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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:ATP2A1-ATXN2L (FusionGDB2 ID:HG487TG11273)

Fusion Gene Summary for ATP2A1-ATXN2L

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP2A1-ATXN2L
Fusion gene ID: hg487tg11273
HgeneTgene
Gene symbol

ATP2A1

ATXN2L

Gene ID

487

11273

Gene nameATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1ataxin 2 like
SynonymsATP2A|SERCA1A2D|A2LG|A2LP|A2RP
Cytomap('ATP2A1')('ATXN2L')

16p11.2

16p11.2

Type of geneprotein-codingprotein-coding
Descriptionsarcoplasmic/endoplasmic reticulum calcium ATPase 1ATPase, Ca++ transporting, cardiac muscle, fast twitch 1SR Ca(2+)-ATPase 1calcium pump 1calcium-transporting ATPase sarcoplasmic reticulum type, fast twitch skeletal muscle isoformendoplasmic reticulataxin-2-like proteinataxin 2 related proteinataxin-2 domain protein
Modification date2020031320200320
UniProtAcc

O14983

.
Ensembl transtripts involved in fusion geneENST00000357084, ENST00000395503, 
ENST00000536376, ENST00000565042, 
Fusion gene scores* DoF score2 X 2 X 2=85 X 7 X 3=105
# samples 27
** MAII scorelog2(2/8*10)=1.32192809488736log2(7/105*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATP2A1 [Title/Abstract] AND ATXN2L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP2A1(28912237)-ATXN2L(28846379), # samples:2
Anticipated loss of major functional domain due to fusion event.ATP2A1-ATXN2L seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ATP2A1-ATXN2L seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneATP2A1

GO:0031448

positive regulation of fast-twitch skeletal muscle fiber contraction

12479237

HgeneATP2A1

GO:0090076

relaxation of skeletal muscle

8841193

TgeneATXN2L

GO:0010603

regulation of cytoplasmic mRNA processing body assembly

23209657


check buttonFusion gene breakpoints across ATP2A1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across ATXN2L (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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
ChimerDB4CESCTCGA-HM-A6W2-06AATP2A1chr16

28912237

-ATXN2Lchr16

28846379

+
ChimerDB4CESCTCGA-HM-A6W2-06AATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+


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Fusion Gene ORF analysis for ATP2A1-ATXN2L

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-3UTRENST00000357084ENST00000565845ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
5CDS-3UTRENST00000395503ENST00000565845ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
5CDS-3UTRENST00000536376ENST00000565845ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000357084ENST00000325215ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000357084ENST00000336783ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000357084ENST00000340394ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000357084ENST00000382686ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000357084ENST00000395547ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000357084ENST00000564304ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000357084ENST00000570200ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000395503ENST00000325215ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000395503ENST00000336783ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000395503ENST00000340394ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000395503ENST00000382686ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000395503ENST00000395547ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000395503ENST00000564304ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000395503ENST00000570200ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000536376ENST00000325215ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000536376ENST00000336783ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000536376ENST00000340394ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000536376ENST00000382686ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000536376ENST00000395547ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000536376ENST00000564304ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
In-frameENST00000536376ENST00000570200ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3CDSENST00000565042ENST00000325215ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3CDSENST00000565042ENST00000336783ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3CDSENST00000565042ENST00000340394ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3CDSENST00000565042ENST00000382686ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3CDSENST00000565042ENST00000395547ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3CDSENST00000565042ENST00000564304ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3CDSENST00000565042ENST00000570200ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+
intron-3UTRENST00000565042ENST00000565845ATP2A1chr16

28912237

+ATXN2Lchr16

28846379

+

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 ATP2A1-ATXN2L


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)
ATP2A1chr1628912237+ATXN2Lchr1628846378+0.0001970230.999803
ATP2A1chr1628912237+ATXN2Lchr1628846378+0.0001970230.999803

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for ATP2A1-ATXN2L


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/chr16:28912237/chr16:28846379)
- 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
ATP2A1

O14983

.
FUNCTION: Key regulator of striated muscle performance by acting as the major Ca(2+) ATPase responsible for the reuptake of cytosolic Ca(2+) into the sarcoplasmic reticulum. Catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen (By similarity). Contributes to calcium sequestration involved in muscular excitation/contraction (PubMed:10914677). {ECO:0000250|UniProtKB:P04191, ECO:0000269|PubMed:10914677}.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
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522625_6277001002.0Nucleotide bindingATP
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523625_6277001004.3333333333334Nucleotide bindingATP
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522254_2737001002.0TransmembraneHelical%3B Name%3D3
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522296_3137001002.0TransmembraneHelical%3B Name%3D4
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+152249_697001002.0TransmembraneHelical%3B Name%3D1
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+152290_1107001002.0TransmembraneHelical%3B Name%3D2
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523254_2737001004.3333333333334TransmembraneHelical%3B Name%3D3
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523296_3137001004.3333333333334TransmembraneHelical%3B Name%3D4
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+152349_697001004.3333333333334TransmembraneHelical%3B Name%3D1
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+152390_1107001004.3333333333334TransmembraneHelical%3B Name%3D2

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522758_7777001002.0TransmembraneHelical%3B Name%3D5
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522829_8517001002.0TransmembraneHelical%3B Name%3D7
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522898_9177001002.0TransmembraneHelical%3B Name%3D8
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522931_9497001002.0TransmembraneHelical%3B Name%3D9
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522965_9857001002.0TransmembraneHelical%3B Name%3D10
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523758_7777001004.3333333333334TransmembraneHelical%3B Name%3D5
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523829_8517001004.3333333333334TransmembraneHelical%3B Name%3D7
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523898_9177001004.3333333333334TransmembraneHelical%3B Name%3D8
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523931_9497001004.3333333333334TransmembraneHelical%3B Name%3D9
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523965_9857001004.3333333333334TransmembraneHelical%3B Name%3D10
TgeneATXN2Lchr16:28912237chr16:28846379ENST0000032521517234_848111063.0Compositional biasNote=Pro-rich
TgeneATXN2Lchr16:28912237chr16:28846379ENST0000033678317224_848111076.0Compositional biasNote=Pro-rich
TgeneATXN2Lchr16:28912237chr16:28846379ENST0000034039417234_848111045.0Compositional biasNote=Pro-rich
TgeneATXN2Lchr16:28912237chr16:28846379ENST0000038268617234_848111045.0Compositional biasNote=Pro-rich
TgeneATXN2Lchr16:28912237chr16:28846379ENST0000039554717244_848111112.6666666666667Compositional biasNote=Pro-rich
TgeneATXN2Lchr16:28912237chr16:28846379ENST0000057020017234_848111063.0Compositional biasNote=Pro-rich


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Fusion Gene Sequence for ATP2A1-ATXN2L


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 ATP2A1-ATXN2L


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
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522788_808700.01002.0PLN
HgeneATP2A1chr16:28912237chr16:28846379ENST00000357084+1522932_943700.01002.0PLN
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523788_808700.01004.3333333333334PLN
HgeneATP2A1chr16:28912237chr16:28846379ENST00000395503+1523932_943700.01004.3333333333334PLN
TgeneATXN2Lchr16:28912237chr16:28846379ENST00000325215172398_121811.01063.0MPL
TgeneATXN2Lchr16:28912237chr16:28846379ENST00000336783172298_121811.01076.0MPL
TgeneATXN2Lchr16:28912237chr16:28846379ENST00000340394172398_121811.01045.0MPL
TgeneATXN2Lchr16:28912237chr16:28846379ENST00000382686172398_121811.01045.0MPL
TgeneATXN2Lchr16:28912237chr16:28846379ENST00000395547172498_121811.01112.6666666666667MPL
TgeneATXN2Lchr16:28912237chr16:28846379ENST00000570200172398_121811.01063.0MPL


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 ATP2A1-ATXN2L


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneATP2A1O14983DB00228EnfluraneInhibitor|StimulatorSmall moleculeApproved|Investigational|Vet_approved

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Related Diseases for ATP2A1-ATXN2L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATP2A1C1832918Brody myopathy3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneATP2A1C0018801Heart failure1CTD_human
HgeneATP2A1C0018802Congestive heart failure1CTD_human
HgeneATP2A1C0023212Left-Sided Heart Failure1CTD_human
HgeneATP2A1C0235527Heart Failure, Right-Sided1CTD_human
HgeneATP2A1C1959583Myocardial Failure1CTD_human
HgeneATP2A1C1961112Heart Decompensation1CTD_human