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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:FN1-LYN (FusionGDB2 ID:30824)

Fusion Gene Summary for FN1-LYN

check button Fusion gene summary
Fusion gene informationFusion gene name: FN1-LYN
Fusion gene ID: 30824
HgeneTgene
Gene symbol

FN1

LYN

Gene ID

2335

4067

Gene namefibronectin 1LYN proto-oncogene, Src family tyrosine kinase
SynonymsCIG|ED-B|FINC|FN|FNZ|GFND|GFND2|LETS|MSF|SMDCFJTK8|p53Lyn|p56Lyn
Cytomap

2q35

8q12.1

Type of geneprotein-codingprotein-coding
Descriptionfibronectincold-insoluble globulinepididymis secretory sperm binding proteinmigration-stimulating factortyrosine-protein kinase Lynlck/Yes-related novel protein tyrosine kinasev-yes-1 Yamaguchi sarcoma viral related oncogene homolog
Modification date2020032920200327
UniProtAcc

P02751

P0DP58

Ensembl transtripts involved in fusion geneENST00000323926, ENST00000336916, 
ENST00000345488, ENST00000346544, 
ENST00000354785, ENST00000356005, 
ENST00000357009, ENST00000357867, 
ENST00000359671, ENST00000421182, 
ENST00000426059, ENST00000432072, 
ENST00000443816, ENST00000446046, 
ENST00000490833, 		ENST00000519728, 
ENST00000520220, ENST00000420292, 
Fusion gene scores* DoF score47 X 49 X 13=2993913 X 14 X 7=1274
# samples 4815
** MAII scorelog2(48/29939*10)=-5.96284781832542
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1274*10)=-3.08633087176042
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FN1 [Title/Abstract] AND LYN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFN1(216248136)-LYN(56922700), # samples:1
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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneFN1

GO:0001932

regulation of protein phosphorylation

11792823

HgeneFN1

GO:0008284

positive regulation of cell proliferation

25834989

HgeneFN1

GO:0010628

positive regulation of gene expression

25834989

HgeneFN1

GO:0018149

peptide cross-linking

3997886

HgeneFN1

GO:0034446

substrate adhesion-dependent cell spreading

16236823

HgeneFN1

GO:0035987

endodermal cell differentiation

23154389

HgeneFN1

GO:0048146

positive regulation of fibroblast proliferation

25834989

HgeneFN1

GO:0051702

interaction with symbiont

12167537|12421310|19429745

HgeneFN1

GO:0070372

regulation of ERK1 and ERK2 cascade

11792823

HgeneFN1

GO:1901166

neural crest cell migration involved in autonomic nervous system development

26571399

HgeneFN1

GO:1904237

positive regulation of substrate-dependent cell migration, cell attachment to substrate

25834989

HgeneFN1

GO:2001202

negative regulation of transforming growth factor-beta secretion

25834989

TgeneLYN

GO:0006468

protein phosphorylation

11517336

TgeneLYN

GO:0006974

cellular response to DNA damage stimulus

10891478|11517336

TgeneLYN

GO:0018108

peptidyl-tyrosine phosphorylation

7682714|11782428

TgeneLYN

GO:0046777

protein autophosphorylation

7682714

TgeneLYN

GO:0051272

positive regulation of cellular component movement

16467205

TgeneLYN

GO:0070304

positive regulation of stress-activated protein kinase signaling cascade

10891478


check buttonFusion gene breakpoints across FN1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

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
ChiTaRS5.0N/ACN419543FN1chr2

216248136

-LYNchr8

56922700

+


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Fusion Gene ORF analysis for FN1-LYN

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
intron-3UTRENST00000323926ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000323926ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000336916ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000336916ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000345488ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000345488ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000346544ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000346544ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000354785ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000354785ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000356005ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000356005ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000357009ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000357009ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000357867ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000357867ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000359671ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000359671ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000421182ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000421182ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000426059ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000426059ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000432072ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000432072ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000443816ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000443816ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000446046ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000446046ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000490833ENST00000519728FN1chr2

216248136

-LYNchr8

56922700

+
intron-3UTRENST00000490833ENST00000520220FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000323926ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000336916ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000345488ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000346544ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000354785ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000356005ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000357009ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000357867ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000359671ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000421182ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000426059ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000432072ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000443816ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000446046ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+
intron-intronENST00000490833ENST00000420292FN1chr2

216248136

-LYNchr8

56922700

+

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)

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

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Fusion Genomic Features for FN1-LYN


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.

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 FN1-LYN


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/:216248136/:56922700)
- 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
FN1

P02751

LYN

P0DP58

FUNCTION: Fibronectins bind cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin (PubMed:3024962, PubMed:3900070, PubMed:3593230, PubMed:7989369). Fibronectins are involved in cell adhesion, cell motility, opsonization, wound healing, and maintenance of cell shape (PubMed:3024962, PubMed:3900070, PubMed:3593230, PubMed:7989369). Involved in osteoblast compaction through the fibronectin fibrillogenesis cell-mediated matrix assembly process, essential for osteoblast mineralization (By similarity). Participates in the regulation of type I collagen deposition by osteoblasts (By similarity). Acts as a ligand for the LILRB4 receptor, inhibiting FCGR1A/CD64-mediated monocyte activation (PubMed:34089617). {ECO:0000250|UniProtKB:P11276, ECO:0000269|PubMed:3024962, ECO:0000269|PubMed:34089617, ECO:0000269|PubMed:3593230, ECO:0000269|PubMed:3900070, ECO:0000269|PubMed:7989369}.; FUNCTION: [Anastellin]: Binds fibronectin and induces fibril formation. This fibronectin polymer, named superfibronectin, exhibits enhanced adhesive properties. Both anastellin and superfibronectin inhibit tumor growth, angiogenesis and metastasis. Anastellin activates p38 MAPK and inhibits lysophospholipid signaling. {ECO:0000269|PubMed:11209058, ECO:0000269|PubMed:15665290, ECO:0000269|PubMed:19379667, ECO:0000269|PubMed:8114919}.FUNCTION: Acts in different tissues through interaction to nicotinic acetylcholine receptors (nAChRs) (PubMed:21252236). The proposed role as modulator of nAChR activity seems to be dependent on the nAChR subtype and stoichiometry, and to involve an effect on nAChR trafficking and its cell surface expression, and on single channel properties of the nAChR inserted in the plasma membrane. Modulates functional properties of nicotinic acetylcholine receptors (nAChRs) to prevent excessive excitation, and hence neurodegeneration. Enhances desensitization by increasing both the rate and extent of desensitization of alpha-4:beta-2-containing nAChRs and slowing recovery from desensitization. Promotes large amplitude ACh-evoked currents through alpha-4:beta-2 nAChRs. Is involved in regulation of the nAChR pentameric assembly in the endoplasmic reticulum. Shifts stoichiometry from high sensitivity alpha-4(2):beta-2(3) to low sensitivity alpha-4(3):beta-2(2) nAChR (By similarity). In vitro modulates alpha-3:beta-4-containing nAChRs. Reduces cell surface expression of (alpha-3:beta-4)(2):beta-4 and (alpha-3:beta-4)(2):alpha-5 nAChRs suggesting an interaction with nAChR alpha-3(-):(+)beta-4 subunit interfaces and an allosteric mode. Corresponding single channel effects characterized by decreased unitary conductance, altered burst proportions and enhanced desensitization/inactivation seem to depend on nAChR alpha:alpha subunit interfaces and are greater in (alpha-3:beta-2)(2):alpha-3 when compared to (alpha-3:beta-2)(2):alpha-5 nAChRs (PubMed:28100642). Prevents plasticity in the primary visual cortex late in life (By similarity). {ECO:0000250|UniProtKB:P0DP60, ECO:0000269|PubMed:21252236, ECO:0000269|PubMed:28100642}.

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


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Fusion Gene Sequence for FN1-LYN


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.

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Fusion Gene PPI Analysis for FN1-LYN


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


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 FN1-LYN


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 FN1-LYN


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