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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:FNIP1-IL5 (FusionGDB2 ID:30952)

Fusion Gene Summary for FNIP1-IL5

Fusion gene summary

Fusion gene information	Fusion gene name: FNIP1-IL5
	Fusion gene ID: 30952
		Hgene	Tgene
	Gene symbol	FNIP1	IL5
	Gene ID	96459	3567
	Gene name	folliculin interacting protein 1	interleukin 5
	Synonyms	-	EDF\|IL-5\|TRF
	Cytomap	5q31.1	5q31.1
	Type of gene	protein-coding	protein-coding
	Description	folliculin-interacting protein 1	interleukin-5B-cell differentiation factor IT-cell replacing factorcolony-stimulating factor, eosinophileosinophil differentiation factor
	Modification date	20200327	20200329
	UniProtAcc	Q8TF40	Q01344
	Ensembl transtripts involved in fusion gene	ENST00000307954, ENST00000307968, ENST00000510461, ENST00000511848,	ENST00000231454,
Fusion gene scores	* DoF score	15 X 11 X 10=1650	2 X 2 X 2=8
	# samples	18	2
	** MAII score	log2(18/1650*10)=-3.1963972128035 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(2/8*10)=1.32192809488736
Context	PubMed: FNIP1 [Title/Abstract] AND IL5 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	FNIP1(131132523)-IL5(131878818), # samples:2
Anticipated loss of major functional domain due to fusion event.

* 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	FNIP1	GO:0000122	negative regulation of transcription by RNA polymerase II	21209915
Hgene	FNIP1	GO:0001932	regulation of protein phosphorylation	18663353
Hgene	FNIP1	GO:0031334	positive regulation of protein complex assembly	25126726
Hgene	FNIP1	GO:0033138	positive regulation of peptidyl-serine phosphorylation	19914239
Tgene	IL5	GO:0071803	positive regulation of podosome assembly	15220135

Fusion gene breakpoints across FNIP1 (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 IL5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	BLCA	TCGA-FJ-A3ZF-01A	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-

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Fusion Gene ORF analysis for FNIP1-IL5

Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
In-frame	ENST00000307954	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-
In-frame	ENST00000307968	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-
In-frame	ENST00000510461	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-
In-frame	ENST00000511848	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)
ENST00000307968	FNIP1	chr5	131132523	-	ENST00000231454	IL5	chr5	131878818	-	720	92	80	352	90
ENST00000307954	FNIP1	chr5	131132523	-	ENST00000231454	IL5	chr5	131878818	-	749	121	109	381	90
ENST00000510461	FNIP1	chr5	131132523	-	ENST00000231454	IL5	chr5	131878818	-	816	188	283	2	94
ENST00000511848	FNIP1	chr5	131132523	-	ENST00000231454	IL5	chr5	131878818	-	815	187	282	1	94

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
ENST00000307968	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-	0.95818335	0.04181662
ENST00000307954	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-	0.96010923	0.03989076
ENST00000510461	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-	0.9589114	0.041088585
ENST00000511848	ENST00000231454	FNIP1	chr5	131132523	-	IL5	chr5	131878818	-	0.9612355	0.038764454

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Fusion Genomic Features for FNIP1-IL5

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for FNIP1-IL5

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:131132523/chr5:131878818)
- 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
FNIP1 Q8TF40	IL5 Q01344
FUNCTION: Binding partner of the GTPase-activating protein FLCN: involved in the cellular response to amino acid availability by regulating the mTORC1 signaling cascade controlling the MiT/TFE factors TFEB and TFE3 (PubMed:17028174, PubMed:18663353, PubMed:24081491). In low-amino acid conditions, component of the lysosomal folliculin complex (LFC) on the membrane of lysosomes, which inhibits the GTPase-activating activity of FLCN, thereby inactivating mTORC1 and promoting nuclear translocation of TFEB and TFE3 (By similarity). Upon amino acid restimulation, disassembly of the LFC complex liberates the GTPase-activating activity of FLCN, leading to activation of mTORC1 and subsequent cytoplasmic retention of TFEB and TFE3 (By similarity). Required to promote FLCN recruitment to lysosomes and interaction with Rag GTPases (PubMed:24081491). Together with FLCN, regulates autophagy: following phosphorylation by ULK1, interacts with GABARAP and promotes autophagy (PubMed:25126726). In addition to its role in mTORC1 signaling, also acts as a co-chaperone of HSP90AA1/Hsp90: following gradual phosphorylation by CK2, inhibits the ATPase activity of HSP90AA1/Hsp90, leading to activate both kinase and non-kinase client proteins of HSP90AA1/Hsp90 (PubMed:27353360, PubMed:30699359). Acts as a scaffold to load client protein FLCN onto HSP90AA1/Hsp90 (PubMed:27353360). Competes with the activating co-chaperone AHSA1 for binding to HSP90AA1, thereby providing a reciprocal regulatory mechanism for chaperoning of client proteins (PubMed:27353360). Required for B-cell development (By similarity). {ECO:0000250\|UniProtKB:Q68FD7, ECO:0000250\|UniProtKB:Q9P278, ECO:0000269\|PubMed:17028174, ECO:0000269\|PubMed:18663353, ECO:0000269\|PubMed:24081491, ECO:0000269\|PubMed:25126726, ECO:0000269\|PubMed:27353360, ECO:0000269\|PubMed:30699359}.	FUNCTION: This is the receptor for interleukin-5. The alpha chain binds to IL5.

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.

- In-frame and 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

- In-frame and 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

FNIP1

chr5:131132523

chr5:131878818

ENST00000307968

96_99

1139.0

Compositional bias

Note=Poly-Ser

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000510461

96_99

1167.0

Compositional bias

Note=Poly-Ser

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000511848

96_99

509.0

Compositional bias

Note=Poly-Ser

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000307968

1102_1157

1139.0

Domain

dDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000307968

37_478

1139.0

Domain

uDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000307968

486_1092

1139.0

Domain

cDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000510461

1102_1157

1167.0

Domain

dDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000510461

37_478

1167.0

Domain

uDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000510461

486_1092

1167.0

Domain

cDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000511848

1102_1157

509.0

Domain

dDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000511848

37_478

509.0

Domain

uDENN FNIP1/2-type

Hgene

FNIP1

chr5:131132523

chr5:131878818

ENST00000511848

486_1092

509.0

Domain

cDENN FNIP1/2-type

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Fusion Gene Sequence for FNIP1-IL5

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>30952_30952_1_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000307954_IL5_chr5_131878818_ENST00000231454_length(transcript)=749nt_BP=121nt
GGAGCGACCCCTGCCTGGCCGTGGCTAGCATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCC
GCGACGCCCGGGACCCAGATTGCGGGTTCAGACTCTGAGGATTCCTGTTCCTGTACATAAAAATCACCAACTGTGCACTGAAGAAATCTT
TCAGGGAATAGGCACACTGGAGAGTCAAACTGTGCAAGGGGGTACTGTGGAAAGACTATTCAAAAACTTGTCCTTAATAAAGAAATACAT
TGACGGCCAAAAAAAAAAGTGTGGAGAAGAAAGACGGAGAGTAAACCAATTCCTAGACTACCTGCAAGAGTTTCTTGGTGTAATGAACAC
CGAGTGGATAATAGAAAGTTGAGACTAAACTGGTTTGTTGCAGCCAAAGATTTTGGAGGAGAAGGACATTTTACTGCAGTGAGAATGAGG
GCCAAGAAAGAGTCAGGCCTTAATTTTCAGTATAATTTAACTTCAGAGGGAAAGTAAATATTTCAGGCATACTGACACTTTGCCAGAAAG
CATAAAATTCTTAAAATATATTTCAGATATCAGAATCATTGAAGTATTTTCCTCCAGGCAAAATTGATATACTTTTTTCTTATTTAACTT
AACATTCTGTAAAATGTCTGTTAACTTAATAGTATTTATGAAATGGTTAAGAATTTGGTAAATTAGTATTTATTTAATGTTATGTTGTGT

>30952_30952_1_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000307954_IL5_chr5_131878818_ENST00000231454_length(amino acids)=90AA_BP=3
MRVQTLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEWIIES

--------------------------------------------------------------
>30952_30952_2_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000307968_IL5_chr5_131878818_ENST00000231454_length(transcript)=720nt_BP=92nt
ATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCCGCGACGCCCGGGACCCAGATTGCGGGTTC
AGACTCTGAGGATTCCTGTTCCTGTACATAAAAATCACCAACTGTGCACTGAAGAAATCTTTCAGGGAATAGGCACACTGGAGAGTCAAA
CTGTGCAAGGGGGTACTGTGGAAAGACTATTCAAAAACTTGTCCTTAATAAAGAAATACATTGACGGCCAAAAAAAAAAGTGTGGAGAAG
AAAGACGGAGAGTAAACCAATTCCTAGACTACCTGCAAGAGTTTCTTGGTGTAATGAACACCGAGTGGATAATAGAAAGTTGAGACTAAA
CTGGTTTGTTGCAGCCAAAGATTTTGGAGGAGAAGGACATTTTACTGCAGTGAGAATGAGGGCCAAGAAAGAGTCAGGCCTTAATTTTCA
GTATAATTTAACTTCAGAGGGAAAGTAAATATTTCAGGCATACTGACACTTTGCCAGAAAGCATAAAATTCTTAAAATATATTTCAGATA
TCAGAATCATTGAAGTATTTTCCTCCAGGCAAAATTGATATACTTTTTTCTTATTTAACTTAACATTCTGTAAAATGTCTGTTAACTTAA
TAGTATTTATGAAATGGTTAAGAATTTGGTAAATTAGTATTTATTTAATGTTATGTTGTGTTCTAATAAAACAAAAATAGACAACTGTTC

>30952_30952_2_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000307968_IL5_chr5_131878818_ENST00000231454_length(amino acids)=90AA_BP=3
MRVQTLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEWIIES

--------------------------------------------------------------
>30952_30952_3_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000510461_IL5_chr5_131878818_ENST00000231454_length(transcript)=816nt_BP=188nt
ATATGACTGAGGCGCCCATGGGGGTGGCGGGGCGGCTGTAGGAGCAGGGGCCTAGCAAGCGCCCAGCGGAGCGACCCCTGCCTGGCCGTG
GCTAGCATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCCGCGACGCCCGGGACCCAGATTGC
GGGTTCAGACTCTGAGGATTCCTGTTCCTGTACATAAAAATCACCAACTGTGCACTGAAGAAATCTTTCAGGGAATAGGCACACTGGAGA
GTCAAACTGTGCAAGGGGGTACTGTGGAAAGACTATTCAAAAACTTGTCCTTAATAAAGAAATACATTGACGGCCAAAAAAAAAAGTGTG
GAGAAGAAAGACGGAGAGTAAACCAATTCCTAGACTACCTGCAAGAGTTTCTTGGTGTAATGAACACCGAGTGGATAATAGAAAGTTGAG
ACTAAACTGGTTTGTTGCAGCCAAAGATTTTGGAGGAGAAGGACATTTTACTGCAGTGAGAATGAGGGCCAAGAAAGAGTCAGGCCTTAA
TTTTCAGTATAATTTAACTTCAGAGGGAAAGTAAATATTTCAGGCATACTGACACTTTGCCAGAAAGCATAAAATTCTTAAAATATATTT
CAGATATCAGAATCATTGAAGTATTTTCCTCCAGGCAAAATTGATATACTTTTTTCTTATTTAACTTAACATTCTGTAAAATGTCTGTTA
ACTTAATAGTATTTATGAAATGGTTAAGAATTTGGTAAATTAGTATTTATTTAATGTTATGTTGTGTTCTAATAAAACAAAAATAGACAA

>30952_30952_3_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000510461_IL5_chr5_131878818_ENST00000231454_length(amino acids)=94AA_BP=1
MHSLTLQCAYSLKDFFSAQLVIFMYRNRNPQSLNPQSGSRASRPGAPSPVLLLKSFWNSVGAMLATARQGSLRWALARPLLLQPPRHPHG

--------------------------------------------------------------
>30952_30952_4_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000511848_IL5_chr5_131878818_ENST00000231454_length(transcript)=815nt_BP=187nt
TATGACTGAGGCGCCCATGGGGGTGGCGGGGCGGCTGTAGGAGCAGGGGCCTAGCAAGCGCCCAGCGGAGCGACCCCTGCCTGGCCGTGG
CTAGCATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCCGCGACGCCCGGGACCCAGATTGCG
GGTTCAGACTCTGAGGATTCCTGTTCCTGTACATAAAAATCACCAACTGTGCACTGAAGAAATCTTTCAGGGAATAGGCACACTGGAGAG
TCAAACTGTGCAAGGGGGTACTGTGGAAAGACTATTCAAAAACTTGTCCTTAATAAAGAAATACATTGACGGCCAAAAAAAAAAGTGTGG
AGAAGAAAGACGGAGAGTAAACCAATTCCTAGACTACCTGCAAGAGTTTCTTGGTGTAATGAACACCGAGTGGATAATAGAAAGTTGAGA
CTAAACTGGTTTGTTGCAGCCAAAGATTTTGGAGGAGAAGGACATTTTACTGCAGTGAGAATGAGGGCCAAGAAAGAGTCAGGCCTTAAT
TTTCAGTATAATTTAACTTCAGAGGGAAAGTAAATATTTCAGGCATACTGACACTTTGCCAGAAAGCATAAAATTCTTAAAATATATTTC
AGATATCAGAATCATTGAAGTATTTTCCTCCAGGCAAAATTGATATACTTTTTTCTTATTTAACTTAACATTCTGTAAAATGTCTGTTAA
CTTAATAGTATTTATGAAATGGTTAAGAATTTGGTAAATTAGTATTTATTTAATGTTATGTTGTGTTCTAATAAAACAAAAATAGACAAC

>30952_30952_4_FNIP1-IL5_FNIP1_chr5_131132523_ENST00000511848_IL5_chr5_131878818_ENST00000231454_length(amino acids)=94AA_BP=1
MHSLTLQCAYSLKDFFSAQLVIFMYRNRNPQSLNPQSGSRASRPGAPSPVLLLKSFWNSVGAMLATARQGSLRWALARPLLLQPPRHPHG

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

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Fusion Gene PPI Analysis for FNIP1-IL5

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Hgene	FNIP1	chr5:131132523	chr5:131878818	ENST00000307968	-	1	17	929_1166	30.666666666666668	1139.0	HSP90AA1
Hgene	FNIP1	chr5:131132523	chr5:131878818	ENST00000510461	-	1	18	929_1166	30.666666666666668	1167.0	HSP90AA1
Hgene	FNIP1	chr5:131132523	chr5:131878818	ENST00000511848	-	1	13	929_1166	30.666666666666668	509.0	HSP90AA1

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for FNIP1-IL5

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for FNIP1-IL5

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source