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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:ATP1A1-PEX19

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ATP1A1-PEX19
FusionPDB ID: 7786
FusionGDB2.0 ID: 7786
HgeneTgene
Gene symbol

ATP1A1

PEX19

Gene ID

480

5824

Gene nameATPase Na+/K+ transporting subunit alpha 4peroxisomal biogenesis factor 19
SynonymsATP1A1|ATP1AL2D1S2223E|HK33|PBD12A|PMP1|PMPI|PXF|PXMP1
Cytomap

1q23.2

1q23.2

Type of geneprotein-codingprotein-coding
Descriptionsodium/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 superoxisomal biogenesis factor 1933 kDa housekeeping proteinhousekeeping gene, 33kDperoxin-19peroxisomal farnesylated protein
Modification date2020031320200313
UniProtAcc

Q5TC04

.
Ensembl transtripts involved in fusion geneENST idsENST00000295598, ENST00000369496, 
ENST00000537345, ENST00000491156, 
ENST00000532508, ENST00000368072, 
ENST00000440949, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 18 X 7=20166 X 8 X 3=144
# samples 239
** MAII scorelog2(23/2016*10)=-3.13178987255554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/144*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ATP1A1 [Title/Abstract] AND PEX19 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATP1A1(116930113)-PEX19(160251990), # samples:1
Anticipated loss of major functional domain due to fusion event.ATP1A1-PEX19 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.
ATP1A1-PEX19 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.
ATP1A1-PEX19 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.
ATP1A1-PEX19 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
HgeneATP1A1

GO:0030317

flagellated sperm motility

12112599

HgeneATP1A1

GO:0030641

regulation of cellular pH

12112599

TgenePEX19

GO:0006625

protein targeting to peroxisome

16344115|16763195

TgenePEX19

GO:0045046

protein import into peroxisome membrane

11402059|14709540

TgenePEX19

GO:0050821

protein stabilization

14709540|16344115

TgenePEX19

GO:0061077

chaperone-mediated protein folding

14709540

TgenePEX19

GO:0072321

chaperone-mediated protein transport

11402059|14709540

TgenePEX19

GO:1900131

negative regulation of lipid binding

19715730


check buttonFusion gene breakpoints across ATP1A1 (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 PEX19 (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
ChimerDB4SKCMTCGA-EE-A29D-06AATP1A1chr1

116930113

+PEX19chr1

160251990

-


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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)
ENST00000295598ATP1A1chr1116930113+ENST00000368072PEX19chr1160251990-38466392371106289
ENST00000295598ATP1A1chr1116930113+ENST00000440949PEX19chr1160251990-21776392371106289
ENST00000537345ATP1A1chr1116930113+ENST00000368072PEX19chr1160251990-39577503181217299
ENST00000537345ATP1A1chr1116930113+ENST00000440949PEX19chr1160251990-22887503181217299
ENST00000369496ATP1A1chr1116930113+ENST00000368072PEX19chr1160251990-37665591631026287
ENST00000369496ATP1A1chr1116930113+ENST00000440949PEX19chr1160251990-20975591631026287

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
ENST00000295598ENST00000368072ATP1A1chr1116930113+PEX19chr1160251990-0.0007704490.99922955
ENST00000295598ENST00000440949ATP1A1chr1116930113+PEX19chr1160251990-0.0026325390.99736744
ENST00000537345ENST00000368072ATP1A1chr1116930113+PEX19chr1160251990-0.0006063620.9993936
ENST00000537345ENST00000440949ATP1A1chr1116930113+PEX19chr1160251990-0.0020716860.99792826
ENST00000369496ENST00000368072ATP1A1chr1116930113+PEX19chr1160251990-0.0008654150.9991346
ENST00000369496ENST00000440949ATP1A1chr1116930113+PEX19chr1160251990-0.0024487320.99755126

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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

>7786_7786_1_ATP1A1-PEX19_ATP1A1_chr1_116930113_ENST00000295598_PEX19_chr1_160251990_ENST00000368072_length(amino acids)=289AA_BP=134
MSTATMGKGVGRDKYEPAAVSEQGDKKGKKGKKDRDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILARDGPNALTPPPT
TPEWIKFCRQLFGGFSMLLWIGAILCFLAYSIQAATEEEPQNDNNSSMSEEELTKAMEGLGMDEGDGEGNILPIMQSIMQNLLSKDVLYP
SLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFDL

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

>7786_7786_2_ATP1A1-PEX19_ATP1A1_chr1_116930113_ENST00000295598_PEX19_chr1_160251990_ENST00000440949_length(amino acids)=289AA_BP=134
MSTATMGKGVGRDKYEPAAVSEQGDKKGKKGKKDRDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILARDGPNALTPPPT
TPEWIKFCRQLFGGFSMLLWIGAILCFLAYSIQAATEEEPQNDNNSSMSEEELTKAMEGLGMDEGDGEGNILPIMQSIMQNLLSKDVLYP
SLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFDL

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

>7786_7786_3_ATP1A1-PEX19_ATP1A1_chr1_116930113_ENST00000369496_PEX19_chr1_160251990_ENST00000368072_length(amino acids)=287AA_BP=132
MPKDTLLVGRDKYEPAAVSEQGDKKGKKGKKDRDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILARDGPNALTPPPTTP
EWIKFCRQLFGGFSMLLWIGAILCFLAYSIQAATEEEPQNDNNSSMSEEELTKAMEGLGMDEGDGEGNILPIMQSIMQNLLSKDVLYPSL
KEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFDLDA

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

>7786_7786_4_ATP1A1-PEX19_ATP1A1_chr1_116930113_ENST00000369496_PEX19_chr1_160251990_ENST00000440949_length(amino acids)=287AA_BP=132
MPKDTLLVGRDKYEPAAVSEQGDKKGKKGKKDRDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILARDGPNALTPPPTTP
EWIKFCRQLFGGFSMLLWIGAILCFLAYSIQAATEEEPQNDNNSSMSEEELTKAMEGLGMDEGDGEGNILPIMQSIMQNLLSKDVLYPSL
KEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFDLDA

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

>7786_7786_5_ATP1A1-PEX19_ATP1A1_chr1_116930113_ENST00000537345_PEX19_chr1_160251990_ENST00000368072_length(amino acids)=299AA_BP=144
MGGLVPERVCLHCPKMAFKVGRDKYEPAAVSEQGDKKGKKGKKDRDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILARD
GPNALTPPPTTPEWIKFCRQLFGGFSMLLWIGAILCFLAYSIQAATEEEPQNDNNSSMSEEELTKAMEGLGMDEGDGEGNILPIMQSIMQ
NLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAG

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

>7786_7786_6_ATP1A1-PEX19_ATP1A1_chr1_116930113_ENST00000537345_PEX19_chr1_160251990_ENST00000440949_length(amino acids)=299AA_BP=144
MGGLVPERVCLHCPKMAFKVGRDKYEPAAVSEQGDKKGKKGKKDRDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILARD
GPNALTPPPTTPEWIKFCRQLFGGFSMLLWIGAILCFLAYSIQAATEEEPQNDNNSSMSEEELTKAMEGLGMDEGDGEGNILPIMQSIMQ
NLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAG

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

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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/chr1:116930113/chr1:160251990)
- 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
ATP1A1

Q5TC04

.
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
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+42382_84129.01024.0RegionPhosphoinositide-3 kinase binding
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+42382_8498.0993.0RegionPhosphoinositide-3 kinase binding
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+42382_84129.01024.0RegionPhosphoinositide-3 kinase binding
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423109_131129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+4236_87129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+4236_8798.0993.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423109_131129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+4236_87129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+42388_108129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+42388_108129.01024.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+4231007_1023129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423153_288129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423309_320129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423339_772129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423793_802129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423824_843129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423867_918129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423939_951129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423971_985129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+4231007_102398.0993.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423109_13198.0993.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423153_28898.0993.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423309_32098.0993.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423339_77298.0993.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423793_80298.0993.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423824_84398.0993.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423867_91898.0993.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423939_95198.0993.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423971_98598.0993.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+4231007_1023129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423153_288129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423309_320129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423339_772129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423793_802129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423824_843129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423867_918129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423939_951129.01024.0Topological domainCytoplasmic
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423971_985129.01024.0Topological domainExtracellular
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423132_152129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423289_308129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423321_338129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423773_792129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423803_823129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423844_866129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423919_938129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423952_970129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000295598+423986_1006129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423132_15298.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423289_30898.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423321_33898.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423773_79298.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423803_82398.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423844_86698.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+42388_10898.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423919_93898.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423952_97098.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000369496+423986_100698.0993.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423132_152129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423289_308129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423321_338129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423773_792129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423803_823129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423844_866129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423919_938129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423952_970129.01024.0TransmembraneHelical
HgeneATP1A1chr1:116930113chr1:160251990ENST00000537345+423986_1006129.01024.0TransmembraneHelical
TgenePEX19chr1:116930113chr1:160251990ENST00000368072382_56144.0300.0RegionNote=Docking to the peroxisome membrane and binding to PEX3
TgenePEX19chr1:116930113chr1:160251990ENST00000368072382_91144.0300.0RegionNote=Necessary for PEX19 function on peroxisome biogenesis


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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
ATP1A1
PEX19


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


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Related Drugs to ATP1A1-PEX19


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 ATP1A1-PEX19


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