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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:FNIP1-CYP3A4 (FusionGDB2 ID:30948)

Fusion Gene Summary for FNIP1-CYP3A4

check button Fusion gene summary
Fusion gene informationFusion gene name: FNIP1-CYP3A4
Fusion gene ID: 30948
HgeneTgene
Gene symbol

FNIP1

CYP3A4

Gene ID

96459

1576

Gene namefolliculin interacting protein 1cytochrome P450 family 3 subfamily A member 4
Synonyms-CP33|CP34|CYP3A|CYP3A3|CYPIIIA3|CYPIIIA4|HLP|NF-25|P450C3|P450PCN1
Cytomap

5q31.1

7q22.1

Type of geneprotein-codingprotein-coding
Descriptionfolliculin-interacting protein 1cytochrome P450 3A41,4-cineole 2-exo-monooxygenase1,8-cineole 2-exo-monooxygenaseP450-III, steroid induciblealbendazole monooxygenasealbendazole monooxygenase (sulfoxide-forming)albendazole sulfoxidasecholesterol 25-hydroxylasecytochrome P450 3A3
Modification date2020032720200327
UniProtAcc

Q8TF40

Q9HB55

Ensembl transtripts involved in fusion geneENST00000307954, ENST00000307968, 
ENST00000510461, ENST00000511848, 
ENST00000354593, ENST00000336411, 
Fusion gene scores* DoF score15 X 11 X 10=16504 X 4 X 3=48
# samples 184
** MAII scorelog2(18/1650*10)=-3.1963972128035
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

PubMed: FNIP1 [Title/Abstract] AND CYP3A4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFNIP1(131132523)-CYP3A4(99355851), # samples:1
Anticipated loss of major functional domain due to fusion event.FNIP1-CYP3A4 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
FNIP1-CYP3A4 seems lost the major protein functional domain in Tgene 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneFNIP1

GO:0000122

negative regulation of transcription by RNA polymerase II

21209915

HgeneFNIP1

GO:0001932

regulation of protein phosphorylation

18663353

HgeneFNIP1

GO:0031334

positive regulation of protein complex assembly

25126726

HgeneFNIP1

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19914239

TgeneCYP3A4

GO:0002933

lipid hydroxylation

14559847

TgeneCYP3A4

GO:0008202

steroid metabolic process

14559847

TgeneCYP3A4

GO:0008210

estrogen metabolic process

11555828|12865317|14559847

TgeneCYP3A4

GO:0009822

alkaloid catabolic process

15039299

TgeneCYP3A4

GO:0016098

monoterpenoid metabolic process

16401082

TgeneCYP3A4

GO:0017144

drug metabolic process

15327587|19219744

TgeneCYP3A4

GO:0042572

retinol metabolic process

10681376

TgeneCYP3A4

GO:0042573

retinoic acid metabolic process

11093772

TgeneCYP3A4

GO:0042737

drug catabolic process

15039299

TgeneCYP3A4

GO:0042738

exogenous drug catabolic process

18619574

TgeneCYP3A4

GO:0046483

heterocycle metabolic process

15327587

TgeneCYP3A4

GO:0055114

oxidation-reduction process

16401082|19219744

TgeneCYP3A4

GO:0070989

oxidative demethylation

15039299|18619574


check buttonFusion 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.
all structure

check buttonFusion gene breakpoints across CYP3A4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LIHCTCGA-DD-A73F-01AFNIP1chr5

131132523

-CYP3A4chr7

99355851

-


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Fusion Gene ORF analysis for FNIP1-CYP3A4

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000307954ENST00000354593FNIP1chr5

131132523

-CYP3A4chr7

99355851

-
Frame-shiftENST00000307968ENST00000354593FNIP1chr5

131132523

-CYP3A4chr7

99355851

-
Frame-shiftENST00000510461ENST00000354593FNIP1chr5

131132523

-CYP3A4chr7

99355851

-
Frame-shiftENST00000511848ENST00000354593FNIP1chr5

131132523

-CYP3A4chr7

99355851

-
In-frameENST00000307954ENST00000336411FNIP1chr5

131132523

-CYP3A4chr7

99355851

-
In-frameENST00000307968ENST00000336411FNIP1chr5

131132523

-CYP3A4chr7

99355851

-
In-frameENST00000510461ENST00000336411FNIP1chr5

131132523

-CYP3A4chr7

99355851

-
In-frameENST00000511848ENST00000336411FNIP1chr5

131132523

-CYP3A4chr7

99355851

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000307968FNIP1chr5131132523-ENST00000336411CYP3A4chr799355851-64592161054
ENST00000307954FNIP1chr5131132523-ENST00000336411CYP3A4chr799355851-674121190263
ENST00000510461FNIP1chr5131132523-ENST00000336411CYP3A4chr799355851-7411882575168
ENST00000511848FNIP1chr5131132523-ENST00000336411CYP3A4chr799355851-7401872565068

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000307968ENST00000336411FNIP1chr5131132523-CYP3A4chr799355851-0.96798130.032018688
ENST00000307954ENST00000336411FNIP1chr5131132523-CYP3A4chr799355851-0.97640250.023597522
ENST00000510461ENST00000336411FNIP1chr5131132523-CYP3A4chr799355851-0.91458370.085416354
ENST00000511848ENST00000336411FNIP1chr5131132523-CYP3A4chr799355851-0.93124190.068758085

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Fusion Genomic Features for FNIP1-CYP3A4


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution 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.
genomic feature

check buttonDistribution 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-CYP3A4


check button 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/chr7:99355851)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
FNIP1

Q8TF40

CYP3A4

Q9HB55

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: Exhibits low testosterone 6-beta-hydroxylase activity.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneFNIP1chr5:131132523chr7:99355851ENST00000307968-11796_99301139.0Compositional biasNote=Poly-Ser
HgeneFNIP1chr5:131132523chr7:99355851ENST00000510461-11896_99301167.0Compositional biasNote=Poly-Ser
HgeneFNIP1chr5:131132523chr7:99355851ENST00000511848-11396_9930509.0Compositional biasNote=Poly-Ser
HgeneFNIP1chr5:131132523chr7:99355851ENST00000307968-1171102_1157301139.0DomaindDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000307968-11737_478301139.0DomainuDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000307968-117486_1092301139.0DomaincDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000510461-1181102_1157301167.0DomaindDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000510461-11837_478301167.0DomainuDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000510461-118486_1092301167.0DomaincDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000511848-1131102_115730509.0DomaindDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000511848-11337_47830509.0DomainuDENN FNIP1/2-type
HgeneFNIP1chr5:131132523chr7:99355851ENST00000511848-113486_109230509.0DomaincDENN FNIP1/2-type
TgeneCYP3A4chr5:131132523chr7:99355851ENST0000033641111132_22472504.0TransmembraneHelical


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Fusion Gene Sequence for FNIP1-CYP3A4


check button 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.
>30948_30948_1_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000307954_CYP3A4_chr7_99355851_ENST00000336411_length(transcript)=674nt_BP=121nt
GGAGCGACCCCTGCCTGGCCGTGGCTAGCATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCC
GCGACGCCCGGGACCCAGATTGCGGGTTCAGATCCCCCTGAAATTAAGCTTAGGAGGACTTCTTCAACCAGAAAAACCCGTTGTTCTAAA
GGTTGAGTCAAGGGATGGCACCGTAAGTGGAGCCTGAATTTTCCTAAGGACTTCTGCTTTGCTCTTCAAGAAATCTGTGCCTGAGAACAC
CAGAGACCTCAAATTACTTTGTGAATAGAACTCTGAAATGAAGATGGGCTTCATCCAATGGACTGCATAAATAACCGGGGATTCTGTACA
TGCATTGAGCTCTCTCATTGTCTGTGTAGAGTGTTATACTTGGGAATATAAAGGAGGTGACCAAATCAGTGTGAGGAGGTAGATTTGGCT
CCTCTGCTTCTCACGGGACTATTTCCACCACCCCCAGTTAGCACCATTAACTCCTCCTGAGCTCTGATAAGAGAATCAACATTTCTCAAT
AATTTCCTCCACAAATTATTAATGAAAATAAGAATTATTTTGATGGCTCTAACAATGACATTTATATCACATGTTTTCTCTGGAGTATTC

>30948_30948_1_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000307954_CYP3A4_chr7_99355851_ENST00000336411_length(amino acids)=63AA_BP=1

--------------------------------------------------------------
>30948_30948_2_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000307968_CYP3A4_chr7_99355851_ENST00000336411_length(transcript)=645nt_BP=92nt
ATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCCGCGACGCCCGGGACCCAGATTGCGGGTTC
AGATCCCCCTGAAATTAAGCTTAGGAGGACTTCTTCAACCAGAAAAACCCGTTGTTCTAAAGGTTGAGTCAAGGGATGGCACCGTAAGTG
GAGCCTGAATTTTCCTAAGGACTTCTGCTTTGCTCTTCAAGAAATCTGTGCCTGAGAACACCAGAGACCTCAAATTACTTTGTGAATAGA
ACTCTGAAATGAAGATGGGCTTCATCCAATGGACTGCATAAATAACCGGGGATTCTGTACATGCATTGAGCTCTCTCATTGTCTGTGTAG
AGTGTTATACTTGGGAATATAAAGGAGGTGACCAAATCAGTGTGAGGAGGTAGATTTGGCTCCTCTGCTTCTCACGGGACTATTTCCACC
ACCCCCAGTTAGCACCATTAACTCCTCCTGAGCTCTGATAAGAGAATCAACATTTCTCAATAATTTCCTCCACAAATTATTAATGAAAAT
AAGAATTATTTTGATGGCTCTAACAATGACATTTATATCACATGTTTTCTCTGGAGTATTCTATAAGTTTTATGTTAAATCAATAAAGAC

>30948_30948_2_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000307968_CYP3A4_chr7_99355851_ENST00000336411_length(amino acids)=54AA_BP=1

--------------------------------------------------------------
>30948_30948_3_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000510461_CYP3A4_chr7_99355851_ENST00000336411_length(transcript)=741nt_BP=188nt
ATATGACTGAGGCGCCCATGGGGGTGGCGGGGCGGCTGTAGGAGCAGGGGCCTAGCAAGCGCCCAGCGGAGCGACCCCTGCCTGGCCGTG
GCTAGCATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCCGCGACGCCCGGGACCCAGATTGC
GGGTTCAGATCCCCCTGAAATTAAGCTTAGGAGGACTTCTTCAACCAGAAAAACCCGTTGTTCTAAAGGTTGAGTCAAGGGATGGCACCG
TAAGTGGAGCCTGAATTTTCCTAAGGACTTCTGCTTTGCTCTTCAAGAAATCTGTGCCTGAGAACACCAGAGACCTCAAATTACTTTGTG
AATAGAACTCTGAAATGAAGATGGGCTTCATCCAATGGACTGCATAAATAACCGGGGATTCTGTACATGCATTGAGCTCTCTCATTGTCT
GTGTAGAGTGTTATACTTGGGAATATAAAGGAGGTGACCAAATCAGTGTGAGGAGGTAGATTTGGCTCCTCTGCTTCTCACGGGACTATT
TCCACCACCCCCAGTTAGCACCATTAACTCCTCCTGAGCTCTGATAAGAGAATCAACATTTCTCAATAATTTCCTCCACAAATTATTAAT
GAAAATAAGAATTATTTTGATGGCTCTAACAATGACATTTATATCACATGTTTTCTCTGGAGTATTCTATAAGTTTTATGTTAAATCAAT

>30948_30948_3_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000510461_CYP3A4_chr7_99355851_ENST00000336411_length(amino acids)=68AA_BP=1

--------------------------------------------------------------
>30948_30948_4_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000511848_CYP3A4_chr7_99355851_ENST00000336411_length(transcript)=740nt_BP=187nt
TATGACTGAGGCGCCCATGGGGGTGGCGGGGCGGCTGTAGGAGCAGGGGCCTAGCAAGCGCCCAGCGGAGCGACCCCTGCCTGGCCGTGG
CTAGCATGGCCCCTACGCTGTTCCAGAAGCTCTTCAGCAAGAGGACCGGGCTGGGCGCGCCCGGCCGCGACGCCCGGGACCCAGATTGCG
GGTTCAGATCCCCCTGAAATTAAGCTTAGGAGGACTTCTTCAACCAGAAAAACCCGTTGTTCTAAAGGTTGAGTCAAGGGATGGCACCGT
AAGTGGAGCCTGAATTTTCCTAAGGACTTCTGCTTTGCTCTTCAAGAAATCTGTGCCTGAGAACACCAGAGACCTCAAATTACTTTGTGA
ATAGAACTCTGAAATGAAGATGGGCTTCATCCAATGGACTGCATAAATAACCGGGGATTCTGTACATGCATTGAGCTCTCTCATTGTCTG
TGTAGAGTGTTATACTTGGGAATATAAAGGAGGTGACCAAATCAGTGTGAGGAGGTAGATTTGGCTCCTCTGCTTCTCACGGGACTATTT
CCACCACCCCCAGTTAGCACCATTAACTCCTCCTGAGCTCTGATAAGAGAATCAACATTTCTCAATAATTTCCTCCACAAATTATTAATG
AAAATAAGAATTATTTTGATGGCTCTAACAATGACATTTATATCACATGTTTTCTCTGGAGTATTCTATAAGTTTTATGTTAAATCAATA

>30948_30948_4_FNIP1-CYP3A4_FNIP1_chr5_131132523_ENST00000511848_CYP3A4_chr7_99355851_ENST00000336411_length(amino acids)=68AA_BP=1

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

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Fusion Gene PPI Analysis for FNIP1-CYP3A4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneFNIP1chr5:131132523chr7:99355851ENST00000307968-117929_116630.6666666666666681139.0HSP90AA1
HgeneFNIP1chr5:131132523chr7:99355851ENST00000510461-118929_116630.6666666666666681167.0HSP90AA1
HgeneFNIP1chr5:131132523chr7:99355851ENST00000511848-113929_116630.666666666666668509.0HSP90AA1


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for FNIP1-CYP3A4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for FNIP1-CYP3A4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource