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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:PI4K2A-AS3MT

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PI4K2A-AS3MT
FusionPDB ID: 65052
FusionGDB2.0 ID: 65052
HgeneTgene
Gene symbol

PI4K2A

AS3MT

Gene ID

55361

57412

Gene namephosphatidylinositol 4-kinase type 2 alphaarsenite methyltransferase
SynonymsPI4KII|PIK42ACYT19
Cytomap

10q24.2

10q24.32

Type of geneprotein-codingprotein-coding
Descriptionphosphatidylinositol 4-kinase type 2-alphaphosphatidylinositol 4-kinase type II (PI4KII)phosphatidylinositol 4-kinase type II-alphaarsenite methyltransferaseS-adenosyl-L-methionine:arsenic(III) methyltransferaseS-adenosylmethionine:arsenic (III) methyltransferasearsenic (+3 oxidation state) methyltransferasemethylarsonite methyltransferasemethyltransferase cyt19
Modification date2020031320200329
UniProtAcc.

Q9HBK9

Ensembl transtripts involved in fusion geneENST idsENST00000370631, ENST00000370649, 
ENST00000555577, 
ENST00000369880, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 4 X 4=641 X 1 X 1=1
# samples 41
** MAII scorelog2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context (manual curation of fusion genes in FusionPDB)

PubMed: PI4K2A [Title/Abstract] AND AS3MT [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PI4K2A(99426877)-AS3MT(104650301), # samples:3
Anticipated loss of major functional domain due to fusion event.PI4K2A-AS3MT 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.
PI4K2A-AS3MT 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.
PI4K2A-AS3MT 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.
PI4K2A-AS3MT 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
HgenePI4K2A

GO:0006661

phosphatidylinositol biosynthetic process

11279162

HgenePI4K2A

GO:0046854

phosphatidylinositol phosphorylation

25168678

TgeneAS3MT

GO:0009404

toxin metabolic process

25997655

TgeneAS3MT

GO:0018872

arsonoacetate metabolic process

25997655

TgeneAS3MT

GO:0032259

methylation

25997655


check buttonFusion gene breakpoints across PI4K2A (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 AS3MT (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
ChimerDB4PRADTCGA-J9-A8CK-01API4K2Achr10

99426877

+AS3MTchr10

104650301

+
ChimerDB4PRADTCGA-J9-A8CKPI4K2Achr10

99426877

+AS3MTchr10

104650301

+


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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)
ENST00000555577PI4K2Achr1099426877+ENST00000369880AS3MTchr10104650301+296015183061760484
ENST00000370649PI4K2Achr1099426877+ENST00000369880AS3MTchr10104650301+296015183061760484
ENST00000370631PI4K2Achr1099426877+ENST00000369880AS3MTchr10104650301+27771335571577506

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
ENST00000555577ENST00000369880PI4K2Achr1099426877+AS3MTchr10104650301+0.0028582680.99714166
ENST00000370649ENST00000369880PI4K2Achr1099426877+AS3MTchr10104650301+0.0028582680.99714166
ENST00000370631ENST00000369880PI4K2Achr1099426877+AS3MTchr10104650301+0.0024795260.9975205

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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

>65052_65052_1_PI4K2A-AS3MT_PI4K2A_chr10_99426877_ENST00000370631_AS3MT_chr10_104650301_ENST00000369880_length(amino acids)=506AA_BP=426
MDETSPLVSPERAQPPDYTFPSGSGAHFPQVPGGAVRVAAAAGSGPSPPGSPGHDRERQPLLDRARGAAAQGQTQTVAAQAQALAAQAAA
AAHAAQAHRERNEFPEDPEFEAVVRQAELAIERCIFPERIYQGSSGSYFVKDPQGRIIAVFKPKNEEPYGHLNPKWTKWLQKLCCPCCFG
RDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEKVPKVGQRFNRIGLPPKVGSFQLFVEGYKDA
DYWLRRFEAEPLPENTNRQLLLQFERLVVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWR
AYPFYWAWLPQAKVPFSQEIKDLILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQEGEIVEVDEETAAILKNSRFAQDF

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

>65052_65052_2_PI4K2A-AS3MT_PI4K2A_chr10_99426877_ENST00000370649_AS3MT_chr10_104650301_ENST00000369880_length(amino acids)=484AA_BP=404
MCFRPPAEMLGPQVWSSVRQGLSRSLSRNVGVWASGEGKKVDIAGIYPPVTTPFTATAEVDYGKLEENLHKLGTFPFRGAVGGVCALANV
LGAQVCQLERLCCTGQWEDAQKLQHRLIEPNAARIIAVFKPKNEEPYGHLNPKWTKWLQKLCCPCCFGRDCLVLNQGYLSEAGASLVDQK
LELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEKVPKVGQRFNRIGLPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLL
QFERLVVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWRAYPFYWAWLPQAKVPFSQEIKD
LILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQEGEIVEVDEETAAILKNSRFAQDFLIRPIGEKLPTSGGCSALELKD

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

>65052_65052_3_PI4K2A-AS3MT_PI4K2A_chr10_99426877_ENST00000555577_AS3MT_chr10_104650301_ENST00000369880_length(amino acids)=484AA_BP=404
MCFRPPAEMLGPQVWSSVRQGLSRSLSRNVGVWASGEGKKVDIAGIYPPVTTPFTATAEVDYGKLEENLHKLGTFPFRGAVGGVCALANV
LGAQVCQLERLCCTGQWEDAQKLQHRLIEPNAARIIAVFKPKNEEPYGHLNPKWTKWLQKLCCPCCFGRDCLVLNQGYLSEAGASLVDQK
LELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEKVPKVGQRFNRIGLPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLL
QFERLVVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWRAYPFYWAWLPQAKVPFSQEIKD
LILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQEGEIVEVDEETAAILKNSRFAQDFLIRPIGEKLPTSGGCSALELKD

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

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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/chr10:99426877/chr10:104650301)
- 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
.AS3MT

Q9HBK9

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.FUNCTION: Catalyzes the transfer of a methyl group from AdoMet to trivalent arsenicals producing methylated and dimethylated arsenicals (PubMed:16407288, PubMed:25997655). It methylates arsenite to form methylarsonate, Me-AsO(3)H(2), which is reduced by methylarsonate reductase to methylarsonite, Me-As(OH)2 (PubMed:16407288, PubMed:25997655). Methylarsonite is also a substrate and it is converted into the much less toxic compound dimethylarsinate (cacodylate), Me(2)As(O)-OH (PubMed:16407288, PubMed:25997655). {ECO:0000269|PubMed:16407288, ECO:0000269|PubMed:25997655}.

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
HgenePI4K2Achr10:99426877chr10:104650301ENST00000370631+8939_42426.0480.0Compositional biasNote=Poly-Ala
HgenePI4K2Achr10:99426877chr10:104650301ENST00000370631+8965_97426.0480.0Compositional biasNote=Ala-rich
HgenePI4K2Achr10:99426877chr10:104650301ENST00000370631+89131_137426.0480.0Nucleotide bindingATP
HgenePI4K2Achr10:99426877chr10:104650301ENST00000370631+89261_264426.0480.0Nucleotide bindingATP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePI4K2Achr10:99426877chr10:104650301ENST00000370631+89133_438426.0480.0DomainNote=PI3K/PI4K


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1078_PI4K2A_99426877_AS3MT_104650301_1078_PI4K2A_99426877_AS3MT_104650301_ranked_0.pdbPI4K2A9942687799426877ENST00000369880AS3MTchr10104650301+
MDETSPLVSPERAQPPDYTFPSGSGAHFPQVPGGAVRVAAAAGSGPSPPGSPGHDRERQPLLDRARGAAAQGQTQTVAAQAQALAAQAAA
AAHAAQAHRERNEFPEDPEFEAVVRQAELAIERCIFPERIYQGSSGSYFVKDPQGRIIAVFKPKNEEPYGHLNPKWTKWLQKLCCPCCFG
RDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEKVPKVGQRFNRIGLPPKVGSFQLFVEGYKDA
DYWLRRFEAEPLPENTNRQLLLQFERLVVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWR
AYPFYWAWLPQAKVPFSQEIKDLILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQEGEIVEVDEETAAILKNSRFAQDF
506


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
PI4K2A_pLDDT.png
all structure
all structure
AS3MT_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
PI4K2A
AS3MT


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 PI4K2A-AS3MT


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 PI4K2A-AS3MT


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