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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:RSF1-CLNS1A (FusionGDB2 ID:78394)

Fusion Gene Summary for RSF1-CLNS1A

check button Fusion gene summary
Fusion gene informationFusion gene name: RSF1-CLNS1A
Fusion gene ID: 78394
HgeneTgene
Gene symbol

RSF1

CLNS1A

Gene ID

51773

1207

Gene nameremodeling and spacing factor 1chloride nucleotide-sensitive channel 1A
SynonymsHBXAP|RSF-1|XAP8|p325CLCI|CLNS1B|ICln
Cytomap

11q14.1

11q14.1

Type of geneprotein-codingprotein-coding
Descriptionremodeling and spacing factor 1HBV pX-associated protein 8hepatitis B virus x-associated proteinp325 subunit of RSF chromatin-remodeling complexmethylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein ICln
Modification date2020031320200313
UniProtAcc.

P54105

Ensembl transtripts involved in fusion geneENST00000308488, ENST00000360355, 
ENST00000530604, ENST00000480887, 
ENST00000263309, ENST00000525064, 
ENST00000528364, ENST00000532069, 
ENST00000533957, ENST00000525428, 
Fusion gene scores* DoF score24 X 20 X 11=528010 X 8 X 6=480
# samples 3213
** MAII scorelog2(32/5280*10)=-4.04439411935845
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/480*10)=-1.88452278258006
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RSF1 [Title/Abstract] AND CLNS1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRSF1(77451776)-CLNS1A(77340944), # samples:2
Anticipated loss of major functional domain due to fusion event.RSF1-CLNS1A seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
RSF1-CLNS1A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
RSF1-CLNS1A seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
RSF1-CLNS1A seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
* 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
HgeneRSF1

GO:0006334

nucleosome assembly

12972596

HgeneRSF1

GO:0006338

chromatin remodeling

9836642

HgeneRSF1

GO:0006352

DNA-templated transcription, initiation

9836642

HgeneRSF1

GO:0016584

nucleosome positioning

9836642

HgeneRSF1

GO:0043392

negative regulation of DNA binding

12972596

HgeneRSF1

GO:0045892

negative regulation of transcription, DNA-templated

11944984

HgeneRSF1

GO:0045893

positive regulation of transcription, DNA-templated

11788598

HgeneRSF1

GO:0050434

positive regulation of viral transcription

11788598

TgeneCLNS1A

GO:0000387

spliceosomal snRNP assembly

18984161


check buttonFusion gene breakpoints across RSF1 (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 CLNS1A (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
ChimerDB4LIHCTCGA-DD-AADP-01ARSF1chr11

77451776

-CLNS1Achr11

77340944

-
ChimerDB4LIHCTCGA-DD-AADPRSF1chr11

77451776

-CLNS1Achr11

77340944

-
ChimerDB4STADTCGA-B7-5818-01ARSF1chr11

77531574

-CLNS1Achr11

77336115

-
ChimerDB4STADTCGA-B7-5818-01ARSF1chr11

77531574

-CLNS1Achr11

77336863

-


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Fusion Gene ORF analysis for RSF1-CLNS1A

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-intronENST00000308488ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000308488ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000308488ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5CDS-intronENST00000308488ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000308488ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5CDS-intronENST00000308488ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000308488ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-
5CDS-intronENST00000308488ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5CDS-intronENST00000308488ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000360355ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000360355ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000360355ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5CDS-intronENST00000360355ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000360355ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5CDS-intronENST00000360355ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5CDS-intronENST00000360355ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-
5CDS-intronENST00000360355ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5CDS-intronENST00000360355ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5UTR-3CDSENST00000530604ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5UTR-3CDSENST00000530604ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5UTR-3CDSENST00000530604ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5UTR-3CDSENST00000530604ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5UTR-intronENST00000530604ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5UTR-intronENST00000530604ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5UTR-intronENST00000530604ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5UTR-intronENST00000530604ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5UTR-intronENST00000530604ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5UTR-intronENST00000530604ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336863

-
5UTR-intronENST00000530604ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336115

-
5UTR-intronENST00000530604ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336863

-
Frame-shiftENST00000308488ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000308488ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336115

-
Frame-shiftENST00000308488ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000308488ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336115

-
Frame-shiftENST00000308488ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000308488ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336115

-
Frame-shiftENST00000308488ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336863

-
Frame-shiftENST00000308488ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000308488ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000360355ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000360355ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336115

-
Frame-shiftENST00000360355ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000360355ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336115

-
Frame-shiftENST00000360355ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000360355ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336115

-
Frame-shiftENST00000360355ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336863

-
Frame-shiftENST00000360355ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shiftENST00000360355ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336115

-
intron-3CDSENST00000480887ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336115

-
intron-3CDSENST00000480887ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336115

-
intron-3CDSENST00000480887ENST00000525428RSF1chr11

77531574

-CLNS1Achr11

77336863

-
intron-3CDSENST00000480887ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-intronENST00000480887ENST00000263309RSF1chr11

77531574

-CLNS1Achr11

77336863

-
intron-intronENST00000480887ENST00000525064RSF1chr11

77531574

-CLNS1Achr11

77336863

-
intron-intronENST00000480887ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336115

-
intron-intronENST00000480887ENST00000528364RSF1chr11

77531574

-CLNS1Achr11

77336863

-
intron-intronENST00000480887ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336115

-
intron-intronENST00000480887ENST00000532069RSF1chr11

77531574

-CLNS1Achr11

77336863

-
intron-intronENST00000480887ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-intronENST00000480887ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336115

-
intron-intronENST00000480887ENST00000533957RSF1chr11

77531574

-CLNS1Achr11

77336863

-
intron-intronENST00000530604ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-

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 RSF1-CLNS1A


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 RSF1-CLNS1A


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/:77451776/:77340944)
- 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
.CLNS1A

P54105

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: Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (PubMed:21081503, PubMed:18984161). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway. {ECO:0000269|PubMed:10330151, ECO:0000269|PubMed:11713266, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:21081503}.

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 RSF1-CLNS1A


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 RSF1-CLNS1A


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 RSF1-CLNS1A


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 RSF1-CLNS1A


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