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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:RBFOX1-LAMA5 (FusionGDB2 ID:HG54715TG3911)

Fusion Gene Summary for RBFOX1-LAMA5

Fusion gene summary

Fusion gene information	Fusion gene name: RBFOX1-LAMA5
	Fusion gene ID: hg54715tg3911
		Hgene	Tgene
	Gene symbol	RBFOX1	LAMA5
	Gene ID	54715	3911
	Gene name	RNA binding fox-1 homolog 1	laminin subunit alpha 5
	Synonyms	2BP1\|A2BP1\|FOX-1\|FOX1\|HRNBP1	-
	Cytomap	('RBFOX1')('LAMA5') 16p13.3	20q13.33
	Type of gene	protein-coding	protein-coding
	Description	RNA binding protein fox-1 homolog 1RNA binding protein, fox-1 homolog 1ataxin 2-binding protein 1fox-1 homolog Afox-1-like RNA-binding protein 1hexaribonucleotide binding protein 1 isoform alphahexaribonucleotide binding protein 1 isoform betahexar	laminin subunit alpha-5laminin alpha-5 chainlaminin-10 subunit alphalaminin-11 subunit alphalaminin-15 subunit alpha
	Modification date	20200313	20200313
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000311745, ENST00000340209, ENST00000355637, ENST00000422070, ENST00000436368, ENST00000535565, ENST00000547338, ENST00000547372, ENST00000547427, ENST00000550418, ENST00000552089, ENST00000553186,
Fusion gene scores	* DoF score	19 X 19 X 1=361	12 X 14 X 8=1344
	# samples	19	15
	** MAII score	log2(19/361*10)=-0.925999418556223 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/1344*10)=-3.16349873228288 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: RBFOX1 [Title/Abstract] AND LAMA5 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	RBFOX1(7331837)-LAMA5(60886103), # 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)

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
Tgene	LAMA5	GO:0016477	cell migration	11821406
Tgene	LAMA5	GO:0034446	substrate adhesion-dependent cell spreading	16236823

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
ChiTaRS5.0	N/A	EC556353	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+

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Fusion Gene ORF analysis for RBFOX1-LAMA5

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
intron-intron	ENST00000311745	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000311745	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000311745	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000311745	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000340209	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000340209	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000340209	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000340209	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000355637	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000355637	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000355637	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000355637	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000422070	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000422070	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000422070	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000422070	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000436368	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000436368	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000436368	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000436368	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000535565	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000535565	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000535565	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000535565	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547338	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547338	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547338	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547338	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547372	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547372	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547372	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547372	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547427	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547427	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547427	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000547427	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000550418	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000550418	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000550418	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000550418	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000552089	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000552089	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000552089	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000552089	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000553186	ENST00000252999	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000553186	ENST00000370677	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000553186	ENST00000370692	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+
intron-intron	ENST00000553186	ENST00000492698	RBFOX1	chr16	7331837	-	LAMA5	chr20	60886103	+

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)

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

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Fusion Genomic Features for RBFOX1-LAMA5

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)

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Fusion Protein Features for RBFOX1-LAMA5

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:7331837/:60886103)
- 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
.	.
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: 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}.

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

- 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

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Fusion Gene Sequence for RBFOX1-LAMA5

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 RBFOX1-LAMA5

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

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Related Drugs for RBFOX1-LAMA5

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 RBFOX1-LAMA5

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	RBFOX1	C0004352	Autistic Disorder	2	CTD_human
Hgene	RBFOX1	C0022333	Jacksonian Seizure	1	CTD_human
Hgene	RBFOX1	C0036572	Seizures	1	CTD_human
Hgene	RBFOX1	C0149958	Complex partial seizures	1	CTD_human
Hgene	RBFOX1	C0234533	Generalized seizures	1	CTD_human
Hgene	RBFOX1	C0234535	Clonic Seizures	1	CTD_human
Hgene	RBFOX1	C0270824	Visual seizure	1	CTD_human
Hgene	RBFOX1	C0270844	Tonic Seizures	1	CTD_human
Hgene	RBFOX1	C0270846	Epileptic drop attack	1	CTD_human
Hgene	RBFOX1	C0422850	Seizures, Somatosensory	1	CTD_human
Hgene	RBFOX1	C0422852	Seizures, Auditory	1	CTD_human
Hgene	RBFOX1	C0422853	Olfactory seizure	1	CTD_human
Hgene	RBFOX1	C0422854	Gustatory seizure	1	CTD_human
Hgene	RBFOX1	C0422855	Vertiginous seizure	1	CTD_human
Hgene	RBFOX1	C0494475	Tonic - clonic seizures	1	CTD_human
Hgene	RBFOX1	C0751056	Non-epileptic convulsion	1	CTD_human
Hgene	RBFOX1	C0751110	Single Seizure	1	CTD_human
Hgene	RBFOX1	C0751123	Atonic Absence Seizures	1	CTD_human
Hgene	RBFOX1	C0751494	Convulsive Seizures	1	CTD_human
Hgene	RBFOX1	C0751495	Seizures, Focal	1	CTD_human
Hgene	RBFOX1	C0751496	Seizures, Sensory	1	CTD_human
Hgene	RBFOX1	C3495874	Nonepileptic Seizures	1	CTD_human
Hgene	RBFOX1	C4048158	Convulsions	1	CTD_human
Hgene	RBFOX1	C4316903	Absence Seizures	1	CTD_human
Hgene	RBFOX1	C4317109	Epileptic Seizures	1	CTD_human
Hgene	RBFOX1	C4317123	Myoclonic Seizures	1	CTD_human
Hgene	RBFOX1	C4505436	Generalized Absence Seizures	1	CTD_human
Tgene		C0027726	Nephrotic Syndrome	1	GENOMICS_ENGLAND

Fusion Gene Studies in Kim Lab

Fusion gene:RBFOX1-LAMA5 (FusionGDB2 ID:HG54715TG3911)

Fusion Gene Summary for RBFOX1-LAMA5

Fusion Gene ORF analysis for RBFOX1-LAMA5

Fusion Genomic Features for RBFOX1-LAMA5

Fusion Protein Features for RBFOX1-LAMA5

Fusion Gene Sequence for RBFOX1-LAMA5

Fusion Gene PPI Analysis for RBFOX1-LAMA5

Related Drugs for RBFOX1-LAMA5

Related Diseases for RBFOX1-LAMA5

Fusion Gene Studies
in Kim Lab