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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:CTBP1-FGFR3 (FusionGDB2 ID:20035)

Fusion Gene Summary for CTBP1-FGFR3

check button Fusion gene summary
Fusion gene informationFusion gene name: CTBP1-FGFR3
Fusion gene ID: 20035
HgeneTgene
Gene symbol

CTBP1

FGFR3

Gene ID

1487

2261

Gene nameC-terminal binding protein 1fibroblast growth factor receptor 3
SynonymsBARS|HADDTSACH|CD333|CEK2|HSFGFR3EX|JTK4
Cytomap

4p16.3

4p16.3

Type of geneprotein-codingprotein-coding
DescriptionC-terminal-binding protein 1brefeldin A-ribosylated substratefibroblast growth factor receptor 3FGFR-3fibroblast growth factor receptor 3 variant 4fibroblast growth factor receptor 3-Shydroxyaryl-protein kinasetyrosine kinase JTK4
Modification date2020032820200313
UniProtAcc

Q13363

P22607

Ensembl transtripts involved in fusion geneENST00000290921, ENST00000382952, 
ENST00000515690, ENST00000510568, 
ENST00000260795, ENST00000340107, 
ENST00000352904, ENST00000412135, 
ENST00000440486, ENST00000474521, 
ENST00000481110, 
Fusion gene scores* DoF score14 X 12 X 7=11766 X 11 X 9=594
# samples 149
** MAII scorelog2(14/1176*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/594*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTBP1 [Title/Abstract] AND FGFR3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTBP1(1225500)-FGFR3(1803203), # samples:1
CTBP1(1225866)-FGFR3(1801538), # samples:1
CTBP1(1231970)-FGFR3(1802494), # 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
TgeneFGFR3

GO:0008543

fibroblast growth factor receptor signaling pathway

8663044

TgeneFGFR3

GO:0018108

peptidyl-tyrosine phosphorylation

11294897

TgeneFGFR3

GO:0046777

protein autophosphorylation

11294897


check buttonFusion gene breakpoints across CTBP1 (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 FGFR3 (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
ChimerDB4BRCATCGA-D8-A1JG-01BCTBP1chr4

1225500

-FGFR3chr4

1803203

-
ChimerDB4BRCATCGA-D8-A1JG-01BCTBP1chr4

1225866

-FGFR3chr4

1801538

-
ChimerDB4BRCATCGA-D8-A1JG-01BCTBP1chr4

1231970

-FGFR3chr4

1802494

-


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Fusion Gene ORF analysis for CTBP1-FGFR3

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
5CDS-intronENST00000290921ENST00000260795CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000290921ENST00000340107CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000290921ENST00000352904CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000290921ENST00000412135CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000290921ENST00000440486CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000290921ENST00000474521CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000290921ENST00000481110CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000382952ENST00000260795CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000382952ENST00000340107CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000382952ENST00000352904CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000382952ENST00000412135CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000382952ENST00000440486CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000382952ENST00000474521CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5CDS-intronENST00000382952ENST00000481110CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5UTR-intronENST00000515690ENST00000260795CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5UTR-intronENST00000515690ENST00000340107CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5UTR-intronENST00000515690ENST00000352904CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5UTR-intronENST00000515690ENST00000412135CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5UTR-intronENST00000515690ENST00000440486CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5UTR-intronENST00000515690ENST00000474521CTBP1chr4

1231970

-FGFR3chr4

1802494

-
5UTR-intronENST00000515690ENST00000481110CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-3CDSENST00000290921ENST00000260795CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000290921ENST00000340107CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000290921ENST00000352904CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000290921ENST00000412135CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000290921ENST00000440486CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000290921ENST00000481110CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000382952ENST00000260795CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000382952ENST00000340107CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000382952ENST00000352904CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000382952ENST00000412135CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000382952ENST00000440486CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000382952ENST00000481110CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000510568ENST00000260795CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000510568ENST00000340107CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000510568ENST00000352904CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000510568ENST00000412135CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000510568ENST00000440486CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000510568ENST00000481110CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000515690ENST00000260795CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000515690ENST00000340107CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000515690ENST00000352904CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000515690ENST00000412135CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000515690ENST00000440486CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-3CDSENST00000515690ENST00000481110CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-intronENST00000290921ENST00000260795CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000290921ENST00000340107CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000290921ENST00000352904CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000290921ENST00000412135CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000290921ENST00000440486CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000290921ENST00000474521CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-intronENST00000290921ENST00000474521CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000290921ENST00000481110CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000382952ENST00000260795CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000382952ENST00000340107CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000382952ENST00000352904CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000382952ENST00000412135CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000382952ENST00000440486CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000382952ENST00000474521CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-intronENST00000382952ENST00000474521CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000382952ENST00000481110CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000260795CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000260795CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-intronENST00000510568ENST00000340107CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000340107CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-intronENST00000510568ENST00000352904CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000352904CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-intronENST00000510568ENST00000412135CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000412135CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-intronENST00000510568ENST00000440486CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000440486CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-intronENST00000510568ENST00000474521CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-intronENST00000510568ENST00000474521CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000474521CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-intronENST00000510568ENST00000481110CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000510568ENST00000481110CTBP1chr4

1231970

-FGFR3chr4

1802494

-
intron-intronENST00000515690ENST00000260795CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000515690ENST00000340107CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000515690ENST00000352904CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000515690ENST00000412135CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000515690ENST00000440486CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000515690ENST00000474521CTBP1chr4

1225500

-FGFR3chr4

1803203

-
intron-intronENST00000515690ENST00000474521CTBP1chr4

1225866

-FGFR3chr4

1801538

-
intron-intronENST00000515690ENST00000481110CTBP1chr4

1225866

-FGFR3chr4

1801538

-

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 CTBP1-FGFR3


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 CTBP1-FGFR3


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/:1225500/:1803203)
- 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
CTBP1

Q13363

FGFR3

P22607

FUNCTION: Corepressor targeting diverse transcription regulators such as GLIS2 or BCL6. Has dehydrogenase activity. Involved in controlling the equilibrium between tubular and stacked structures in the Golgi complex. Functions in brown adipose tissue (BAT) differentiation. {ECO:0000269|PubMed:12419229, ECO:0000269|PubMed:15542832, ECO:0000269|PubMed:18212045, ECO:0000269|PubMed:19103759, ECO:0000269|PubMed:9858600}.FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation and apoptosis. Plays an essential role in the regulation of chondrocyte differentiation, proliferation and apoptosis, and is required for normal skeleton development. Regulates both osteogenesis and postnatal bone mineralization by osteoblasts. Promotes apoptosis in chondrocytes, but can also promote cancer cell proliferation. Required for normal development of the inner ear. Phosphorylates PLCG1, CBL and FRS2. 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. Plays a role in the regulation of vitamin D metabolism. Mutations that lead to constitutive kinase activation or impair normal FGFR3 maturation, internalization and degradation lead to aberrant signaling. Over-expressed or constitutively activated FGFR3 promotes activation of PTPN11/SHP2, STAT1, STAT5A and STAT5B. Secreted isoform 3 retains its capacity to bind FGF1 and FGF2 and hence may interfere with FGF signaling. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:11294897, ECO:0000269|PubMed:11703096, ECO:0000269|PubMed:14534538, ECO:0000269|PubMed:16410555, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17145761, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17509076, ECO:0000269|PubMed:17561467, ECO:0000269|PubMed:19088846, ECO:0000269|PubMed:19286672, ECO:0000269|PubMed:8663044}.

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 CTBP1-FGFR3


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 CTBP1-FGFR3


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 CTBP1-FGFR3


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 CTBP1-FGFR3


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