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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:CNTNAP3-FRG1 (FusionGDB2 ID:HG79937TG2483)

Fusion Gene Summary for CNTNAP3-FRG1

Fusion gene summary

Fusion gene information	Fusion gene name: CNTNAP3-FRG1
	Fusion gene ID: hg79937tg2483
		Hgene	Tgene
	Gene symbol	CNTNAP3	FRG1
	Gene ID	79937	2483
	Gene name	contactin associated protein family member 3	FSHD region gene 1
	Synonyms	CASPR3\|CNTNAP3A	FRG1A\|FSG1
	Cytomap	('CNTNAP3')('FRG1') 9p12	4q35.2
	Type of gene	protein-coding	protein-coding
	Description	contactin-associated protein-like 3cell recognition molecule Caspr3contactin associated protein like 3	protein FRG1FSHD region gene 1 proteinfacioscapulohumeral muscular dystrophy region gene-1
	Modification date	20200329	20200313
	UniProtAcc	.	Q14331
	Ensembl transtripts involved in fusion gene	ENST00000297668, ENST00000323947, ENST00000358144, ENST00000377656, ENST00000377659, ENST00000377653,
Fusion gene scores	* DoF score	1 X 1 X 1=1	5 X 3 X 5=75
	# samples	1	5
	** MAII score	log2(1/1*10)=3.32192809488736	log2(5/75*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CNTNAP3 [Title/Abstract] AND FRG1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CNTNAP3(39238990)-FRG1(190878553), # samples:1 CNTNAP3(39238990)-FRG1(190881903), # samples:1
Anticipated loss of major functional domain due to fusion event.	CNTNAP3-FRG1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CNTNAP3-FRG1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CNTNAP3-FRG1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. CNTNAP3-FRG1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* 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

Fusion gene breakpoints across CNTNAP3 (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 FRG1 (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-XF-A9T4	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
ChimerDB4	BLCA	TCGA-XF-A9T4	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+

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Fusion Gene ORF analysis for CNTNAP3-FRG1

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
5CDS-3UTR	ENST00000297668	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
5CDS-3UTR	ENST00000323947	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
5CDS-3UTR	ENST00000358144	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
5CDS-3UTR	ENST00000377656	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
5CDS-3UTR	ENST00000377659	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
5CDS-intron	ENST00000297668	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
5CDS-intron	ENST00000323947	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
5CDS-intron	ENST00000358144	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
5CDS-intron	ENST00000377656	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
5CDS-intron	ENST00000377659	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
5UTR-3CDS	ENST00000377653	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
5UTR-3CDS	ENST00000377653	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
5UTR-3UTR	ENST00000377653	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
5UTR-intron	ENST00000377653	ENST00000514482	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
In-frame	ENST00000297668	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
In-frame	ENST00000297668	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
In-frame	ENST00000323947	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
In-frame	ENST00000323947	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
In-frame	ENST00000358144	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
In-frame	ENST00000358144	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
In-frame	ENST00000377656	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
In-frame	ENST00000377656	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+
In-frame	ENST00000377659	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+
In-frame	ENST00000377659	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+

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)
ENST00000297668	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190878553	+	884	464	59	808	249
ENST00000377656	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190878553	+	954	534	129	878	249
ENST00000358144	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190878553	+	602	182	32	526	164
ENST00000323947	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190878553	+	841	421	16	765	249
ENST00000377659	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190878553	+	1049	629	224	973	249
ENST00000297668	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190881903	+	779	464	59	703	214
ENST00000377656	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190881903	+	849	534	129	773	214
ENST00000358144	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190881903	+	497	182	478	14	154
ENST00000323947	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190881903	+	736	421	16	660	214
ENST00000377659	CNTNAP3	chr9	39238990	-	ENST00000226798	FRG1	chr4	190881903	+	944	629	224	868	214

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
ENST00000297668	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+	0.008831367	0.9911686
ENST00000377656	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+	0.011184157	0.9888158
ENST00000358144	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+	0.015236977	0.98476297
ENST00000323947	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+	0.00737954	0.99262047
ENST00000377659	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190878553	+	0.011300257	0.98869973
ENST00000297668	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+	0.021643687	0.9783563
ENST00000377656	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+	0.02690384	0.9730962
ENST00000358144	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+	0.08888291	0.91111714
ENST00000323947	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+	0.016678648	0.9833213
ENST00000377659	ENST00000226798	CNTNAP3	chr9	39238990	-	FRG1	chr4	190881903	+	0.02202492	0.97797513

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Fusion Genomic Features for CNTNAP3-FRG1

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)
CNTNAP3	chr9	39238989	-	FRG1	chr4	190881902	+	0.45564675	0.54435325
CNTNAP3	chr9	39238989	-	FRG1	chr4	190878552	+	0.115748495	0.88425153
CNTNAP3	chr9	39238989	-	FRG1	chr4	190881902	+	0.45564675	0.54435325
CNTNAP3	chr9	39238989	-	FRG1	chr4	190878552	+	0.115748495	0.88425153

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 CNTNAP3-FRG1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:39238990/chr4:190878553)
- 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
.	FRG1 Q14331
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}.	FUNCTION: Binds to mRNA in a sequence-independent manner. May play a role in regulation of pre-mRNA splicing or in the assembly of rRNA into ribosomal subunits. May be involved in mRNA transport. May be involved in epigenetic regulation of muscle differentiation through regulation of activity of the histone-lysine N-methyltransferase KMT5B. {ECO:0000269\|PubMed:11991638, ECO:0000269\|PubMed:15060122, ECO:0000269\|PubMed:20970242, ECO:0000269\|PubMed:21699900, ECO:0000269\|PubMed:23720823}.

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

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

42_48

130

1289.0

Compositional bias

Note=Poly-Ser

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

42_48

130

1289.0

Compositional bias

Note=Poly-Ser

Tgene

FRG1

chr9:39238990

chr4:190878553

ENST00000226798

235_251

144

259.0

Motif

Bipartite nuclear localization signal

Tgene

FRG1

chr9:39238990

chr4:190881903

ENST00000226798

235_251

179

259.0

Motif

Bipartite nuclear localization signal

- 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

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

1015_1203

130

1289.0

Domain

Laminin G-like 4

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

183_364

130

1289.0

Domain

Laminin G-like 1

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

370_545

130

1289.0

Domain

Laminin G-like 2

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

551_583

130

1289.0

Domain

EGF-like 1

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

584_792

130

1289.0

Domain

Fibrinogen C-terminal

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

793_958

130

1289.0

Domain

Laminin G-like 3

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

962_996

130

1289.0

Domain

EGF-like 2

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

1015_1203

130

1289.0

Domain

Laminin G-like 4

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

183_364

130

1289.0

Domain

Laminin G-like 1

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

370_545

130

1289.0

Domain

Laminin G-like 2

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

551_583

130

1289.0

Domain

EGF-like 1

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

584_792

130

1289.0

Domain

Fibrinogen C-terminal

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

793_958

130

1289.0

Domain

Laminin G-like 3

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

962_996

130

1289.0

Domain

EGF-like 2

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

1267_1288

130

1289.0

Topological domain

Cytoplasmic

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

26_1245

130

1289.0

Topological domain

Extracellular

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

1267_1288

130

1289.0

Topological domain

Cytoplasmic

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

26_1245

130

1289.0

Topological domain

Extracellular

Hgene

CNTNAP3

chr9:39238990

chr4:190878553

ENST00000297668

1246_1266

130

1289.0

Transmembrane

Helical

Hgene

CNTNAP3

chr9:39238990

chr4:190881903

ENST00000297668

1246_1266

130

1289.0

Transmembrane

Helical

Tgene

FRG1

chr9:39238990

chr4:190878553

ENST00000226798

8_32

144

259.0

Compositional bias

Note=Lys-rich

Tgene

FRG1

chr9:39238990

chr4:190881903

ENST00000226798

8_32

179

259.0

Compositional bias

Note=Lys-rich

Tgene

FRG1

chr9:39238990

chr4:190878553

ENST00000226798

22_32

144

259.0

Motif

Nuclear localization signal

Tgene

FRG1

chr9:39238990

chr4:190881903

ENST00000226798

22_32

179

259.0

Motif

Nuclear localization signal

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Fusion Gene Sequence for CNTNAP3-FRG1

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.

>17925_17925_1_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000297668_FRG1_chr4_190878553_ENST00000226798_length(transcript)=884nt_BP=464nt
CGGGAGTGAGAGCAGGAGCGACGCAGAGCGGCCGTCGCCGTGCCCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCT
GGGCCGTCCTCAAGGTGCTGCTGCTTCTCCCCACTCAGACTTGGAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGG
CCTCTGCCTTGCCTAGGTCATCCTTCAGCAGCTCCTCAGAGCTGTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATG
GAGCTGGTGGCTGGACTCCACTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCA
CCCAAGGAGGATATGGGAGCTCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAG
AAGAAAGCATCTGGGGGAAAATGGCTTTGTTGGCCTCAAATAGCTGCTTTATTAGATGCAATGAAGCAGGGGACATAGAAGCAAAAAGTA
AAACAGCAGGAGAAGAAGAAATGATCAAGATTAGATCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAG
GAAATGTAAAACAATGTGAAATCAATTATGTAAAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAA
TTCTTAAAAAGGCTCGGAAAGATGGATTTTTGCATGAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGAC

>17925_17925_1_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000297668_FRG1_chr4_190878553_ENST00000226798_length(amino acids)=249AA_BP=135
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWGKMALLASNSCFIRCNEAGDIEAKSKTAGEEEMIKIRSCAERETK

--------------------------------------------------------------
>17925_17925_2_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000297668_FRG1_chr4_190881903_ENST00000226798_length(transcript)=779nt_BP=464nt
CGGGAGTGAGAGCAGGAGCGACGCAGAGCGGCCGTCGCCGTGCCCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCT
GGGCCGTCCTCAAGGTGCTGCTGCTTCTCCCCACTCAGACTTGGAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGG
CCTCTGCCTTGCCTAGGTCATCCTTCAGCAGCTCCTCAGAGCTGTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATG
GAGCTGGTGGCTGGACTCCACTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCA
CCCAAGGAGGATATGGGAGCTCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAG
AAGAAAGCATCTGGATTAGATCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAAT
GTGAAATCAATTATGTAAAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTC
GGAAAGATGGATTTTTGCATGAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTC

>17925_17925_2_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000297668_FRG1_chr4_190881903_ENST00000226798_length(amino acids)=214AA_BP=133
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWIRSCAERETKKKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKIS

--------------------------------------------------------------
>17925_17925_3_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000323947_FRG1_chr4_190878553_ENST00000226798_length(transcript)=841nt_BP=421nt
CCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCTGGGCCGTCCTCAAGGTGCTGCTGCTTCTCCCCACTCAGACTTG
GAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGGCCTCTGCCTTGCCTAGGTCATCCTTCAGCAGCTCCTCAGAGCT
GTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATGGAGCTGGTGGCTGGACTCCACTTGTGTCAAATAAATACCAATG
GCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGATATGGGAGCTCTGACTGGGTGACCAGCTACCT
CCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCTGGGGGAAAATGGCTTTGTTGGCCTCAAATAG
CTGCTTTATTAGATGCAATGAAGCAGGGGACATAGAAGCAAAAAGTAAAACAGCAGGAGAAGAAGAAATGATCAAGATTAGATCCTGTGC
TGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAATGTGAAATCAATTATGTAAAGAAATTTCA
GAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTCGGAAAGATGGATTTTTGCATGAGACGCT
TCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTCTGCCTTATCTTTCTGTGTTTTTTTCTGA

>17925_17925_3_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000323947_FRG1_chr4_190878553_ENST00000226798_length(amino acids)=249AA_BP=135
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWGKMALLASNSCFIRCNEAGDIEAKSKTAGEEEMIKIRSCAERETK

--------------------------------------------------------------
>17925_17925_4_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000323947_FRG1_chr4_190881903_ENST00000226798_length(transcript)=736nt_BP=421nt
CCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCTGGGCCGTCCTCAAGGTGCTGCTGCTTCTCCCCACTCAGACTTG
GAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGGCCTCTGCCTTGCCTAGGTCATCCTTCAGCAGCTCCTCAGAGCT
GTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATGGAGCTGGTGGCTGGACTCCACTTGTGTCAAATAAATACCAATG
GCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGATATGGGAGCTCTGACTGGGTGACCAGCTACCT
CCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCTGGATTAGATCCTGTGCTGAAAGAGAAACCAA
GAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAATGTGAAATCAATTATGTAAAGAAATTTCAGAGCTTCCAAGACCA
CAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTCGGAAAGATGGATTTTTGCATGAGACGCTTCTGGACAGGAGAGC
CAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTCTGCCTTATCTTTCTGTGTTTTTTTCTGAATAAAATATTCAGAG

>17925_17925_4_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000323947_FRG1_chr4_190881903_ENST00000226798_length(amino acids)=214AA_BP=133
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWIRSCAERETKKKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKIS

--------------------------------------------------------------
>17925_17925_5_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000358144_FRG1_chr4_190878553_ENST00000226798_length(transcript)=602nt_BP=182nt
GGACTCCACTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGAT
ATGGGAGCTCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCT
GGGGGAAAATGGCTTTGTTGGCCTCAAATAGCTGCTTTATTAGATGCAATGAAGCAGGGGACATAGAAGCAAAAAGTAAAACAGCAGGAG
AAGAAGAAATGATCAAGATTAGATCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAAC
AATGTGAAATCAATTATGTAAAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGG
CTCGGAAAGATGGATTTTTGCATGAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGT

>17925_17925_5_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000358144_FRG1_chr4_190878553_ENST00000226798_length(amino acids)=164AA_BP=50
MQIDLGERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWGKMALLASNSCFIRCNEAGDIEAKSKTAGEEEMIKIRSCA

--------------------------------------------------------------
>17925_17925_6_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000358144_FRG1_chr4_190881903_ENST00000226798_length(transcript)=497nt_BP=182nt
GGACTCCACTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGAT
ATGGGAGCTCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCT
GGATTAGATCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAATGTGAAATCAATT
ATGTAAAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTCGGAAAGATGGAT
TTTTGCATGAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTCTGCCTTATCTTT

>17925_17925_6_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000358144_FRG1_chr4_190881903_ENST00000226798_length(amino acids)=154AA_BP=1
MNILFRKKHRKIRQKQKSQSLAVSVGFQFGSPVQKRLMQKSIFPSLFKNFTVFFTYFKFVVLEALKFLYIIDFTLFYISFVFFWNVIFFL

--------------------------------------------------------------
>17925_17925_7_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377656_FRG1_chr4_190878553_ENST00000226798_length(transcript)=954nt_BP=534nt
GCTGGTGCGTGAGGAAGAGAGCTAGAGACTGGACAGGGGAGGCAGAGCAGCGTCAGAGCCGCGCAGGGGACGGGAGTGAGAGCAGGAGCG
ACGCAGAGCGGCCGTCGCCGTGCCCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCTGGGCCGTCCTCAAGGTGCTG
CTGCTTCTCCCCACTCAGACTTGGAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGGCCTCTGCCTTGCCTAGGTCA
TCCTTCAGCAGCTCCTCAGAGCTGTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATGGAGCTGGTGGCTGGACTCCA
CTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGATATGGGAGC
TCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCTGGGGGAAA
ATGGCTTTGTTGGCCTCAAATAGCTGCTTTATTAGATGCAATGAAGCAGGGGACATAGAAGCAAAAAGTAAAACAGCAGGAGAAGAAGAA
ATGATCAAGATTAGATCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAATGTGAA
ATCAATTATGTAAAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTCGGAAA
GATGGATTTTTGCATGAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTCTGCCT

>17925_17925_7_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377656_FRG1_chr4_190878553_ENST00000226798_length(amino acids)=249AA_BP=135
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWGKMALLASNSCFIRCNEAGDIEAKSKTAGEEEMIKIRSCAERETK

--------------------------------------------------------------
>17925_17925_8_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377656_FRG1_chr4_190881903_ENST00000226798_length(transcript)=849nt_BP=534nt
GCTGGTGCGTGAGGAAGAGAGCTAGAGACTGGACAGGGGAGGCAGAGCAGCGTCAGAGCCGCGCAGGGGACGGGAGTGAGAGCAGGAGCG
ACGCAGAGCGGCCGTCGCCGTGCCCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCTGGGCCGTCCTCAAGGTGCTG
CTGCTTCTCCCCACTCAGACTTGGAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGGCCTCTGCCTTGCCTAGGTCA
TCCTTCAGCAGCTCCTCAGAGCTGTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATGGAGCTGGTGGCTGGACTCCA
CTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGATATGGGAGC
TCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCTGGATTAGA
TCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAATGTGAAATCAATTATGTAAAG
AAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTCGGAAAGATGGATTTTTGCAT
GAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTCTGCCTTATCTTTCTGTGTTT

>17925_17925_8_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377656_FRG1_chr4_190881903_ENST00000226798_length(amino acids)=214AA_BP=133
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWIRSCAERETKKKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKIS

--------------------------------------------------------------
>17925_17925_9_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377659_FRG1_chr4_190878553_ENST00000226798_length(transcript)=1049nt_BP=629nt
AGAAAGCTGCGGCGCGAGTCCGCGGGGCCGACCTCGGAGACGCAGCTGGGGCCGGGCGCGGCTTGGCGGGAGGGTCTGCAGCGCCGAGGG
AGGCTGCTGGTGCGTGAGGAAGAGAGCTAGAGACTGGACAGGGGAGGCAGAGCAGCGTCAGAGCCGCGCAGGGGACGGGAGTGAGAGCAG
GAGCGACGCAGAGCGGCCGTCGCCGTGCCCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCTGGGCCGTCCTCAAGG
TGCTGCTGCTTCTCCCCACTCAGACTTGGAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGGCCTCTGCCTTGCCTA
GGTCATCCTTCAGCAGCTCCTCAGAGCTGTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATGGAGCTGGTGGCTGGA
CTCCACTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGATATG
GGAGCTCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCTGGG
GGAAAATGGCTTTGTTGGCCTCAAATAGCTGCTTTATTAGATGCAATGAAGCAGGGGACATAGAAGCAAAAAGTAAAACAGCAGGAGAAG
AAGAAATGATCAAGATTAGATCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAAT
GTGAAATCAATTATGTAAAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTC
GGAAAGATGGATTTTTGCATGAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTC

>17925_17925_9_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377659_FRG1_chr4_190878553_ENST00000226798_length(amino acids)=249AA_BP=135
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWGKMALLASNSCFIRCNEAGDIEAKSKTAGEEEMIKIRSCAERETK

--------------------------------------------------------------
>17925_17925_10_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377659_FRG1_chr4_190881903_ENST00000226798_length(transcript)=944nt_BP=629nt
AGAAAGCTGCGGCGCGAGTCCGCGGGGCCGACCTCGGAGACGCAGCTGGGGCCGGGCGCGGCTTGGCGGGAGGGTCTGCAGCGCCGAGGG
AGGCTGCTGGTGCGTGAGGAAGAGAGCTAGAGACTGGACAGGGGAGGCAGAGCAGCGTCAGAGCCGCGCAGGGGACGGGAGTGAGAGCAG
GAGCGACGCAGAGCGGCCGTCGCCGTGCCCGGGTCTCAGGGCGCCTGGCTGAAGTGAGCATGGCTTCAGTGGCCTGGGCCGTCCTCAAGG
TGCTGCTGCTTCTCCCCACTCAGACTTGGAGCCCCGTGGGAGCAGGAAATCCACCTGACTGTGATGCCCCACTGGCCTCTGCCTTGCCTA
GGTCATCCTTCAGCAGCTCCTCAGAGCTGTCCAGCAGCCACGGCCCGGGGTTTTCAAGGCTTAATCGAAGAGATGGAGCTGGTGGCTGGA
CTCCACTTGTGTCAAATAAATACCAATGGCTGCAAATTGACCTTGGAGAGAGAATGGAGGTCACTGCTGTCGCCACCCAAGGAGGATATG
GGAGCTCTGACTGGGTGACCAGCTACCTCCTGATGTTCAGTGATGGTGGGAGAAACTGGAAGCAGTATCGCCGAGAAGAAAGCATCTGGA
TTAGATCCTGTGCTGAAAGAGAAACCAAGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAATGTGAAATCAATTATG
TAAAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGACAGTAAAATTCTTAAAAAGGCTCGGAAAGATGGATTTT
TGCATGAGACGCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACAGATACTGCAAGTGACTGGGATTTTTGTTTCTGCCTTATCTTTCTG

>17925_17925_10_CNTNAP3-FRG1_CNTNAP3_chr9_39238990_ENST00000377659_FRG1_chr4_190881903_ENST00000226798_length(amino acids)=214AA_BP=133
MAEVSMASVAWAVLKVLLLLPTQTWSPVGAGNPPDCDAPLASALPRSSFSSSSELSSSHGPGFSRLNRRDGAGGWTPLVSNKYQWLQIDL
GERMEVTAVATQGGYGSSDWVTSYLLMFSDGGRNWKQYRREESIWIRSCAERETKKKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKIS

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

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Fusion Gene PPI Analysis for CNTNAP3-FRG1

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

- 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

Top

Related Drugs for CNTNAP3-FRG1

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 CNTNAP3-FRG1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene		C0238288	Muscular Dystrophy, Facioscapulohumeral	3	ORPHANET

Fusion Gene Studies in Kim Lab

Fusion gene:CNTNAP3-FRG1 (FusionGDB2 ID:HG79937TG2483)

Fusion Gene Summary for CNTNAP3-FRG1

Fusion Gene ORF analysis for CNTNAP3-FRG1

Fusion Genomic Features for CNTNAP3-FRG1

Fusion Protein Features for CNTNAP3-FRG1

Fusion Gene Sequence for CNTNAP3-FRG1

Fusion Gene PPI Analysis for CNTNAP3-FRG1

Related Drugs for CNTNAP3-FRG1

Related Diseases for CNTNAP3-FRG1

Fusion Gene Studies
in Kim Lab