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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:SET-UTP11L

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SET-UTP11L
	FusionPDB ID: 80972
	FusionGDB2.0 ID: 80972
		Hgene	Tgene
	Gene symbol	SET	UTP11L
	Gene ID	6418	51118
	Gene name	SET nuclear proto-oncogene	UTP11 small subunit processome component
	Synonyms	2PP2A\|I2PP2A\|IGAAD\|IPP2A2\|MRD58\|PHAPII\|TAF-I\|TAF-IBETA	CGI-94\|CGI94\|UTP11L
	Cytomap	9q34.11	1p34.3
	Type of gene	protein-coding	protein-coding
	Description	protein SETHLA-DR-associated protein IISET nuclear oncogeneSET translocation (myeloid leukemia-associated)Template-Activating Factor-I, chromatin remodelling factorchromatin remodelling factorinhibitor of granzyme A-activated DNaseinhibitor-2 of pr	probable U3 small nucleolar RNA-associated protein 11U3 snoRNA-associated protein 11UTP11, small subunit processome component homologUTP11-like proteinUTP11-like, U3 small nucleolar ribonucleoprotein
	Modification date	20200313	20200313
	UniProtAcc	Q9BYW2	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000477806, ENST00000322030, ENST00000372688, ENST00000372692, ENST00000409104,	ENST00000373014, ENST00000537711, ENST00000488453,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 14 X 3=672	3 X 3 X 3=27
	# samples	17	4
	** MAII score	log2(17/672*10)=-1.98292648664106 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/27*10)=0.567040592723894 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SET [Title/Abstract] AND UTP11L [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SET(131453506)-UTP11L(38483340), # samples:1
Anticipated loss of major functional domain due to fusion event.	SET-UTP11L 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. SET-UTP11L 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	SET	GO:0045892	negative regulation of transcription, DNA-templated	19343227

Fusion gene breakpoints across SET (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 UTP11L (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	STAD	TCGA-BR-8078-01A	SET	chr9	131453506	+	UTP11L	chr1	38483340	+

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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)
ENST00000372692	SET	chr9	131453506	+	ENST00000373014	UTP11L	chr1	38483340	+	2244	411	241	1047	268
ENST00000372692	SET	chr9	131453506	+	ENST00000537711	UTP11L	chr1	38483340	+	1137	411	241	732	163
ENST00000409104	SET	chr9	131453506	+	ENST00000373014	UTP11L	chr1	38483340	+	2022	189	85	825	246
ENST00000409104	SET	chr9	131453506	+	ENST00000537711	UTP11L	chr1	38483340	+	915	189	85	510	141
ENST00000322030	SET	chr9	131453506	+	ENST00000373014	UTP11L	chr1	38483340	+	2321	488	357	1124	255
ENST00000322030	SET	chr9	131453506	+	ENST00000537711	UTP11L	chr1	38483340	+	1214	488	487	2	162
ENST00000372688	SET	chr9	131453506	+	ENST00000373014	UTP11L	chr1	38483340	+	1931	98	0	734	244
ENST00000372688	SET	chr9	131453506	+	ENST00000537711	UTP11L	chr1	38483340	+	824	98	0	419	139

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
ENST00000372692	ENST00000373014	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.000772628	0.9992274
ENST00000372692	ENST00000537711	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.006297492	0.99370253
ENST00000409104	ENST00000373014	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.001009723	0.99899024
ENST00000409104	ENST00000537711	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.011314304	0.9886857
ENST00000322030	ENST00000373014	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.000995171	0.9990049
ENST00000322030	ENST00000537711	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.005525249	0.9944747
ENST00000372688	ENST00000373014	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.00045038	0.99954957
ENST00000372688	ENST00000537711	SET	chr9	131453506	+	UTP11L	chr1	38483340	+	0.005454534	0.99454546

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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

>80972_80972_1_SET-UTP11L_SET_chr9_131453506_ENST00000322030_UTP11L_chr1_38483340_ENST00000373014_length(amino acids)=255AA_BP=43
MSAPAAKVSKKELNSNHDGADETSEKEQQEAIEHIDEVQNEIDSDYRKKQEYLKALRKKALEKNPDEFYYKMTRVKLQDGVHIIKETKEE
VTPEQLKLMRTQDVKYIEMKRVAEAKKIERLKSELHLLDFQGKQQNKHVFFFDTKKEVEQFDVATHLQTAPELVDRVFNRPRIETLQKEK

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

>80972_80972_2_SET-UTP11L_SET_chr9_131453506_ENST00000322030_UTP11L_chr1_38483340_ENST00000537711_length(amino acids)=162AA_BP=
MSISFCTSSMCSIASCCSFSEVSSAPSWLELSSFLLTLAAGADMVLLRGRGGSGEGERREGEGGGQAASPHATRAGARSVRPPPPGARSL

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

>80972_80972_3_SET-UTP11L_SET_chr9_131453506_ENST00000372688_UTP11L_chr1_38483340_ENST00000373014_length(amino acids)=244AA_BP=32
MMPRSHQPPPPPHEKEQQEAIEHIDEVQNEIDSDYRKKQEYLKALRKKALEKNPDEFYYKMTRVKLQDGVHIIKETKEEVTPEQLKLMRT
QDVKYIEMKRVAEAKKIERLKSELHLLDFQGKQQNKHVFFFDTKKEVEQFDVATHLQTAPELVDRVFNRPRIETLQKEKVKGVTNQTGLK

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

>80972_80972_4_SET-UTP11L_SET_chr9_131453506_ENST00000372688_UTP11L_chr1_38483340_ENST00000537711_length(amino acids)=139AA_BP=32
MMPRSHQPPPPPHEKEQQEAIEHIDEVQNEIDSDYRKKQEYLKALRKKALEKNPDEFYYKMTRVKLQDGVHIIKETKEEVTPEQLKLMRT

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

>80972_80972_5_SET-UTP11L_SET_chr9_131453506_ENST00000372692_UTP11L_chr1_38483340_ENST00000373014_length(amino acids)=268AA_BP=56
MAPKRQSPLPPQKKKPRPPPALGPEETSASAGLPKKGEKEQQEAIEHIDEVQNEIDSDYRKKQEYLKALRKKALEKNPDEFYYKMTRVKL
QDGVHIIKETKEEVTPEQLKLMRTQDVKYIEMKRVAEAKKIERLKSELHLLDFQGKQQNKHVFFFDTKKEVEQFDVATHLQTAPELVDRV

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

>80972_80972_6_SET-UTP11L_SET_chr9_131453506_ENST00000372692_UTP11L_chr1_38483340_ENST00000537711_length(amino acids)=163AA_BP=56
MAPKRQSPLPPQKKKPRPPPALGPEETSASAGLPKKGEKEQQEAIEHIDEVQNEIDSDYRKKQEYLKALRKKALEKNPDEFYYKMTRVKL

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

>80972_80972_7_SET-UTP11L_SET_chr9_131453506_ENST00000409104_UTP11L_chr1_38483340_ENST00000373014_length(amino acids)=246AA_BP=34
MGCRDLLPSLKPTLLEKEQQEAIEHIDEVQNEIDSDYRKKQEYLKALRKKALEKNPDEFYYKMTRVKLQDGVHIIKETKEEVTPEQLKLM
RTQDVKYIEMKRVAEAKKIERLKSELHLLDFQGKQQNKHVFFFDTKKEVEQFDVATHLQTAPELVDRVFNRPRIETLQKEKVKGVTNQTG

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

>80972_80972_8_SET-UTP11L_SET_chr9_131453506_ENST00000409104_UTP11L_chr1_38483340_ENST00000537711_length(amino acids)=141AA_BP=34
MGCRDLLPSLKPTLLEKEQQEAIEHIDEVQNEIDSDYRKKQEYLKALRKKALEKNPDEFYYKMTRVKLQDGVHIIKETKEEVTPEQLKLM

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

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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/chr9:131453506/chr1:38483340)
- 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
SET Q9BYW2	.
FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using dimethylated 'Lys-36' (H3K36me2) as substrate (PubMed:16118227, PubMed:19141475, PubMed:21526191, PubMed:21792193, PubMed:23043551, PubMed:27474439). It is capable of trimethylating unmethylated H3K36 (H3K36me0) in vitro (PubMed:19332550). Represents the main enzyme generating H3K36me3, a specific tag for epigenetic transcriptional activation (By similarity). Plays a role in chromatin structure modulation during elongation by coordinating recruitment of the FACT complex and by interacting with hyperphosphorylated POLR2A (PubMed:23325844). Acts as a key regulator of DNA mismatch repair in G1 and early S phase by generating H3K36me3, a mark required to recruit MSH6 subunit of the MutS alpha complex: early recruitment of the MutS alpha complex to chromatin to be replicated allows a quick identification of mismatch DNA to initiate the mismatch repair reaction (PubMed:23622243). Required for DNA double-strand break repair in response to DNA damage: acts by mediating formation of H3K36me3, promoting recruitment of RAD51 and DNA repair via homologous recombination (HR) (PubMed:24843002). Acts as a tumor suppressor (PubMed:24509477). H3K36me3 also plays an essential role in the maintenance of a heterochromatic state, by recruiting DNA methyltransferase DNMT3A (PubMed:27317772). H3K36me3 is also enhanced in intron-containing genes, suggesting that SETD2 recruitment is enhanced by splicing and that splicing is coupled to recruitment of elongating RNA polymerase (PubMed:21792193). Required during angiogenesis (By similarity). Required for endoderm development by promoting embryonic stem cell differentiation toward endoderm: acts by mediating formation of H3K36me3 in distal promoter regions of FGFR3, leading to regulate transcription initiation of FGFR3 (By similarity). In addition to histones, also mediates methylation of other proteins, such as tubulins and STAT1 (PubMed:27518565, PubMed:28753426). Trimethylates 'Lys-40' of alpha-tubulins such as TUBA1B (alpha-TubK40me3); alpha-TubK40me3 is required for normal mitosis and cytokinesis and may be a specific tag in cytoskeletal remodeling (PubMed:27518565). Involved in interferon-alpha-induced antiviral defense by mediating both monomethylation of STAT1 at 'Lys-525' and catalyzing H3K36me3 on promoters of some interferon-stimulated genes (ISGs) to activate gene transcription (PubMed:28753426). {ECO:0000250\|UniProtKB:E9Q5F9, ECO:0000269\|PubMed:16118227, ECO:0000269\|PubMed:19141475, ECO:0000269\|PubMed:21526191, ECO:0000269\|PubMed:21792193, ECO:0000269\|PubMed:23043551, ECO:0000269\|PubMed:23325844, ECO:0000269\|PubMed:23622243, ECO:0000269\|PubMed:24509477, ECO:0000269\|PubMed:24843002, ECO:0000269\|PubMed:27317772, ECO:0000269\|PubMed:27474439, ECO:0000269\|PubMed:27518565, ECO:0000269\|PubMed:28753426}.; FUNCTION: (Microbial infection) Recruited to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression. {ECO:0000269\|PubMed:11461154}.	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

SET

chr9:131453506

chr1:38483340

ENST00000322030

239_290

43.666666666666664

278.0

Compositional bias

Note=Asp/Glu-rich (highly acidic)

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000372688

239_290

32.666666666666664

267.0

Compositional bias

Note=Asp/Glu-rich (highly acidic)

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000372692

239_290

56.666666666666664

291.0

Compositional bias

Note=Asp/Glu-rich (highly acidic)

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000409104

239_290

34.666666666666664

269.0

Compositional bias

Note=Asp/Glu-rich (highly acidic)

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000322030

31_78

43.666666666666664

278.0

Region

Note=Dimerization

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000322030

79_225

43.666666666666664

278.0

Region

Note=Earmuff domain

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000372688

31_78

32.666666666666664

267.0

Region

Note=Dimerization

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000372688

79_225

32.666666666666664

267.0

Region

Note=Earmuff domain

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000372692

31_78

56.666666666666664

291.0

Region

Note=Dimerization

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000372692

79_225

56.666666666666664

291.0

Region

Note=Earmuff domain

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000409104

31_78

34.666666666666664

269.0

Region

Note=Dimerization

Hgene

SET

chr9:131453506

chr1:38483340

ENST00000409104

79_225

34.666666666666664

269.0

Region

Note=Earmuff domain

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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
SET
UTP11L

- 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 SET-UTP11L

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 SET-UTP11L

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