	UCEC	TCGA-PG-A5BC	RFWD2	chr1	176118141	-	FBXO28	chr1	224318173	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000367669	RFWD2	chr1	176118141	-	ENST00000366862	FBXO28	chr1	224318173	+	6487	1346	515	2185	556
ENST00000367669	RFWD2	chr1	176118141	-	ENST00000424254	FBXO28	chr1	224318173	+	2394	1346	515	1618	367
ENST00000308769	RFWD2	chr1	176118141	-	ENST00000366862	FBXO28	chr1	224318173	+	5960	819	0	1658	552
ENST00000308769	RFWD2	chr1	176118141	-	ENST00000424254	FBXO28	chr1	224318173	+	1867	819	0	1091	363

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000367669	ENST00000366862	RFWD2	chr1	176118141	-	FBXO28	chr1	224318173	+	0.000204907	0.99979514
ENST00000367669	ENST00000424254	RFWD2	chr1	176118141	-	FBXO28	chr1	224318173	+	0.003908418	0.99609154
ENST00000308769	ENST00000366862	RFWD2	chr1	176118141	-	FBXO28	chr1	224318173	+	0.000218582	0.9997814
ENST00000308769	ENST00000424254	RFWD2	chr1	176118141	-	FBXO28	chr1	224318173	+	0.003419001	0.996581

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>73670_73670_1_RFWD2-FBXO28_RFWD2_chr1_176118141_ENST00000308769_FBXO28_chr1_224318173_ENST00000366862_length(amino acids)=552AA_BP=273
MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAVSAAALVSGGVAQAAGSGGLGGPVRPVLVAPAVSGSGGGAVSTGLSRHS
CAARPSAGVGGSSSSLGSGSRKRPLLAPLCNGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNI
DHLYPNFLVNELILKQKQRFEEKRFKLDHSNGHRWQIFQDWLGTDQDNLDLANVNLMLELLVQKKKQLEAESHAAQLQILMEFLKVARRN
KREVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESERRNHSLARHADILAAVETRLSLLNMTFMKYVDSNLCCFIPGKVIDE
IYRVLRYVNSTRAPQRAHEVLQELRDISSMAMEYFDEKIVPILKRKLPGSDVSGRLMGSPPVPGPSAALTTMQLFSKQNPSRQEVTKLQQ
QVKTNGAGVTVLRREISELRTKVQEQQKQLQDQDQKLLEQTQIIGEQNARLAELERKLREVMESAVGNSSGSGQNEESPRKRKKATEAID

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

>73670_73670_2_RFWD2-FBXO28_RFWD2_chr1_176118141_ENST00000308769_FBXO28_chr1_224318173_ENST00000424254_length(amino acids)=363AA_BP=273
MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAVSAAALVSGGVAQAAGSGGLGGPVRPVLVAPAVSGSGGGAVSTGLSRHS
CAARPSAGVGGSSSSLGSGSRKRPLLAPLCNGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNI
DHLYPNFLVNELILKQKQRFEEKRFKLDHSNGHRWQIFQDWLGTDQDNLDLANVNLMLELLVQKKKQLEAESHAAQLQILMEFLKVARRN
KREVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESERRNHSLARHADILAAVETRLSLLNMTFMKYVDSNLCCFIPGKFQDR

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

>73670_73670_3_RFWD2-FBXO28_RFWD2_chr1_176118141_ENST00000367669_FBXO28_chr1_224318173_ENST00000366862_length(amino acids)=556AA_BP=277
MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAVSAAALVSGGVAQAAGSGGLGGPVRPVLVAPAVSGSGGGAVSTGLSRHS
CAARPSAGVGGSSSSLGSGSRKRPLLAPLCNGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNI
DHLYPNFLVNELILKQKQRFEEKRFKLDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNLMLELLVQKKKQLEAESHAAQLQILMEFLKV
ARRNKREVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESERRNHSLARHADILAAVETRLSLLNMTFMKYVDSNLCCFIPGK
VIDEIYRVLRYVNSTRAPQRAHEVLQELRDISSMAMEYFDEKIVPILKRKLPGSDVSGRLMGSPPVPGPSAALTTMQLFSKQNPSRQEVT
KLQQQVKTNGAGVTVLRREISELRTKVQEQQKQLQDQDQKLLEQTQIIGEQNARLAELERKLREVMESAVGNSSGSGQNEESPRKRKKAT

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

>73670_73670_4_RFWD2-FBXO28_RFWD2_chr1_176118141_ENST00000367669_FBXO28_chr1_224318173_ENST00000424254_length(amino acids)=367AA_BP=277
MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAVSAAALVSGGVAQAAGSGGLGGPVRPVLVAPAVSGSGGGAVSTGLSRHS
CAARPSAGVGGSSSSLGSGSRKRPLLAPLCNGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNI
DHLYPNFLVNELILKQKQRFEEKRFKLDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNLMLELLVQKKKQLEAESHAAQLQILMEFLKV
ARRNKREVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESERRNHSLARHADILAAVETRLSLLNMTFMKYVDSNLCCFIPGK

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:176118141/chr1:224318173)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	FBXO28 Q9NVF7
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.	FUNCTION: Probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. {ECO:0000250}.

Retention 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.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

2_110

273.0

708.0

Compositional bias

Note=Ser-rich

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

2_110

277.0

732.0

Compositional bias

Note=Ser-rich

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

109_113

273.0

708.0

Motif

Note=Nuclear localization signal 1

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

195_206

273.0

708.0

Motif

Note=Nuclear localization signal 2

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

235_245

273.0

708.0

Motif

Nuclear export signal

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

109_113

277.0

732.0

Motif

Note=Nuclear localization signal 1

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

195_206

277.0

732.0

Motif

Note=Nuclear localization signal 2

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

235_245

277.0

732.0

Motif

Nuclear export signal

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

136_174

273.0

708.0

Zinc finger

RING-type

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

136_174

277.0

732.0

Zinc finger

RING-type

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

233_301

273.0

708.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

233_301

277.0

732.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

419_458

273.0

708.0

Repeat

Note=WD 1

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

468_508

273.0

708.0

Repeat

Note=WD 2

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

511_551

273.0

708.0

Repeat

Note=WD 3

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

553_593

273.0

708.0

Repeat

Note=WD 4

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

597_635

273.0

708.0

Repeat

Note=WD 5

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

638_677

273.0

708.0

Repeat

Note=WD 6

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000308769

691_729

273.0

708.0

Repeat

Note=WD 7

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

419_458

277.0

732.0

Repeat

Note=WD 1

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

468_508

277.0

732.0

Repeat

Note=WD 2

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

511_551

277.0

732.0

Repeat

Note=WD 3

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

553_593

277.0

732.0

Repeat

Note=WD 4

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

597_635

277.0

732.0

Repeat

Note=WD 5

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

638_677

277.0

732.0

Repeat

Note=WD 6

Hgene

RFWD2

chr1:176118141

chr1:224318173

ENST00000367669

691_729

277.0

732.0

Repeat

Note=WD 7

Tgene

FBXO28

chr1:176118141

chr1:224318173

ENST00000366862

61_109

89.0

369.0

Domain

F-box

Tgene

FBXO28

chr1:176118141

chr1:224318173

ENST00000424254

61_109

89.0

180.0

Domain

F-box

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
RFWD2
FBXO28

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Hgene	RFWD2	chr1:176118141	chr1:224318173	ENST00000308769	-	6	19	643_645	273.0	708.0	TRIB1
Hgene	RFWD2	chr1:176118141	chr1:224318173	ENST00000367669	-	6	20	643_645	277.0	732.0	TRIB1

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Related Drugs to RFWD2-FBXO28

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to RFWD2-FBXO28

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source