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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:USP47-RRAS2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: USP47-RRAS2
	FusionPDB ID: 97509
	FusionGDB2.0 ID: 97509
		Hgene	Tgene
	Gene symbol	USP47	RRAS2
	Gene ID	55031	22800
	Gene name	ubiquitin specific peptidase 47	RAS related 2
	Synonyms	TRFP	NS12\|TC21
	Cytomap	11p15.3	11p15.2
	Type of gene	protein-coding	protein-coding
	Description	ubiquitin carboxyl-terminal hydrolase 47Trf (TATA binding protein-related factor)-proximal homologdeubiquitinating enzyme 47ubiquitin thioesterase 47ubiquitin thiolesterase 47ubiquitin-specific-processing protease 47	ras-related protein R-Ras2ras-like protein TC21related RAS viral (r-ras) oncogene homolog 2teratocarcinoma oncogene
	Modification date	20200313	20200315
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000339865, ENST00000399455, ENST00000527733, ENST00000539466, ENST00000305481,	ENST00000256196, ENST00000526063, ENST00000529237, ENST00000532814, ENST00000534746, ENST00000414023, ENST00000537760, ENST00000545643,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 6 X 5=270	5 X 2 X 5=50
	# samples	9	5
	** MAII score	log2(9/270*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/50*10)=0
Context (manual curation of fusion genes in FusionPDB)	PubMed: USP47 [Title/Abstract] AND RRAS2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	USP47(11863771)-RRAS2(14317401), # samples:4
Anticipated loss of major functional domain due to fusion event.	USP47-RRAS2 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. USP47-RRAS2 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. USP47-RRAS2 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. USP47-RRAS2 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	USP47	GO:0035520	monoubiquitinated protein deubiquitination	21362556

Fusion gene breakpoints across USP47 (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 RRAS2 (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	SKCM	TCGA-EB-A82C-01A	USP47	chr11	11863771	-	RRAS2	chr11	14317401	-
ChimerDB4	SKCM	TCGA-EB-A82C-01A	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-
ChimerDB4	SKCM	TCGA-EB-A82C	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-

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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)
ENST00000339865	USP47	chr11	11863771	+	ENST00000545643	RRAS2	chr11	14317401	-	2720	802	842	417	141
ENST00000339865	USP47	chr11	11863771	+	ENST00000537760	RRAS2	chr11	14317401	-	2720	802	763	1308	181
ENST00000339865	USP47	chr11	11863771	+	ENST00000414023	RRAS2	chr11	14317401	-	2686	802	674	1312	212
ENST00000527733	USP47	chr11	11863771	+	ENST00000545643	RRAS2	chr11	14317401	-	2168	250	2133	1903	76
ENST00000527733	USP47	chr11	11863771	+	ENST00000537760	RRAS2	chr11	14317401	-	2168	250	211	756	181
ENST00000527733	USP47	chr11	11863771	+	ENST00000414023	RRAS2	chr11	14317401	-	2134	250	122	760	212
ENST00000399455	USP47	chr11	11863771	+	ENST00000545643	RRAS2	chr11	14317401	-	2077	159	2042	1812	76
ENST00000399455	USP47	chr11	11863771	+	ENST00000537760	RRAS2	chr11	14317401	-	2077	159	120	665	181
ENST00000399455	USP47	chr11	11863771	+	ENST00000414023	RRAS2	chr11	14317401	-	2043	159	31	669	212

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
ENST00000339865	ENST00000545643	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.9207496	0.07925042
ENST00000339865	ENST00000537760	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.000604699	0.99939525
ENST00000339865	ENST00000414023	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.009779502	0.9902204
ENST00000527733	ENST00000545643	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.056678437	0.9433216
ENST00000527733	ENST00000537760	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.000466121	0.9995339
ENST00000527733	ENST00000414023	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.003850453	0.99614954
ENST00000399455	ENST00000545643	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.12625825	0.8737418
ENST00000399455	ENST00000537760	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.000330296	0.9996697
ENST00000399455	ENST00000414023	USP47	chr11	11863771	+	RRAS2	chr11	14317401	-	0.005425469	0.9945746

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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

>97509_97509_1_USP47-RRAS2_USP47_chr11_11863771_ENST00000339865_RRAS2_chr11_14317401_ENST00000414023_length(amino acids)=212AA_BP=43
MPLPFSLELASRRHPPPSPGRAERSGRSQRWCPARRTNWSRKRQSYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQY
MRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELV

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

>97509_97509_2_USP47-RRAS2_USP47_chr11_11863771_ENST00000339865_RRAS2_chr11_14317401_ENST00000537760_length(amino acids)=181AA_BP=13
MVPGEENQLVPKESYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILR
VKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVIRKFQEQECPPSPEPTRKEKDKKGCHCVI

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

>97509_97509_3_USP47-RRAS2_USP47_chr11_11863771_ENST00000339865_RRAS2_chr11_14317401_ENST00000545643_length(amino acids)=141AA_BP=
MVLVKEDIPALEISSFGTSWFSSPGTIADSGRSSPPCRGRVEGGGGSLAQERMAAAVILSAACAPAIAEASAWASDTSAQTPTQGSAAAA

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

>97509_97509_4_USP47-RRAS2_USP47_chr11_11863771_ENST00000399455_RRAS2_chr11_14317401_ENST00000414023_length(amino acids)=212AA_BP=43
MPLPFSLELASRRHPPPSPGRAERSGRSQRWCPARRTNWSRKRQSYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQY
MRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELV

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

>97509_97509_5_USP47-RRAS2_USP47_chr11_11863771_ENST00000399455_RRAS2_chr11_14317401_ENST00000537760_length(amino acids)=181AA_BP=13
MVPGEENQLVPKESYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILR
VKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVIRKFQEQECPPSPEPTRKEKDKKGCHCVI

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

>97509_97509_6_USP47-RRAS2_USP47_chr11_11863771_ENST00000399455_RRAS2_chr11_14317401_ENST00000545643_length(amino acids)=76AA_BP=1

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

>97509_97509_7_USP47-RRAS2_USP47_chr11_11863771_ENST00000527733_RRAS2_chr11_14317401_ENST00000414023_length(amino acids)=212AA_BP=43
MPLPFSLELASRRHPPPSPGRAERSGRSQRWCPARRTNWSRKRQSYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQY
MRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELV

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

>97509_97509_8_USP47-RRAS2_USP47_chr11_11863771_ENST00000527733_RRAS2_chr11_14317401_ENST00000537760_length(amino acids)=181AA_BP=13
MVPGEENQLVPKESYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILR
VKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVIRKFQEQECPPSPEPTRKEKDKKGCHCVI

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

>97509_97509_9_USP47-RRAS2_USP47_chr11_11863771_ENST00000527733_RRAS2_chr11_14317401_ENST00000545643_length(amino acids)=76AA_BP=1

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

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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/chr11:11863771/chr11:14317401)
- 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
.	.
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: 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.

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

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000256196

43_51

36.0

205.0

Motif

Note=Effector region

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000414023

-1

43_51

128.0

Motif

Note=Effector region

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000526063

43_51

128.0

Motif

Note=Effector region

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000529237

43_51

128.0

Motif

Note=Effector region

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000532814

43_51

128.0

Motif

Note=Effector region

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000534746

43_51

128.0

Motif

Note=Effector region

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000537760

43_51

1.0

170.0

Motif

Note=Effector region

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000256196

127_130

36.0

205.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000256196

157_159

36.0

205.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000256196

68_72

36.0

205.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000414023

-1

127_130

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000414023

-1

157_159

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000414023

-1

21_29

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000414023

-1

68_72

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000526063

127_130

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000526063

157_159

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000526063

21_29

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000526063

68_72

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000529237

127_130

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000529237

157_159

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000529237

21_29

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000529237

68_72

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000532814

127_130

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000532814

157_159

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000532814

21_29

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000532814

68_72

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000534746

127_130

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000534746

157_159

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000534746

21_29

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000534746

68_72

128.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000537760

127_130

1.0

170.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000537760

157_159

1.0

170.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000537760

21_29

1.0

170.0

Nucleotide binding

GTP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000537760

68_72

1.0

170.0

Nucleotide binding

GTP

- 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

USP47

chr11:11863771

chr11:14317401

ENST00000339865

188_564

13.0

1288.0

Domain

Note=USP

Hgene

USP47

chr11:11863771

chr11:14317401

ENST00000399455

188_564

13.0

1376.0

Domain

Note=USP

Hgene

USP47

chr11:11863771

chr11:14317401

ENST00000539466

188_564

158.0

Domain

Note=USP

Tgene

RRAS2

chr11:11863771

chr11:14317401

ENST00000256196

21_29

36.0

205.0

Nucleotide binding

GTP

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>308_USP47_11863771_RRAS2_14317401_ranked_0.pdb	USP47	11863771	11863771	ENST00000414023	RRAS2	chr11	14317401	-	MPLPFSLELASRRHPPPSPGRAERSGRSQRWCPARRTNWSRKRQSYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQY MRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELV	212

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

USP47_pLDDT.png

RRAS2_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
USP47
RRAS2

- 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

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Related Drugs to USP47-RRAS2

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 USP47-RRAS2

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