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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:SNRNP40-EPB41

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SNRNP40-EPB41
	FusionPDB ID: 84727
	FusionGDB2.0 ID: 84727
		Hgene	Tgene
	Gene symbol	SNRNP40	EPB41
	Gene ID	9410	2035
	Gene name	small nuclear ribonucleoprotein U5 subunit 40	erythrocyte membrane protein band 4.1
	Synonyms	40K\|HPRP8BP\|PRP8BP\|PRPF8BP\|SPF38\|WDR57	4.1R\|EL1\|HE
	Cytomap	1p35.2	1p35.3
	Type of gene	protein-coding	protein-coding
	Description	U5 small nuclear ribonucleoprotein 40 kDa protein38 kDa-splicing factorPrp8-binding proteinU5 snRNP 40 kDa proteinU5 snRNP-specific 40 kDa protein (hPrp8-binding)U5-40KU5-40kD proteinWD repeat domain 57 (U5 snRNP specific)WD repeat-containing prot	protein 4.1EPB4.1P4.1band 4.1elliptocytosis 1, RH-linkederythrocyte surface protein band 4.1
	Modification date	20200313	20200320
	UniProtAcc	.	Q9HCM4
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000263694, ENST00000446633, ENST00000373720, ENST00000489853,	ENST00000460378, ENST00000343067, ENST00000347529, ENST00000349460, ENST00000356093, ENST00000373797, ENST00000373798, ENST00000373800, ENST00000398863,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 6 X 6=252	13 X 13 X 6=1014
	# samples	7	15
	** MAII score	log2(7/252*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/1014*10)=-2.75702324650746 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SNRNP40 [Title/Abstract] AND EPB41 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SNRNP40(31762101)-EPB41(29365766), # samples:2
Anticipated loss of major functional domain due to fusion event.	SNRNP40-EPB41 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. SNRNP40-EPB41 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. SNRNP40-EPB41 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. SNRNP40-EPB41 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. SNRNP40-EPB41 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. SNRNP40-EPB41 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. SNRNP40-EPB41 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. SNRNP40-EPB41 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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)

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
Tgene	EPB41	GO:0032092	positive regulation of protein binding	3693401

Fusion gene breakpoints across SNRNP40 (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 EPB41 (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	HNSC	TCGA-DQ-7591-01A	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+

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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)
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000356093	EPB41	chr1	29365766	+	4836	595	560	1627	355
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000398863	EPB41	chr1	29365766	+	4644	595	560	1435	291
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000343067	EPB41	chr1	29365766	+	4935	595	560	1726	388
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000349460	EPB41	chr1	29365766	+	1987	595	560	1684	374
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000373800	EPB41	chr1	29365766	+	1828	595	560	1525	321
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000347529	EPB41	chr1	29365766	+	1867	595	560	1564	334
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000373798	EPB41	chr1	29365766	+	4956	595	560	1726	388
ENST00000446633	SNRNP40	chr1	31762101	-	ENST00000373797	EPB41	chr1	29365766	+	1337	595	560	1294	244

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
ENST00000446633	ENST00000356093	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.001918024	0.99808204
ENST00000446633	ENST00000398863	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.002488649	0.9975114
ENST00000446633	ENST00000343067	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.001182365	0.9988176
ENST00000446633	ENST00000349460	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.002288303	0.99771166
ENST00000446633	ENST00000373800	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.002420466	0.9975795
ENST00000446633	ENST00000347529	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.002580418	0.9974196
ENST00000446633	ENST00000373798	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.00112889	0.998871
ENST00000446633	ENST00000373797	SNRNP40	chr1	31762101	-	EPB41	chr1	29365766	+	0.002005576	0.9979944

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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

>84727_84727_1_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000343067_length(amino acids)=388AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKVEKTHIEVTVPTSNGDQTQKLAEKTEDLIRMRKKKRERLDG
ENIYIRHSNLMLEDLDKSQEEIKKHHASISELKKNFMESVPEPRPSEWDKRLSTHSPFRTLNINGQIPTGEGPPLVKTQTVTISDNANAV
KSEIPTKDVPIVHTETKTITYEAAQTDDNSGDLDPGVLLTAQTITSETPSSTTTTQITKTVKGGISETRIEKRIVITGDADIDHDQVLVQ

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

>84727_84727_2_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000347529_length(amino acids)=334AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKDLDKSQEEIKKHHASISELKKNFMESVPEPRPSEWDKRLST
HSPFRTLNINGQIPTGEGPPLVKTQTVTISDNANAVKSEIPTKDVPIVHTETKTITYEAAQTDDNSGDLDPGVLLTAQTITSETPSSTTT

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

>84727_84727_3_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000349460_length(amino acids)=374AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKVEKTHIEVTVPTSNGDQTQKKRERLDGENIYIRHSNLMLED
LDKSQEEIKKHHASISELKKNFMESVPEPRPSEWDKRLSTHSPFRTLNINGQIPTGEGPPLVKTQTVTISDNANAVKSEIPTKDVPIVHT
ETKTITYEAAQTDDNSGDLDPGVLLTAQTITSETPSSTTTTQITKTVKGGISETRIEKRIVITGDADIDHDQVLVQAIKEAKEQHPDMSV

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

>84727_84727_4_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000356093_length(amino acids)=355AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKKKRERLDGENIYIRHSNLMLEDLDKSQEEIKKHHASISELK
KNFMESVPEPRPSEWDKRLSTHSPFRTLNINGQIPTGEGPPLVKTQTVTISDNANAVKSEIPTKDVPIVHTETKTITYEAAQTDDNSGDL

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

>84727_84727_5_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000373797_length(amino acids)=244AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKVEKTHIEVTVPTSNGDQTQKKRERLDGENIYIRHSNLMLED

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

>84727_84727_6_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000373798_length(amino acids)=388AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKVEKTHIEVTVPTSNGDQTQKLAEKTEDLIRMRKKKRERLDG
ENIYIRHSNLMLEDLDKSQEEIKKHHASISELKKNFMESVPEPRPSEWDKRLSTHSPFRTLNINGQIPTGEGPPLVKTQTVTISDNANAV
KSEIPTKDVPIVHTETKTITYEAAQTDDNSGDLDPGVLLTAQTITSETPSSTTTTQITKTVKGGISETRIEKRIVITGDADIDHDQVLVQ

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

>84727_84727_7_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000373800_length(amino acids)=321AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKKKRERLDGENIYIRHSNLMLEDLDKSQEEIKKHHASISELK
KNFMESVPEPRPSEWDKRLSTHSPFRTLNINGQIPTGEGPPLVKTQTVTISDNANAVKSEIPTKDVPIVHTETKTITYEAAQTVKGGISE

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

>84727_84727_8_SNRNP40-EPB41_SNRNP40_chr1_31762101_ENST00000446633_EPB41_chr1_29365766_ENST00000398863_length(amino acids)=291AA_BP=11
MSALAVTMAQLRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVDSADRSPRPTSAPAITQ
GQVAEGGVLDASAKKTVVPKAQKETVKAEVKKEDEPPEQAEPEPTEAWKDLDKSQEEIKKHHASISELKKNFMESVPEPRPSEWDKRLST
HSPFRTLNINGQIPTGEGTDDNSGDLDPGVLLTAQTITSETPSSTTTTQITKTVKGGISETRIEKRIVITGDADIDHDQVLVQAIKEAKE

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

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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/chr1:31762101/chr1:29365766)
- 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
.	EPB41 Q9HCM4
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: Plays a role in the formation and organization of tight junctions during the establishment of polarity in epithelial cells. {ECO:0000269\|PubMed:17920587}.

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

SNRNP40

chr1:31762101

chr1:29365766

ENST00000263694

107_146

177.0

358.0

Repeat

Note=WD 2

Hgene

SNRNP40

chr1:31762101

chr1:29365766

ENST00000263694

64_103

177.0

358.0

Repeat

Note=WD 1

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000343067

494_614

487.6666666666667

1892.3333333333333

Region

Note=Hydrophilic

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000343067

615_713

487.6666666666667

1892.3333333333333

Region

Note=Spectrin--actin-binding

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000343067

714_864

487.6666666666667

1892.3333333333333

Region

Note=C-terminal (CTD)

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000347529

494_614

452.6666666666667

861.6666666666666

Region

Note=Hydrophilic

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000347529

615_713

452.6666666666667

861.6666666666666

Region

Note=Spectrin--actin-binding

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000347529

714_864

452.6666666666667

861.6666666666666

Region

Note=C-terminal (CTD)

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000349460

494_614

278.6666666666667

711.6666666666666

Region

Note=Hydrophilic

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000349460

615_713

278.6666666666667

711.6666666666666

Region

Note=Spectrin--actin-binding

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000349460

714_864

278.6666666666667

711.6666666666666

Region

Note=C-terminal (CTD)

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000356093

494_614

487.6666666666667

1859.3333333333333

Region

Note=Hydrophilic

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000356093

615_713

487.6666666666667

1859.3333333333333

Region

Note=Spectrin--actin-binding

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000356093

714_864

487.6666666666667

1859.3333333333333

Region

Note=C-terminal (CTD)

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373797

494_614

487.6666666666667

721.0

Region

Note=Hydrophilic

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373797

615_713

487.6666666666667

721.0

Region

Note=Spectrin--actin-binding

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373797

714_864

487.6666666666667

721.0

Region

Note=C-terminal (CTD)

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373798

494_614

487.6666666666667

1907.0

Region

Note=Hydrophilic

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373798

615_713

487.6666666666667

1907.0

Region

Note=Spectrin--actin-binding

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373798

714_864

487.6666666666667

1907.0

Region

Note=C-terminal (CTD)

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373800

494_614

278.6666666666667

658.6666666666666

Region

Note=Hydrophilic

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373800

615_713

278.6666666666667

658.6666666666666

Region

Note=Spectrin--actin-binding

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373800

714_864

278.6666666666667

658.6666666666666

Region

Note=C-terminal (CTD)

- 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

SNRNP40

chr1:31762101

chr1:29365766

ENST00000263694

149_189

177.0

358.0

Repeat

Note=WD 3

Hgene

SNRNP40

chr1:31762101

chr1:29365766

ENST00000263694

191_230

177.0

358.0

Repeat

Note=WD 4

Hgene

SNRNP40

chr1:31762101

chr1:29365766

ENST00000263694

233_272

177.0

358.0

Repeat

Note=WD 5

Hgene

SNRNP40

chr1:31762101

chr1:29365766

ENST00000263694

283_322

177.0

358.0

Repeat

Note=WD 6

Hgene

SNRNP40

chr1:31762101

chr1:29365766

ENST00000263694

325_357

177.0

358.0

Repeat

Note=WD 7

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000343067

210_491

487.6666666666667

1892.3333333333333

Domain

FERM

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000347529

210_491

452.6666666666667

861.6666666666666

Domain

FERM

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000349460

210_491

278.6666666666667

711.6666666666666

Domain

FERM

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000356093

210_491

487.6666666666667

1859.3333333333333

Domain

FERM

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373797

210_491

487.6666666666667

721.0

Domain

FERM

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373798

210_491

487.6666666666667

1907.0

Domain

FERM

Tgene

EPB41

chr1:31762101

chr1:29365766

ENST00000373800

210_491

278.6666666666667

658.6666666666666

Domain

FERM

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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
SNRNP40
EPB41

- 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 SNRNP40-EPB41

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 SNRNP40-EPB41

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