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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:FDFT1-WDR35

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FDFT1-WDR35
	FusionPDB ID: 30052
	FusionGDB2.0 ID: 30052
		Hgene	Tgene
	Gene symbol	FDFT1	WDR35
	Gene ID	2222	57539
	Gene name	farnesyl-diphosphate farnesyltransferase 1	WD repeat domain 35
	Synonyms	DGPT\|ERG9\|SQS\|SQSD\|SS	CED2\|FAP118\|IFT121\|IFTA1\|SRTD7
	Cytomap	8p23.1	2p24.1
	Type of gene	protein-coding	protein-coding
	Description	squalene synthaseFPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthetase	WD repeat-containing protein 35intraflagellar transport protein 121 homolognaofen
	Modification date	20200320	20200313
	UniProtAcc	P37268	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000446331, ENST00000220584, ENST00000443614, ENST00000525777, ENST00000525900, ENST00000528643, ENST00000528812, ENST00000530664, ENST00000538689,	ENST00000281405, ENST00000345530, ENST00000416055,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 12 X 9=1728	4 X 4 X 3=48
	# samples	20	4
	** MAII score	log2(20/1728*10)=-3.11103131238874 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: FDFT1 [Title/Abstract] AND WDR35 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FDFT1(11695923)-WDR35(20178545), # samples:1
Anticipated loss of major functional domain due to fusion event.	FDFT1-WDR35 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. FDFT1-WDR35 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target 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

Fusion gene breakpoints across FDFT1 (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 WDR35 (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
ChiTaRS5.0	N/A	FN108955	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-

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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)
ENST00000538689	FDFT1	chr8	11695923	-	ENST00000281405	WDR35	chr2	20178545	-	8334	1925	376	1566	396
ENST00000538689	FDFT1	chr8	11695923	-	ENST00000345530	WDR35	chr2	20178545	-	8367	1925	376	1566	396
ENST00000220584	FDFT1	chr8	11695923	-	ENST00000281405	WDR35	chr2	20178545	-	8558	2149	222	1448	408
ENST00000220584	FDFT1	chr8	11695923	-	ENST00000345530	WDR35	chr2	20178545	-	8591	2149	222	1448	408
ENST00000528643	FDFT1	chr8	11695923	-	ENST00000281405	WDR35	chr2	20178545	-	8291	1882	369	1376	335
ENST00000528643	FDFT1	chr8	11695923	-	ENST00000345530	WDR35	chr2	20178545	-	8324	1882	369	1376	335
ENST00000525777	FDFT1	chr8	11695923	-	ENST00000281405	WDR35	chr2	20178545	-	7854	1445	433	1440	335
ENST00000525777	FDFT1	chr8	11695923	-	ENST00000345530	WDR35	chr2	20178545	-	7887	1445	433	1440	335

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
ENST00000538689	ENST00000281405	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.000128077	0.99987185
ENST00000538689	ENST00000345530	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.000127713	0.9998723
ENST00000220584	ENST00000281405	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.00061698	0.999383
ENST00000220584	ENST00000345530	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.000625801	0.9993742
ENST00000528643	ENST00000281405	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.000251249	0.99974877
ENST00000528643	ENST00000345530	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.000247635	0.99975234
ENST00000525777	ENST00000281405	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.000229116	0.99977094
ENST00000525777	ENST00000345530	FDFT1	chr8	11695923	-	WDR35	chr2	20178545	-	0.000226477	0.99977356

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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

>30052_30052_1_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000220584_WDR35_chr2_20178545_ENST00000281405_length(amino acids)=408AA_BP=
MEFVKCLGHPEEFYNLVRFRIGGKRKVMPKMDQDSLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISV
EKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVG
IGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHI
PDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEPSSSKTRQIISTIRTQ

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

>30052_30052_2_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000220584_WDR35_chr2_20178545_ENST00000345530_length(amino acids)=408AA_BP=
MEFVKCLGHPEEFYNLVRFRIGGKRKVMPKMDQDSLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISV
EKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVG
IGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHI
PDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEPSSSKTRQIISTIRTQ

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

>30052_30052_3_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000525777_WDR35_chr2_20178545_ENST00000281405_length(amino acids)=335AA_BP=
MVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVT
SEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENID
LAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYME

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

>30052_30052_4_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000525777_WDR35_chr2_20178545_ENST00000345530_length(amino acids)=335AA_BP=
MVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVT
SEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENID
LAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYME

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

>30052_30052_5_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000528643_WDR35_chr2_20178545_ENST00000281405_length(amino acids)=335AA_BP=
MVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVT
SEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENID
LAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYME

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

>30052_30052_6_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000528643_WDR35_chr2_20178545_ENST00000345530_length(amino acids)=335AA_BP=
MVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVT
SEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENID
LAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYME

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

>30052_30052_7_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000538689_WDR35_chr2_20178545_ENST00000281405_length(amino acids)=396AA_BP=
MKSVRPRTNQFRTHLDSTDSKDSLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHS
FLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEF
EDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRN
QSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEPSSSKTRQIISTIRTQNLPNCQLISRSH

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

>30052_30052_8_FDFT1-WDR35_FDFT1_chr8_11695923_ENST00000538689_WDR35_chr2_20178545_ENST00000345530_length(amino acids)=396AA_BP=
MKSVRPRTNQFRTHLDSTDSKDSLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHS
FLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEF
EDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRN
QSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEPSSSKTRQIISTIRTQNLPNCQLISRSH

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

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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/chr8:11695923/chr2:20178545)
- 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
FDFT1 P37268	.
FUNCTION: Catalyzes the condensation of 2 farnesyl pyrophosphate (FPP) moieties to form squalene. Proceeds in two distinct steps. In the first half-reaction, two molecules of FPP react to form the stable presqualene diphosphate intermediate (PSQPP), with concomitant release of a proton and a molecule of inorganic diphosphate. In the second half-reaction, PSQPP undergoes heterolysis, isomerization, and reduction with NADPH or NADH to form squalene. It is the first committed enzyme of the sterol biosynthesis pathway. {ECO:0000269\|PubMed:10896663, ECO:0000269\|PubMed:24531458}.	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

WDR35

chr8:11695923

chr2:20178545

ENST00000281405

105_143

1171.0

Repeat

Note=WD 3

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000281405

147_185

1171.0

Repeat

Note=WD 4

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000281405

193_241

1171.0

Repeat

Note=WD 5

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000281405

246_288

1171.0

Repeat

Note=WD 6

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000281405

4_43

1171.0

Repeat

Note=WD 1

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000281405

61_100

1171.0

Repeat

Note=WD 2

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000345530

105_143

1182.0

Repeat

Note=WD 3

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000345530

147_185

1182.0

Repeat

Note=WD 4

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000345530

193_241

1182.0

Repeat

Note=WD 5

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000345530

246_288

1182.0

Repeat

Note=WD 6

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000345530

4_43

1182.0

Repeat

Note=WD 1

Tgene

WDR35

chr8:11695923

chr2:20178545

ENST00000345530

61_100

1182.0

Repeat

Note=WD 2

- 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

FDFT1

chr8:11695923

chr2:20178545

ENST00000220584

284_304

418.0

Transmembrane

Helical

Hgene

FDFT1

chr8:11695923

chr2:20178545

ENST00000220584

384_404

418.0

Transmembrane

Helical

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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
FDFT1
WDR35

- 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 FDFT1-WDR35

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 FDFT1-WDR35

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