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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:FDPS-KHSRP

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FDPS-KHSRP
	FusionPDB ID: 30059
	FusionGDB2.0 ID: 30059
		Hgene	Tgene
	Gene symbol	FDPS	KHSRP
	Gene ID	2224	8570
	Gene name	farnesyl diphosphate synthase	KH-type splicing regulatory protein
	Synonyms	FPPS\|FPS\|POROK9	FBP2\|FUBP2\|KSRP\|p75
	Cytomap	1q22	19p13.3
	Type of gene	protein-coding	protein-coding
	Description	farnesyl pyrophosphate synthase(2E,6E)-farnesyl diphosphate synthaseFPP synthaseFPP synthetasefarnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase	far upstream element-binding protein 2FUSE-binding protein 2epididymis secretory sperm binding protein
	Modification date	20200329	20200329
	UniProtAcc	P14324	Q92945
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000487002, ENST00000356657, ENST00000368356, ENST00000447866,	ENST00000398148,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 2 X 6=72	4 X 4 X 3=48
	# samples	7	4
	** MAII score	log2(7/72*10)=-0.0406419844973459 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: FDPS [Title/Abstract] AND KHSRP [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FDPS(155282186)-KHSRP(6422447), # samples:1
Anticipated loss of major functional domain due to fusion event.	FDPS-KHSRP 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. FDPS-KHSRP 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. FDPS-KHSRP 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. FDPS-KHSRP 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
Tgene	KHSRP	GO:0043488	regulation of mRNA stability	16126846
Tgene	KHSRP	GO:0045019	negative regulation of nitric oxide biosynthetic process	16126846
Tgene	KHSRP	GO:0061014	positive regulation of mRNA catabolic process	16126846
Tgene	KHSRP	GO:0061158	3'-UTR-mediated mRNA destabilization	16126846

Fusion gene breakpoints across FDPS (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 KHSRP (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-A4IZ	FDPS	chr1	155282186	+	KHSRP	chr19	6422447	-

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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)
ENST00000447866	FDPS	chr1	155282186	+	ENST00000398148	KHSRP	chr19	6422447	-	3152	501	219	2387	722
ENST00000368356	FDPS	chr1	155282186	+	ENST00000398148	KHSRP	chr19	6422447	-	3246	595	115	2481	788
ENST00000356657	FDPS	chr1	155282186	+	ENST00000398148	KHSRP	chr19	6422447	-	3293	642	162	2528	788

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
ENST00000447866	ENST00000398148	FDPS	chr1	155282186	+	KHSRP	chr19	6422447	-	0.005805729	0.9941943
ENST00000368356	ENST00000398148	FDPS	chr1	155282186	+	KHSRP	chr19	6422447	-	0.002864284	0.99713576
ENST00000356657	ENST00000398148	FDPS	chr1	155282186	+	KHSRP	chr19	6422447	-	0.002336527	0.9976635

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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

>30059_30059_1_FDPS-KHSRP_FDPS_chr1_155282186_ENST00000356657_KHSRP_chr19_6422447_ENST00000398148_length(amino acids)=788AA_BP=160
MPLSRWLRSVGVFLLPAPYWAPRERWLGSLRRPSLVHGYPVLAWHSARCWCQAWTEEPRALCSSLRMNGDQNSDVYAQEKQDFVQHFSQI
VRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELIAAKIGGDAATTVNNSTPDF
GFGGQKRQLEDGDQPESKKLASQGDSISSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVS
LTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPL
RIIGDPYKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM
GPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQ
LPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQ
WQPPAPHDPSKAAAAAADPNAAWAAYYSHYYQQPPGPVPGPAPAPAAPPAQGEPPQPPPTGQSDYTKAWEEYYKKIGQQPQQPGAPPQQD

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

>30059_30059_2_FDPS-KHSRP_FDPS_chr1_155282186_ENST00000368356_KHSRP_chr19_6422447_ENST00000398148_length(amino acids)=788AA_BP=160
MPLSRWLRSVGVFLLPAPYWAPRERWLGSLRRPSLVHGYPVLAWHSARCWCQAWTEEPRALCSSLRMNGDQNSDVYAQEKQDFVQHFSQI
VRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELIAAKIGGDAATTVNNSTPDF
GFGGQKRQLEDGDQPESKKLASQGDSISSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVS
LTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPL
RIIGDPYKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM
GPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQ
LPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQ
WQPPAPHDPSKAAAAAADPNAAWAAYYSHYYQQPPGPVPGPAPAPAAPPAQGEPPQPPPTGQSDYTKAWEEYYKKIGQQPQQPGAPPQQD

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

>30059_30059_3_FDPS-KHSRP_FDPS_chr1_155282186_ENST00000447866_KHSRP_chr19_6422447_ENST00000398148_length(amino acids)=722AA_BP=94
MNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGW
CVELIAAKIGGDAATTVNNSTPDFGFGGQKRQLEDGDQPESKKLASQGDSISSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINK
IQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQL
QERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQ
NDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLV
IGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPGPFNQGPPG
APPHAGGPPPHQYPPQGWGNTYPQWQPPAPHDPSKAAAAAADPNAAWAAYYSHYYQQPPGPVPGPAPAPAAPPAQGEPPQPPPTGQSDYT
KAWEEYYKKIGQQPQQPGAPPQQDYTKAWEEYYKKQAQVATGGGPGAPPGSQPDYSAAWAEYYRQQAAYYGQTPGPGGPQPPPTQQGQQQ

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

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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/chr1:155282186/chr19:6422447)
- 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
FDPS P14324	KHSRP Q92945
FUNCTION: Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.	FUNCTION: Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs. {ECO:0000250, ECO:0000269\|PubMed:11003644, ECO:0000269\|PubMed:8940189, ECO:0000269\|PubMed:9136930}.

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

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

498_612

83.0

712.0

Compositional bias

Note=Ala/Gly/Pro-rich

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

144_208

83.0

712.0

Domain

KH 1

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

233_299

83.0

712.0

Domain

KH 2

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

322_386

83.0

712.0

Domain

KH 3

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

424_491

83.0

712.0

Domain

KH 4

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

571_684

83.0

712.0

Region

Note=4 X 12 AA imperfect repeats

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

571_582

83.0

712.0

Repeat

Note=1

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

617_628

83.0

712.0

Repeat

Note=2

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

643_654

83.0

712.0

Repeat

Note=3

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

673_684

83.0

712.0

Repeat

Note=4

- 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

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

68_496

83.0

712.0

Compositional bias

Note=Gly-rich

Tgene

KHSRP

chr1:155282186

chr19:6422447

ENST00000398148

7_67

83.0

712.0

Compositional bias

Note=Gly/Pro-rich

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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
FDPS
KHSRP

- 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 FDPS-KHSRP

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 FDPS-KHSRP

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