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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 32281

FusionGeneSummary for RSF1_CLNS1A

check button Fusion gene summary
Fusion gene informationFusion gene name: RSF1_CLNS1A
Fusion gene ID: 32281
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 date2018052320180522
UniProtAcc

Q96T23

P54105

Ensembl transtripts involved in fusion geneENST00000308488, ENST00000360355, 
ENST00000480887, ENST00000530604, 
ENST00000525428, ENST00000263309, 
ENST00000525064, ENST00000532069, 
ENST00000528364, ENST00000533957, 
Fusion gene scores* DoF score15 X 8 X 9=10804 X 3 X 3=36
# samples 174
** MAII scorelog2(17/1080*10)=-2.66742466091313
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

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

Functional or gene categories assigned by FusionGDB annotation
* 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 button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDLIHCTCGA-DD-AADP-01ARSF1chr11

77451776

-CLNS1Achr11

77340944

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shitENST00000308488ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000308488ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000308488ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000308488ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000308488ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
5CDS-intronENST00000308488ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000360355ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000360355ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000360355ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000360355ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
Frame-shitENST00000360355ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
5CDS-intronENST00000360355ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000480887ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-intronENST00000480887ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000525428RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000263309RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000525064RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000532069RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-3CDSENST00000530604ENST00000528364RSF1chr11

77451776

-CLNS1Achr11

77340944

-
intron-intronENST00000530604ENST00000533957RSF1chr11

77451776

-CLNS1Achr11

77340944

-

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FusionProtFeatures for RSF1_CLNS1A


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RSF1

Q96T23

CLNS1A

P54105

Required for assembly of regular nucleosome arrays bythe RSF chromatin-remodeling complex (PubMed:12972596).Facilitates transcription of hepatitis B virus (HBV) genes by thepX transcription activator. In case of infection by HBV, togetherwith pX, it represses TNF-alpha induced NF-kappa-B transcriptionactivation. Represses transcription when artificially recruited tochromatin by fusion to a heterogeneous DNA binding domain(PubMed:11944984, PubMed:11788598). {ECO:0000269|PubMed:11788598,ECO:0000269|PubMed:11944984, ECO:0000269|PubMed:12972596}. Involved in both the assembly of spliceosomal snRNPs andthe methylation of Sm proteins (PubMed:21081503, PubMed:18984161).Chaperone that regulates the assembly of spliceosomal U1, U2, U4and U5 small nuclear ribonucleoproteins (snRNPs), the buildingblocks of the spliceosome. Thereby, plays an important role in thesplicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain acommon set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE,SNRPF and SNRPG that assemble in a heptameric protein ring on theSm site of the small nuclear RNA to form the core snRNP. In thecytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPGare trapped in an inactive 6S pICln-Sm complex by the chaperoneCLNS1A that controls the assembly of the core snRNP. Dissociationby the SMN complex of CLNS1A from the trapped Sm proteins andtheir transfer to an SMN-Sm complex triggers the assembly of coresnRNPs and their transport to the nucleus. May also indirectlyparticipate in cellular volume control by activation of aswelling-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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FusionGeneSequence for RSF1_CLNS1A


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI 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
RSF1NFKB1, SMARCA5, CENPA, SIRT7, SP1, COPS6, CSNK2A1, HIST1H2BG, HIST1H3A, EWSR1, MARK2, ATXN3, KAT6A, MCM2CLNS1APRMT5, ITGA2B, SNRPD3, SNRPD1, SNRPB, SNRPD2, SNRPE, WDR77, G3BP1, LSM10, LSM11, AGO3, WDR45, SNRPF, SNRPG, ARRB2, PPP4R2, LGALS1, LGALS3, PTMS, RHOA, OSTF1, PGAM1, SEC24A, PPA1, PDLIM1, UFC1, ATIC, UBXN1, PUM1, NEDD8, TPD52L2, PIR, LPP, RAC1, PLIN3, NDRG1, MIF, SEC24C, PPP2CA, S100A6, UBA2, PDIA6, VBP1, TRIP6, PLS3, MDH2, SNX12, PSMA5, UBA52, UBQLN1, RAD23A, RPS21, MAGOH, EIF4A3, SMURF1, YWHAE, FN1, LSM2, LSM3, LSM6, CSNK2A1, NOS2, UBL4A, PAN2, FBXO6, PDCD10, TRNT1, CTPS1, HSPA5, P4HB, PFDN2, USP5, NFE4, EPB41, GAR1, DDAH2, RPS2, RBFOX2, FBLN7, ADCYAP1, EPB41L3, RPS6KB2, NTRK1, TMEM17, ALKBH3, CRBN, PTPRG, SNRPN, FARP2, RPL15, EPB41L2, CYLD, TRIM25


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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RelatedDrugs for RSF1_CLNS1A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RSF1_CLNS1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCLNS1AC0025202melanoma1CTD_human