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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:NCSTN-ATP1A4

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NCSTN-ATP1A4
FusionPDB ID: 57901
FusionGDB2.0 ID: 57901
HgeneTgene
Gene symbol

NCSTN

ATP1A4

Gene ID

23385

480

Gene namenicastrinATPase Na+/K+ transporting subunit alpha 4
SynonymsATAG1874ATP1A1|ATP1AL2
Cytomap

1q23.2

1q23.2

Type of geneprotein-codingprotein-coding
Descriptionnicastrinanterior pharynx-defective 2sodium/potassium-transporting ATPase subunit alpha-4ATPase, Na+/K+ transporting, alpha 4 polypeptideATPase, Na+/K+ transporting, alpha polypeptide-like 2Na(+)/K(+) ATPase alpha-4 subunitNa+/K+ ATPase 4Na+/K+ ATPase, alpha-D polypeptideNa,K-ATPase su
Modification date2020032720200313
UniProtAcc

Q92542

.
Ensembl transtripts involved in fusion geneENST idsENST00000294785, ENST00000368063, 
ENST00000392212, ENST00000535857, 
ENST00000368065, ENST00000459963, 
ENST00000418334, ENST00000470705, 
ENST00000368081, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 7 X 4=1682 X 2 X 2=8
# samples 72
** MAII scorelog2(7/168*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context (manual curation of fusion genes in FusionPDB)

PubMed: NCSTN [Title/Abstract] AND ATP1A4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NCSTN(160314616)-ATP1A4(160145882), # samples:3
Anticipated loss of major functional domain due to fusion event.NCSTN-ATP1A4 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.
NCSTN-ATP1A4 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.
NCSTN-ATP1A4 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.
NCSTN-ATP1A4 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
HgeneNCSTN

GO:0006509

membrane protein ectodomain proteolysis

15274632

HgeneNCSTN

GO:0016485

protein processing

15274632

HgeneNCSTN

GO:0042982

amyloid precursor protein metabolic process

25043039|26280335

HgeneNCSTN

GO:0043085

positive regulation of catalytic activity

15274632

TgeneATP1A4

GO:0030317

flagellated sperm motility

12112599

TgeneATP1A4

GO:0030641

regulation of cellular pH

12112599


check buttonFusion gene breakpoints across NCSTN (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 ATP1A4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4BRCATCGA-BH-A1FD-01ANCSTNchr1

160314616

-ATP1A4chr1

160145882

+
ChimerDB4BRCATCGA-BH-A1FD-01ANCSTNchr1

160314616

+ATP1A4chr1

160145882

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000294785NCSTNchr1160314616+ENST00000368081ATP1A4chr1160145882+13723151251093322
ENST00000368063NCSTNchr1160314616+ENST00000368081ATP1A4chr1160145882+14674102801188302
ENST00000535857NCSTNchr1160314616+ENST00000368081ATP1A4chr1160145882+125820111979322
ENST00000392212NCSTNchr1160314616+ENST00000368081ATP1A4chr1160145882+11871300908302

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
ENST00000294785ENST00000368081NCSTNchr1160314616+ATP1A4chr1160145882+0.0052961520.9947038
ENST00000368063ENST00000368081NCSTNchr1160314616+ATP1A4chr1160145882+0.0042045270.9957955
ENST00000535857ENST00000368081NCSTNchr1160314616+ATP1A4chr1160145882+0.0050023060.99499774
ENST00000392212ENST00000368081NCSTNchr1160314616+ATP1A4chr1160145882+0.0042873670.99571264

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>57901_57901_1_NCSTN-ATP1A4_NCSTN_chr1_160314616_ENST00000294785_ATP1A4_chr1_160145882_ENST00000368081_length(amino acids)=322AA_BP=64
MATAGGGSGADPGSRGLLRLLSFCVLLAGLCRGNSVERKIYIPLNKTAPCVRLLNATHQIGCQCRLIFDNLKKSIMYTLTSNIPEITPFL
MFIILGIPLPLGTITILCIDLGTDMVPAISLAYESAESDIMKRLPRNPKTDNLVNHRLIGMAYGQIGMIQALAGFFTYFVILAENGFRPV
DLLGIRLHWEDKYLNDLEDSYGQQWTYEQRKVVEFTCQTAFFVTIVVVQWADLIISKTRRNSLFQQGMRNKVLIFGILEETLLAAFLSYT

--------------------------------------------------------------

>57901_57901_2_NCSTN-ATP1A4_NCSTN_chr1_160314616_ENST00000368063_ATP1A4_chr1_160145882_ENST00000368081_length(amino acids)=302AA_BP=44
MDFNLILESLCRGNSVERKIYIPLNKTAPCVRLLNATHQIGCQCRLIFDNLKKSIMYTLTSNIPEITPFLMFIILGIPLPLGTITILCID
LGTDMVPAISLAYESAESDIMKRLPRNPKTDNLVNHRLIGMAYGQIGMIQALAGFFTYFVILAENGFRPVDLLGIRLHWEDKYLNDLEDS
YGQQWTYEQRKVVEFTCQTAFFVTIVVVQWADLIISKTRRNSLFQQGMRNKVLIFGILEETLLAAFLSYTPGMDVALRMYPLKITWWLCA

--------------------------------------------------------------

>57901_57901_3_NCSTN-ATP1A4_NCSTN_chr1_160314616_ENST00000392212_ATP1A4_chr1_160145882_ENST00000368081_length(amino acids)=302AA_BP=44
MDFNLILESLCRGNSVERKIYIPLNKTAPCVRLLNATHQIGCQCRLIFDNLKKSIMYTLTSNIPEITPFLMFIILGIPLPLGTITILCID
LGTDMVPAISLAYESAESDIMKRLPRNPKTDNLVNHRLIGMAYGQIGMIQALAGFFTYFVILAENGFRPVDLLGIRLHWEDKYLNDLEDS
YGQQWTYEQRKVVEFTCQTAFFVTIVVVQWADLIISKTRRNSLFQQGMRNKVLIFGILEETLLAAFLSYTPGMDVALRMYPLKITWWLCA

--------------------------------------------------------------

>57901_57901_4_NCSTN-ATP1A4_NCSTN_chr1_160314616_ENST00000535857_ATP1A4_chr1_160145882_ENST00000368081_length(amino acids)=322AA_BP=64
MATAGGGSGADPGSRGLLRLLSFCVLLAGLCRGNSVERKIYIPLNKTAPCVRLLNATHQIGCQCRLIFDNLKKSIMYTLTSNIPEITPFL
MFIILGIPLPLGTITILCIDLGTDMVPAISLAYESAESDIMKRLPRNPKTDNLVNHRLIGMAYGQIGMIQALAGFFTYFVILAENGFRPV
DLLGIRLHWEDKYLNDLEDSYGQQWTYEQRKVVEFTCQTAFFVTIVVVQWADLIISKTRRNSLFQQGMRNKVLIFGILEETLLAAFLSYT

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr1:160314616/chr1:160145882)
- 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
NCSTN

Q92542

.
FUNCTION: Essential subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors and APP (amyloid-beta precursor protein) (PubMed:10993067, PubMed:12679784, PubMed:25043039, PubMed:26280335, PubMed:30598546, PubMed:30630874). The gamma-secretase complex plays a role in Notch and Wnt signaling cascades and regulation of downstream processes via its role in processing key regulatory proteins, and by regulating cytosolic CTNNB1 levels. {ECO:0000269|PubMed:10993067, ECO:0000269|PubMed:12679784, ECO:0000269|PubMed:25043039, ECO:0000269|PubMed:26280335, ECO:0000269|PubMed:30598546, ECO:0000269|PubMed:30630874}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneATP1A4chr1:160314616chr1:160145882ENST0000036808114221013_1029770.33333333333341030.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422799_808770.33333333333341030.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422830_849770.33333333333341030.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422873_924770.33333333333341030.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422945_957770.33333333333341030.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422977_991770.33333333333341030.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST00000470705051013_10290166.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505117_1390166.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505161_2960166.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST00000470705051_950166.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505317_3280166.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505347_7780166.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505799_8080166.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505830_8490166.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505873_9240166.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505945_9570166.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505977_9910166.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422779_798770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422809_829770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422850_872770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422925_944770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422958_976770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422992_1012770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505140_1600166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505297_3160166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505329_3460166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505779_7980166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505809_8290166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505850_8720166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505925_9440166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505958_9760166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000004707050596_1160166.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST0000047070505992_10120166.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNCSTNchr1:160314616chr1:160145882ENST00000294785+21734_66963.333333333333336710.0Topological domainExtracellular
HgeneNCSTNchr1:160314616chr1:160145882ENST00000294785+217691_70963.333333333333336710.0Topological domainCytoplasmic
HgeneNCSTNchr1:160314616chr1:160145882ENST00000368063+31834_66943.333333333333336690.0Topological domainExtracellular
HgeneNCSTNchr1:160314616chr1:160145882ENST00000368063+318691_70943.333333333333336690.0Topological domainCytoplasmic
HgeneNCSTNchr1:160314616chr1:160145882ENST00000392212+21734_66943.333333333333336690.0Topological domainExtracellular
HgeneNCSTNchr1:160314616chr1:160145882ENST00000392212+217691_70943.333333333333336690.0Topological domainCytoplasmic
HgeneNCSTNchr1:160314616chr1:160145882ENST00000294785+217670_69063.333333333333336710.0TransmembraneHelical
HgeneNCSTNchr1:160314616chr1:160145882ENST00000368063+318670_69043.333333333333336690.0TransmembraneHelical
HgeneNCSTNchr1:160314616chr1:160145882ENST00000392212+217670_69043.333333333333336690.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422117_139770.33333333333341030.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422161_296770.33333333333341030.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST0000036808114221_95770.33333333333341030.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422317_328770.33333333333341030.0Topological domainExtracellular
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422347_778770.33333333333341030.0Topological domainCytoplasmic
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422140_160770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422297_316770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST000003680811422329_346770.33333333333341030.0TransmembraneHelical
TgeneATP1A4chr1:160314616chr1:160145882ENST00000368081142296_116770.33333333333341030.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
NCSTN
ATP1A4


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgeneATP1A4chr1:160314616chr1:160145882ENST00000368081142290_92770.33333333333341030.0phosphoinositide-3 kinase


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Related Drugs to NCSTN-ATP1A4


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to NCSTN-ATP1A4


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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