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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:SIPA1-FLNA (FusionGDB2 ID:HG6494TG2316)

Fusion Gene Summary for SIPA1-FLNA

check button Fusion gene summary
Fusion gene informationFusion gene name: SIPA1-FLNA
Fusion gene ID: hg6494tg2316
HgeneTgene
Gene symbol

SIPA1

FLNA

Gene ID

6494

2316

Gene namesignal-induced proliferation-associated 1filamin A
SynonymsSPA1ABP-280|ABPX|CSBS|CVD1|FGS2|FLN|FLN-A|FLN1|FMD|MNS|NHBP|OPD|OPD1|OPD2|XLVD|XMVD
Cytomap('SIPA1')('FLNA')

11q13.1

Xq28

Type of geneprotein-codingprotein-coding
Descriptionsignal-induced proliferation-associated protein 1GTPase-activating protein Spa-1p130 SPA-1signal-induced proliferation-associated gene 1sipa-1filamin-Aactin binding protein 280alpha-filaminendothelial actin-binding proteinepididymis secretory sperm binding proteinfilamin A, alphafilamin-1non-muscle filamin
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000394224, ENST00000394227, 
ENST00000527525, ENST00000534313, 
Fusion gene scores* DoF score4 X 4 X 4=6425 X 31 X 6=4650
# samples 531
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(31/4650*10)=-3.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SIPA1 [Title/Abstract] AND FLNA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSIPA1(65412600)-FLNA(153585991), # samples:1
Anticipated loss of major functional domain due to fusion event.SIPA1-FLNA seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SIPA1-FLNA seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
SIPA1-FLNA seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SIPA1-FLNA seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneFLNA

GO:0016479

negative regulation of transcription by RNA polymerase I

22307607

TgeneFLNA

GO:0030334

regulation of cell migration

16291724

TgeneFLNA

GO:0031532

actin cytoskeleton reorganization

10051605

TgeneFLNA

GO:0034394

protein localization to cell surface

18322202

TgeneFLNA

GO:0043113

receptor clustering

10692483

TgeneFLNA

GO:0043433

negative regulation of DNA-binding transcription factor activity

15684392

TgeneFLNA

GO:0044319

wound healing, spreading of cells

16291724

TgeneFLNA

GO:0045184

establishment of protein localization

18322202

TgeneFLNA

GO:0051764

actin crosslink formation

10051605

TgeneFLNA

GO:0072659

protein localization to plasma membrane

24951510

TgeneFLNA

GO:0090307

mitotic spindle assembly

18548008

TgeneFLNA

GO:1901381

positive regulation of potassium ion transmembrane transport

24951510



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
ChimerDB4STADTCGA-BR-8059SIPA1chr11

65412600

+FLNAchrX

153585991

-


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Fusion Gene ORF analysis for SIPA1-FLNA

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-5UTRENST00000394224ENST00000344736SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-5UTRENST00000394224ENST00000369856SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-5UTRENST00000394227ENST00000344736SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-5UTRENST00000394227ENST00000369856SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-5UTRENST00000527525ENST00000344736SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-5UTRENST00000527525ENST00000369856SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-5UTRENST00000534313ENST00000344736SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-5UTRENST00000534313ENST00000369856SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-intronENST00000394224ENST00000498491SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-intronENST00000394227ENST00000498491SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-intronENST00000527525ENST00000498491SIPA1chr11

65412600

+FLNAchrX

153585991

-
5CDS-intronENST00000534313ENST00000498491SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000394224ENST00000360319SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000394224ENST00000369850SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000394224ENST00000422373SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000394227ENST00000360319SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000394227ENST00000369850SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000394227ENST00000422373SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000527525ENST00000360319SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000527525ENST00000369850SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000527525ENST00000422373SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000534313ENST00000360319SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000534313ENST00000369850SIPA1chr11

65412600

+FLNAchrX

153585991

-
Frame-shiftENST00000534313ENST00000422373SIPA1chr11

65412600

+FLNAchrX

153585991

-

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 SIPA1-FLNA


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)


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Fusion Protein Features for SIPA1-FLNA


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/:65412600/:153585991)
- 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
..
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}.

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 SIPA1-FLNA


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 SIPA1-FLNA


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 SIPA1-FLNA


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 SIPA1-FLNA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSIPA1C0025202melanoma1CTD_human
TgeneC1848213Periventricular Heterotopia, X-Linked9CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0025237Melnick-Needles Syndrome7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC4707243Familial thoracic aortic aneurysm and aortic dissection7CLINGEN;GENOMICS_ENGLAND
TgeneC0265251Oto-Palato-digital syndrome type 16CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1844696OTOPALATODIGITAL SYNDROME, TYPE II6CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0265293Frontometaphyseal dysplasia5CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC1846129Terminal Osseous Dysplasia and Pigmentary Defects4CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC4281559FRONTOMETAPHYSEAL DYSPLASIA 14GENOMICS_ENGLAND;UNIPROT
TgeneC0262436Cardiac valvular dysplasia, X-linked2CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0543888Epileptic encephalopathy2GENOMICS_ENGLAND
TgeneC1845902FG SYNDROME 22CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1868720Periventricular Nodular Heterotopia2CTD_human
TgeneC2746068Congenital idiopathic intestinal pseudoobstruction2CTD_human;GENOMICS_ENGLAND
TgeneC4551969Bilateral Periventricular Nodular Heterotopia2CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0010701Phyllodes Tumor1CTD_human
TgeneC0013366Dyschondroplasias1CTD_human
TgeneC0014544Epilepsy1CTD_human
TgeneC0021847Intestinal Pseudo-Obstruction1ORPHANET
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0026760Multiple Epiphyseal Dysplasia1CTD_human
TgeneC0029422Osteochondrodysplasias1CTD_human
TgeneC0036391Schwartz-Jampel Syndrome1CTD_human
TgeneC0038015Spondyloepiphyseal Dysplasia1CTD_human
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0220769FG syndrome1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0268341Ehlers-Danlos syndrome type 51ORPHANET
TgeneC0432272Van Buchem disease1CTD_human
TgeneC0600066Malignant Cystosarcoma Phyllodes1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1845235Heterotopia, Periventricular, Ehlers-Danlos Variant1CTD_human
TgeneC1845546FG SYNDROME 4 (disorder)1CTD_human
TgeneC1845567FG SYNDROME 31CTD_human
TgeneC1855733Neuronal intestinal pseudoobstruction1ORPHANET
TgeneC2751260Macrothrombocytopenia1GENOMICS_ENGLAND
TgeneC3541456Spondyloepiphyseal Dysplasia Tarda, X-Linked1CTD_human
TgeneC4551479Schwartz-Jampel Syndrome, Type 11CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human