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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:YPEL3-EXD3

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: YPEL3-EXD3
	FusionPDB ID: 100064
	FusionGDB2.0 ID: 100064
		Hgene	Tgene
	Gene symbol	YPEL3	EXD3
	Gene ID	83719	54932
	Gene name	yippee like 3	exonuclease 3'-5' domain containing 3
	Synonyms	-	Nbr\|mut-7
	Cytomap	16p11.2	9q34.3
	Type of gene	protein-coding	protein-coding
	Description	protein yippee-like 3	exonuclease mut-7 homologexonuclease 3'-5' domain-containing protein 3nibbler homologprobable exonuclease mut-7 homologtesticular tissue protein Li 125
	Modification date	20200320	20200313
	UniProtAcc	.	Q8N9H8
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000398838, ENST00000398841, ENST00000562641, ENST00000563788, ENST00000566134, ENST00000566595, ENST00000565479,	ENST00000465160, ENST00000475006, ENST00000479452, ENST00000340951, ENST00000342129,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 4 X 3=36	10 X 9 X 7=630
	# samples	4	14
	** MAII score	log2(4/36*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(14/630*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: YPEL3 [Title/Abstract] AND EXD3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	YPEL3(30106573)-EXD3(140218595), # samples:3
Anticipated loss of major functional domain due to fusion event.	YPEL3-EXD3 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. YPEL3-EXD3 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. YPEL3-EXD3 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. YPEL3-EXD3 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. YPEL3-EXD3 seems lost the major protein functional domain in Hgene 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
Hgene	YPEL3	GO:2000774	positive regulation of cellular senescence	20388804

Fusion gene breakpoints across YPEL3 (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 EXD3 (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	ACC	TCGA-P6-A5OF-01A	YPEL3	chr16	30106573	-	EXD3	chr9	140218595	-
ChimerDB4	ACC	TCGA-P6-A5OF	YPEL3	chr16	30106572	-	EXD3	chr9	140218595	-

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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)
ENST00000398841	YPEL3	chr16	30106573	-	ENST00000342129	EXD3	chr9	140218595	-	1597	949	628	1542	304
ENST00000398841	YPEL3	chr16	30106573	-	ENST00000340951	EXD3	chr9	140218595	-	1627	949	628	1581	317
ENST00000562641	YPEL3	chr16	30106573	-	ENST00000342129	EXD3	chr9	140218595	-	1409	761	440	1354	304
ENST00000562641	YPEL3	chr16	30106573	-	ENST00000340951	EXD3	chr9	140218595	-	1439	761	440	1393	317
ENST00000398841	YPEL3	chr16	30106572	-	ENST00000342129	EXD3	chr9	140218595	-	1597	949	628	1542	304
ENST00000398841	YPEL3	chr16	30106572	-	ENST00000340951	EXD3	chr9	140218595	-	1627	949	628	1581	317
ENST00000562641	YPEL3	chr16	30106572	-	ENST00000342129	EXD3	chr9	140218595	-	1409	761	440	1354	304
ENST00000562641	YPEL3	chr16	30106572	-	ENST00000340951	EXD3	chr9	140218595	-	1439	761	440	1393	317

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
ENST00000398841	ENST00000342129	YPEL3	chr16	30106573	-	EXD3	chr9	140218595	-	0.28846017	0.71153986
ENST00000398841	ENST00000340951	YPEL3	chr16	30106573	-	EXD3	chr9	140218595	-	0.29353482	0.7064652
ENST00000562641	ENST00000342129	YPEL3	chr16	30106573	-	EXD3	chr9	140218595	-	0.28152356	0.7184764
ENST00000562641	ENST00000340951	YPEL3	chr16	30106573	-	EXD3	chr9	140218595	-	0.2895566	0.7104434
ENST00000398841	ENST00000342129	YPEL3	chr16	30106572	-	EXD3	chr9	140218595	-	0.28846017	0.71153986
ENST00000398841	ENST00000340951	YPEL3	chr16	30106572	-	EXD3	chr9	140218595	-	0.29353482	0.7064652
ENST00000562641	ENST00000342129	YPEL3	chr16	30106572	-	EXD3	chr9	140218595	-	0.28152356	0.7184764
ENST00000562641	ENST00000340951	YPEL3	chr16	30106572	-	EXD3	chr9	140218595	-	0.2895566	0.7104434

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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

>100064_100064_1_YPEL3-EXD3_YPEL3_chr16_30106572_ENST00000398841_EXD3_chr9_140218595_ENST00000340951_length(amino acids)=317AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGDEATQSQAVQEPGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCF

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

>100064_100064_2_YPEL3-EXD3_YPEL3_chr16_30106572_ENST00000398841_EXD3_chr9_140218595_ENST00000342129_length(amino acids)=304AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCFYCCTGCGKVFWDG

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

>100064_100064_3_YPEL3-EXD3_YPEL3_chr16_30106572_ENST00000562641_EXD3_chr9_140218595_ENST00000340951_length(amino acids)=317AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGDEATQSQAVQEPGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCF

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

>100064_100064_4_YPEL3-EXD3_YPEL3_chr16_30106572_ENST00000562641_EXD3_chr9_140218595_ENST00000342129_length(amino acids)=304AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCFYCCTGCGKVFWDG

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

>100064_100064_5_YPEL3-EXD3_YPEL3_chr16_30106573_ENST00000398841_EXD3_chr9_140218595_ENST00000340951_length(amino acids)=317AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGDEATQSQAVQEPGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCF

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

>100064_100064_6_YPEL3-EXD3_YPEL3_chr16_30106573_ENST00000398841_EXD3_chr9_140218595_ENST00000342129_length(amino acids)=304AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCFYCCTGCGKVFWDG

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

>100064_100064_7_YPEL3-EXD3_YPEL3_chr16_30106573_ENST00000562641_EXD3_chr9_140218595_ENST00000340951_length(amino acids)=317AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGDEATQSQAVQEPGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCF

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

>100064_100064_8_YPEL3-EXD3_YPEL3_chr16_30106573_ENST00000562641_EXD3_chr9_140218595_ENST00000342129_length(amino acids)=304AA_BP=107
MVPGEAAGSGERREQPSVTERVPTALGVPRMCVAQVLTAHLLPPRQALGSLCSPWAAPRVGPLPPAPAMVRISKPKTFQAYLDDCHRRYS
CAHCRAHLANHDDLISKVARQEGRIILTSGQPFHKLRAQVGAGRCLSVDCSLKAQQQAKAVLKHFNVRVTHADIFSRCQACNCDQYLKVS
RDMMKQLMWLSSHQEGPRSSGPAPDAAPEGCTYDRPCRWLQMADLRAETPDMLADGTRLQLAGVPVGVLRTPGLRCFYCCTGCGKVFWDG

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

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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/chr16:30106573/chr9:140218595)
- 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
.	EXD3 Q8N9H8
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: Possesses 3'-5' exoribonuclease activity. Required for 3'-end trimming of AGO1-bound miRNAs (By similarity). {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

Tgene

EXD3

chr16:30106572

chr9:140218595

ENST00000342129

517_571

317.0

515.0

Domain

Note=3'-5' exonuclease

Tgene

EXD3

chr16:30106572

chr9:140218595

ENST00000479452

517_571

247.0

Domain

Note=3'-5' exonuclease

Tgene

EXD3

chr16:30106573

chr9:140218595

ENST00000342129

517_571

317.0

515.0

Domain

Note=3'-5' exonuclease

Tgene

EXD3

chr16:30106573

chr9:140218595

ENST00000479452

517_571

247.0

Domain

Note=3'-5' exonuclease

- 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

YPEL3

chr16:30106572

chr9:140218595

ENST00000398838

19_116

39.0

120.0

Domain

Yippee

Hgene

YPEL3

chr16:30106572

chr9:140218595

ENST00000398841

19_116

77.0

158.0

Domain

Yippee

Hgene

YPEL3

chr16:30106572

chr9:140218595

ENST00000563788

19_116

39.0

120.0

Domain

Yippee

Hgene

YPEL3

chr16:30106572

chr9:140218595

ENST00000566595

19_116

39.0

120.0

Domain

Yippee

Hgene

YPEL3

chr16:30106573

chr9:140218595

ENST00000398838

19_116

39.0

120.0

Domain

Yippee

Hgene

YPEL3

chr16:30106573

chr9:140218595

ENST00000398841

19_116

77.0

158.0

Domain

Yippee

Hgene

YPEL3

chr16:30106573

chr9:140218595

ENST00000563788

19_116

39.0

120.0

Domain

Yippee

Hgene

YPEL3

chr16:30106573

chr9:140218595

ENST00000566595

19_116

39.0

120.0

Domain

Yippee

Tgene

EXD3

chr16:30106572

chr9:140218595

ENST00000340951

517_571

666.0

877.0

Domain

Note=3'-5' exonuclease

Tgene

EXD3

chr16:30106573

chr9:140218595

ENST00000340951

517_571

666.0

877.0

Domain

Note=3'-5' exonuclease

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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
YPEL3
EXD3

- 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 YPEL3-EXD3

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 YPEL3-EXD3

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