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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: 34780

FusionGeneSummary for SMARCA1_CNP

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCA1_CNP
Fusion gene ID: 34780
HgeneTgene
Gene symbol

SMARCA1

CNP

Gene ID

6594

1267

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 12',3'-cyclic nucleotide 3' phosphodiesterase
SynonymsISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2LCNP1
Cytomap

Xq25-q26.1

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionprobable global transcription activator SNF2L1ATP-dependent helicase SMARCA1SNF2-like 1global transcription activator homologous sequencenucleosome-remodeling factor subunit SNF2Lsucrose nonfermenting 2-like protein 12',3'-cyclic-nucleotide 3'-phosphodiesterase2', 3' cyclic nucleotide 3' phosphohydrolaseCNPase
Modification date2018051920180523
UniProtAcc

P28370

P09543

Ensembl transtripts involved in fusion geneENST00000371121, ENST00000371122, 
ENST00000371123, ENST00000478420, 
ENST00000393892, ENST00000472031, 
ENST00000591072, ENST00000592446, 
ENST00000393888, 
Fusion gene scores* DoF score4 X 4 X 3=485 X 5 X 3=75
# samples 45
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCA1 [Title/Abstract] AND CNP [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
HgeneSMARCA1

GO:0006338

chromatin remodeling

14609955

HgeneSMARCA1

GO:0043044

ATP-dependent chromatin remodeling

15640247


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
ChiTaRS3.1AA719336SMARCA1chrX

128650434

-CNPchr17

40126540

+
* 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
intron-3UTRENST00000371121ENST00000393892SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371121ENST00000472031SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371121ENST00000591072SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371121ENST00000592446SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-3UTRENST00000371121ENST00000393888SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-3UTRENST00000371122ENST00000393892SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371122ENST00000472031SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371122ENST00000591072SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371122ENST00000592446SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-3UTRENST00000371122ENST00000393888SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-3UTRENST00000371123ENST00000393892SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371123ENST00000472031SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371123ENST00000591072SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000371123ENST00000592446SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-3UTRENST00000371123ENST00000393888SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-3UTRENST00000478420ENST00000393892SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000478420ENST00000472031SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000478420ENST00000591072SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-intronENST00000478420ENST00000592446SMARCA1chrX

128650434

-CNPchr17

40126540

+
intron-3UTRENST00000478420ENST00000393888SMARCA1chrX

128650434

-CNPchr17

40126540

+

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FusionProtFeatures for SMARCA1_CNP


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SMARCA1

P28370

CNP

P09543

Energy-transducing component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor)complexes. Both complexes facilitate the perturbation of chromatinstructure in an ATP-dependent manner. Potentiates neuriteoutgrowth. May be involved in brain development by regulating En-1and En-2 expression. May be involved in the development of lutealcells. {ECO:0000269|PubMed:14609955, ECO:0000269|PubMed:15310751,ECO:0000269|PubMed:15640247, ECO:0000269|PubMed:16740656}. May participate in RNA metabolism in the myelinatingcell, CNP is the third most abundant protein in central nervoussystem myelin. {ECO:0000250}.

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 SMARCA1_CNP


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 SMARCA1_CNP


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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RelatedDrugs for SMARCA1_CNP


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 SMARCA1_CNP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCNPC0036341Schizophrenia5PSYGENET
TgeneCNPC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneCNPC0033975Psychotic Disorders1PSYGENET
TgeneCNPC0041696Unipolar Depression1PSYGENET
TgeneCNPC1269683Major Depressive Disorder1PSYGENET