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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:FGFR1-RAD23A (FusionGDB2 ID:30264)

Fusion Gene Summary for FGFR1-RAD23A

check button Fusion gene summary
Fusion gene informationFusion gene name: FGFR1-RAD23A
Fusion gene ID: 30264
HgeneTgene
Gene symbol

FGFR1

RAD23A

Gene ID

2260

5886

Gene namefibroblast growth factor receptor 1RAD23 homolog A, nucleotide excision repair protein
SynonymsBFGFR|CD331|CEK|ECCL|FGFBR|FGFR-1|FLG|FLT-2|FLT2|HBGFR|HH2|HRTFDS|KAL2|N-SAM|OGD|bFGF-R-1HHR23A|HR23A
Cytomap

8p11.23

19p13.13

Type of geneprotein-codingprotein-coding
Descriptionfibroblast growth factor receptor 1FGFR1/PLAG1 fusionFMS-like tyrosine kinase 2basic fibroblast growth factor receptor 1fms-related tyrosine kinase 2heparin-binding growth factor receptorhydroxyaryl-protein kinaseproto-oncogene c-FgrUV excision repair protein RAD23 homolog ARAD23, yeast homolog, A
Modification date2020032920200322
UniProtAcc

P11362

.
Ensembl transtripts involved in fusion geneENST00000326324, ENST00000335922, 
ENST00000341462, ENST00000356207, 
ENST00000397091, ENST00000397103, 
ENST00000397108, ENST00000397113, 
ENST00000425967, ENST00000447712, 
ENST00000496629, ENST00000532791, 
ENST00000316856, ENST00000586534, 
ENST00000592268, ENST00000541222, 
ENST00000588826, 
Fusion gene scores* DoF score17 X 24 X 9=367213 X 9 X 9=1053
# samples 2015
** MAII scorelog2(20/3672*10)=-4.19849415363908
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1053*10)=-2.81147103052984
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FGFR1 [Title/Abstract] AND RAD23A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFGFR1(38270911)-RAD23A(13064388), # 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
HgeneFGFR1

GO:0008284

positive regulation of cell proliferation

8663044

HgeneFGFR1

GO:0008543

fibroblast growth factor receptor signaling pathway

8663044

HgeneFGFR1

GO:0010863

positive regulation of phospholipase C activity

18480409

HgeneFGFR1

GO:0018108

peptidyl-tyrosine phosphorylation

8622701|18480409

HgeneFGFR1

GO:0043406

positive regulation of MAP kinase activity

8622701|18480409

HgeneFGFR1

GO:0046777

protein autophosphorylation

8622701

HgeneFGFR1

GO:2000546

positive regulation of endothelial cell chemotaxis to fibroblast growth factor

21885851

TgeneRAD23A

GO:0006289

nucleotide-excision repair

9372924

TgeneRAD23A

GO:0032434

regulation of proteasomal ubiquitin-dependent protein catabolic process

12643283


check buttonFusion gene breakpoints across FGFR1 (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 RAD23A (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/ACN276696FGFR1chr8

38270911

-RAD23Achr19

13064388

+


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Fusion Gene ORF analysis for FGFR1-RAD23A

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-3UTRENST00000326324ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000326324ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000326324ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000335922ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000335922ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000335922ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000341462ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000341462ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000341462ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000356207ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000356207ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000356207ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397091ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397091ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397091ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397103ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397103ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397103ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397108ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397108ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397108ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397113ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397113ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000397113ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000425967ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000425967ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000425967ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000447712ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000447712ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000447712ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000496629ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000496629ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000496629ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000532791ENST00000316856FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000532791ENST00000586534FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-3UTRENST00000532791ENST00000592268FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000326324ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000326324ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000335922ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000335922ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000341462ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000341462ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000356207ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000356207ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397091ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397091ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397103ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397103ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397108ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397108ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397113ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000397113ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000425967ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000425967ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000447712ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000447712ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000496629ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000496629ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000532791ENST00000541222FGFR1chr8

38270911

-RAD23Achr19

13064388

+
intron-intronENST00000532791ENST00000588826FGFR1chr8

38270911

-RAD23Achr19

13064388

+

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 FGFR1-RAD23A


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 FGFR1-RAD23A


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/:38270911/:13064388)
- 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
FGFR1

P11362

.
FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of embryonic development, cell proliferation, differentiation and migration. Required for normal mesoderm patterning and correct axial organization during embryonic development, normal skeletogenesis and normal development of the gonadotropin-releasing hormone (GnRH) neuronal system. Phosphorylates PLCG1, FRS2, GAB1 and SHB. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Promotes phosphorylation of SHC1, STAT1 and PTPN11/SHP2. In the nucleus, enhances RPS6KA1 and CREB1 activity and contributes to the regulation of transcription. FGFR1 signaling is down-regulated by IL17RD/SEF, and by FGFR1 ubiquitination, internalization and degradation. {ECO:0000250|UniProtKB:P16092, ECO:0000269|PubMed:10830168, ECO:0000269|PubMed:11353842, ECO:0000269|PubMed:12181353, ECO:0000269|PubMed:1379697, ECO:0000269|PubMed:1379698, ECO:0000269|PubMed:15117958, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17623664, ECO:0000269|PubMed:18480409, ECO:0000269|PubMed:19224897, ECO:0000269|PubMed:19261810, ECO:0000269|PubMed:19665973, ECO:0000269|PubMed:20133753, ECO:0000269|PubMed:20139426, ECO:0000269|PubMed:21765395, ECO:0000269|PubMed:8622701, ECO:0000269|PubMed:8663044}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 FGFR1-RAD23A


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 FGFR1-RAD23A


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 FGFR1-RAD23A


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 FGFR1-RAD23A


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