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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:NMD3-USP40

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NMD3-USP40
	FusionPDB ID: 59403
	FusionGDB2.0 ID: 59403
		Hgene	Tgene
	Gene symbol	NMD3	USP40
	Gene ID	51068	55230
	Gene name	NMD3 ribosome export adaptor	ubiquitin specific peptidase 40
	Synonyms	CGI-07	-
	Cytomap	3q26.1	2q37.1
	Type of gene	protein-coding	protein-coding
	Description	60S ribosomal export protein NMD3NMD3 homologhNMD3	ubiquitin carboxyl-terminal hydrolase 40deubiquitinating enzyme 40ubiquitin specific protease 40ubiquitin thioesterase 40ubiquitin thiolesterase 40ubiquitin-specific-processing protease 40
	Modification date	20200313	20200313
	UniProtAcc	Q96D46	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000478160, ENST00000351193, ENST00000460469, ENST00000472947,	ENST00000251722, ENST00000427112, ENST00000450966, ENST00000409945, ENST00000443711, ENST00000496298,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 9 X 5=405	9 X 9 X 4=324
	# samples	9	9
	** MAII score	log2(9/405*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/324*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: NMD3 [Title/Abstract] AND USP40 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NMD3(160953000)-USP40(234407258), # samples:5
Anticipated loss of major functional domain due to fusion event.	NMD3-USP40 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. NMD3-USP40 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

Fusion gene breakpoints across NMD3 (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 USP40 (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	LIHC	TCGA-ZS-A9CF-01A	NMD3	chr3	160953000	-	USP40	chr2	234407258	-
ChimerDB4	LIHC	TCGA-ZS-A9CF-01A	NMD3	chr3	160953000	+	USP40	chr2	234407258	-
ChimerDB4	LIHC	TCGA-ZS-A9CF-02A	NMD3	chr3	160953000	-	USP40	chr2	234407258	-
ChimerDB4	LIHC	TCGA-ZS-A9CF-02A	NMD3	chr3	160953000	+	USP40	chr2	234407258	-

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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)
ENST00000351193	NMD3	chr3	160953000	+	ENST00000450966	USP40	chr2	234407258	-	3650	717	23	1777	584
ENST00000351193	NMD3	chr3	160953000	+	ENST00000251722	USP40	chr2	234407258	-	3644	717	23	1777	584
ENST00000351193	NMD3	chr3	160953000	+	ENST00000427112	USP40	chr2	234407258	-	1778	717	23	1777	585
ENST00000472947	NMD3	chr3	160953000	+	ENST00000450966	USP40	chr2	234407258	-	3632	699	5	1759	584
ENST00000472947	NMD3	chr3	160953000	+	ENST00000251722	USP40	chr2	234407258	-	3626	699	5	1759	584
ENST00000472947	NMD3	chr3	160953000	+	ENST00000427112	USP40	chr2	234407258	-	1760	699	5	1759	585
ENST00000460469	NMD3	chr3	160953000	+	ENST00000450966	USP40	chr2	234407258	-	3965	1032	455	2092	545
ENST00000460469	NMD3	chr3	160953000	+	ENST00000251722	USP40	chr2	234407258	-	3959	1032	455	2092	545
ENST00000460469	NMD3	chr3	160953000	+	ENST00000427112	USP40	chr2	234407258	-	2093	1032	455	2092	546

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
ENST00000351193	ENST00000450966	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.012558727	0.9874413
ENST00000351193	ENST00000251722	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.012328289	0.98767173
ENST00000351193	ENST00000427112	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.011006687	0.98899335
ENST00000472947	ENST00000450966	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.012194196	0.98780584
ENST00000472947	ENST00000251722	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.011973102	0.98802686
ENST00000472947	ENST00000427112	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.01054416	0.9894559
ENST00000460469	ENST00000450966	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.008196011	0.991804
ENST00000460469	ENST00000251722	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.008105212	0.9918948
ENST00000460469	ENST00000427112	NMD3	chr3	160953000	+	USP40	chr2	234407258	-	0.005961391	0.9940386

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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

>59403_59403_1_NMD3-USP40_NMD3_chr3_160953000_ENST00000351193_USP40_chr2_234407258_ENST00000251722_length(amino acids)=584AA_BP=231
MWRRQPGWQLTGQPGSILLRVFSKSRAGLEARKLKAYRTMEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVS
ISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPLSKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMC
GDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLL
IEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSSWGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFL
EFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGS
LRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQITKRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQ

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

>59403_59403_2_NMD3-USP40_NMD3_chr3_160953000_ENST00000351193_USP40_chr2_234407258_ENST00000427112_length(amino acids)=585AA_BP=231
MWRRQPGWQLTGQPGSILLRVFSKSRAGLEARKLKAYRTMEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVS
ISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPLSKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMC
GDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLL
IEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSSWGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFL
EFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGS
LRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQITKRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQ

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

>59403_59403_3_NMD3-USP40_NMD3_chr3_160953000_ENST00000351193_USP40_chr2_234407258_ENST00000450966_length(amino acids)=584AA_BP=231
MWRRQPGWQLTGQPGSILLRVFSKSRAGLEARKLKAYRTMEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVS
ISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPLSKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMC
GDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLL
IEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSSWGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFL
EFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGS
LRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQITKRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQ

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

>59403_59403_4_NMD3-USP40_NMD3_chr3_160953000_ENST00000460469_USP40_chr2_234407258_ENST00000251722_length(amino acids)=545AA_BP=192
MEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVSISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPL
SKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMCGDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYG
MHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLLIEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSS
WGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFLEFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRR
IEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGSLRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQIT
KRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQRALGRRKSQEALHEQSSYILSSAETPARPRAPETSLSIH

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

>59403_59403_5_NMD3-USP40_NMD3_chr3_160953000_ENST00000460469_USP40_chr2_234407258_ENST00000427112_length(amino acids)=546AA_BP=192
MEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVSISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPL
SKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMCGDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYG
MHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLLIEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSS
WGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFLEFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRR
IEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGSLRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQIT
KRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQRALGRRKSQEALHEQSSYILSSAETPARPRAPETSLSIH

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

>59403_59403_6_NMD3-USP40_NMD3_chr3_160953000_ENST00000460469_USP40_chr2_234407258_ENST00000450966_length(amino acids)=545AA_BP=192
MEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVSISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPL
SKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMCGDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYG
MHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLLIEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSS
WGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFLEFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRR
IEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGSLRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQIT
KRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQRALGRRKSQEALHEQSSYILSSAETPARPRAPETSLSIH

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

>59403_59403_7_NMD3-USP40_NMD3_chr3_160953000_ENST00000472947_USP40_chr2_234407258_ENST00000251722_length(amino acids)=584AA_BP=231
MWRRQPGWQLTGQPGSILLRVFSKSRAGLEARKLKAYRTMEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVS
ISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPLSKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMC
GDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLL
IEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSSWGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFL
EFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGS
LRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQITKRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQ

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

>59403_59403_8_NMD3-USP40_NMD3_chr3_160953000_ENST00000472947_USP40_chr2_234407258_ENST00000427112_length(amino acids)=585AA_BP=231
MWRRQPGWQLTGQPGSILLRVFSKSRAGLEARKLKAYRTMEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVS
ISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPLSKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMC
GDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLL
IEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSSWGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFL
EFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGS
LRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQITKRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQ

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

>59403_59403_9_NMD3-USP40_NMD3_chr3_160953000_ENST00000472947_USP40_chr2_234407258_ENST00000450966_length(amino acids)=584AA_BP=231
MWRRQPGWQLTGQPGSILLRVFSKSRAGLEARKLKAYRTMEYMAESTDRSPGHILCCECGVPISPNPANICVACLRSKVDISQGIPKQVS
ISFCKQCQRYFQPPGTWIQCALESRELLALCLKKIKAPLSKVRLVDAGFVWTEPHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMC
GDCHRVEAKDFWKAVIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHGDAWHLRKMDWCYEAGEPLCEEDATLKELLICSGDTLLL
IEGQLPPLGFLKVPIWWYQLQGPSGHWESHQDQTNCTSSWGRVWRATSSQGASGNEPAQVSLLYLGDIEISEDATLAELKSQAMTLPPFL
EFGVPSPAHLRAWTVERKRPGRLLRTDRQPLREYKLGRRIEICLEPLQKGENLGPQDVLLRTQVRIPGERTYAPALDLVWNAAQGGTAGS
LRQRVADFYRLPVEKIEIAKYFPEKFEWLPISSWNQQITKRKKKKKQDYLQGAPYYLKDGDTIGVKNLLIDDDDDFSTIRDDTGKEKQKQ

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

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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/chr3:160953000/chr2:234407258)
- 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
NMD3 Q96D46	.
FUNCTION: Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit. {ECO:0000269\|PubMed:12724356, ECO:0000269\|PubMed:12773398}.	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

- 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

NMD3

chr3:160953000

chr2:234407258

ENST00000351193

405_422

192.33333333333334

504.0

Motif

Note=Nuclear and nucleolar localization signal

Hgene

NMD3

chr3:160953000

chr2:234407258

ENST00000351193

480_489

192.33333333333334

504.0

Motif

Note=Nuclear export signal

Hgene

NMD3

chr3:160953000

chr2:234407258

ENST00000460469

405_422

192.33333333333334

504.0

Motif

Note=Nuclear and nucleolar localization signal

Hgene

NMD3

chr3:160953000

chr2:234407258

ENST00000460469

480_489

192.33333333333334

504.0

Motif

Note=Nuclear export signal

Hgene

NMD3

chr3:160953000

chr2:234407258

ENST00000351193

425_503

192.33333333333334

504.0

Region

Note=Necessary for the nuclear export of the 60S ribosomal subunit

Hgene

NMD3

chr3:160953000

chr2:234407258

ENST00000460469

425_503

192.33333333333334

504.0

Region

Note=Necessary for the nuclear export of the 60S ribosomal subunit

Tgene

USP40

chr3:160953000

chr2:234407258

ENST00000251722

41_482

882.3333333333334

1236.0

Domain

Note=USP

Tgene

USP40

chr3:160953000

chr2:234407258

ENST00000409945

41_482

58.333333333333336

164.0

Domain

Note=USP

Tgene

USP40

chr3:160953000

chr2:234407258

ENST00000427112

41_482

882.3333333333334

1236.0

Domain

Note=USP

Tgene

USP40

chr3:160953000

chr2:234407258

ENST00000450966

41_482

894.3333333333334

1248.0

Domain

Note=USP

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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)

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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.

NMD3_pLDDT.png

USP40_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
NMD3
USP40

- 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 NMD3-USP40

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 NMD3-USP40

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