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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: 7451

FusionGeneSummary for CLNS1A_SMIM15

check button Fusion gene summary
Fusion gene informationFusion gene name: CLNS1A_SMIM15
Fusion gene ID: 7451
HgeneTgene
Gene symbol

CLNS1A

SMIM15

Gene ID

1207

643155

Gene namechloride nucleotide-sensitive channel 1Asmall integral membrane protein 15
SynonymsCLCI|CLNS1B|IClnC5orf43
Cytomap

11q14.1

5q12.1

Type of geneprotein-codingprotein-coding
Descriptionmethylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein IClnsmall integral membrane protein 15UPF0542 protein C5orf43
Modification date2018052220180329
UniProtAcc

P54105

Q7Z3B0

Ensembl transtripts involved in fusion geneENST00000525428, ENST00000263309, 
ENST00000525064, ENST00000532069, 
ENST00000528364, ENST00000533957, 
ENST00000339020, ENST00000507416, 
Fusion gene scores* DoF score5 X 3 X 3=452 X 2 X 2=8
# samples 62
** MAII scorelog2(6/45*10)=0.415037499278844
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(2/8*10)=1.32192809488736
Context

PubMed: CLNS1A [Title/Abstract] AND SMIM15 [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
HgeneCLNS1A

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
TCGALDLUADTCGA-78-7536-01ACLNS1Achr11

77348635

-SMIM15chr5

60457054

-
* 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
5CDS-5UTRENST00000525428ENST00000339020CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000525428ENST00000507416CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000263309ENST00000339020CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000263309ENST00000507416CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000525064ENST00000339020CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000525064ENST00000507416CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000532069ENST00000339020CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000532069ENST00000507416CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000528364ENST00000339020CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
5CDS-5UTRENST00000528364ENST00000507416CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
intron-5UTRENST00000533957ENST00000339020CLNS1Achr11

77348635

-SMIM15chr5

60457054

-
intron-5UTRENST00000533957ENST00000507416CLNS1Achr11

77348635

-SMIM15chr5

60457054

-

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FusionProtFeatures for CLNS1A_SMIM15


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CLNS1A

P54105

SMIM15

Q7Z3B0

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 CLNS1A_SMIM15


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 CLNS1A_SMIM15


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
CLNS1APRMT5, 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, TRIM25SMIM15


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 CLNS1A_SMIM15


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 CLNS1A_SMIM15


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLNS1AC0025202melanoma1CTD_human