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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:ATP4A-FKBP4 (FusionGDB2 ID:7909)

Fusion Gene Summary for ATP4A-FKBP4

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP4A-FKBP4
Fusion gene ID: 7909
HgeneTgene
Gene symbol

ATP4A

FKBP4

Gene ID

495

63943

Gene nameATPase H+/K+ transporting subunit alphaFKBP prolyl isomerase like
SynonymsATP6ADIR1|FKBP4|NG7|WISP39
Cytomap

19q13.12

6p21.32

Type of geneprotein-codingprotein-coding
Descriptionpotassium-transporting ATPase alpha chain 1ATPase H+/K+ transporting alpha subunitATPase, H+/K+ exchanging, alpha polypeptideATPase, H+/K+ transporting, alpha polypeptideepididymis secretory sperm binding proteingastric H+/K+ ATPase alpha subunitgasFK506-binding protein-likeFK506 binding protein likeWAF-1/CIP1 stabilizing protein 39peptidyl-prolyl cis-trans isomerase
Modification date2020031320200313
UniProtAcc.

Q02790

Ensembl transtripts involved in fusion geneENST00000262623, ENST00000540260, 
ENST00000001008, 
Fusion gene scores* DoF score1 X 1 X 1=12 X 2 X 2=8
# samples 12
** MAII scorelog2(1/1*10)=3.32192809488736log2(2/8*10)=1.32192809488736
Context

PubMed: ATP4A [Title/Abstract] AND FKBP4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP4A(36049894)-FKBP4(2908253), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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

check buttonFusion gene breakpoints across ATP4A (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 FKBP4 (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 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
ChimerDB4ESCATCGA-JY-A939ATP4Achr19

36049894

-FKBP4chr12

2908253

+


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Fusion Gene ORF analysis for ATP4A-FKBP4

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-intronENST00000262623ENST00000540260ATP4Achr19

36049894

-FKBP4chr12

2908253

+
In-frameENST00000262623ENST00000001008ATP4Achr19

36049894

-FKBP4chr12

2908253

+

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)
ENST00000262623ATP4Achr1936049894-ENST00000001008FKBP4chr122908253+28501284292149706

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
ENST00000262623ENST00000001008ATP4Achr1936049894-FKBP4chr122908253+0.0039756010.99602437

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Fusion Genomic Features for ATP4A-FKBP4


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)
ATP4Achr1936049894-FKBP4chr122908253+0.0008160540.99918395
ATP4Achr1936049894-FKBP4chr122908253+0.0008160540.99918395

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 ATP4A-FKBP4


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/chr19:36049894/chr12:2908253)
- 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
.FKBP4

Q02790

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: Immunophilin protein with PPIase and co-chaperone activities. Component of steroid receptors heterocomplexes through interaction with heat-shock protein 90 (HSP90). May play a role in the intracellular trafficking of heterooligomeric forms of steroid hormone receptors between cytoplasm and nuclear compartments. The isomerase activity controls neuronal growth cones via regulation of TRPC1 channel opening. Acts also as a regulator of microtubule dynamics by inhibiting MAPT/TAU ability to promote microtubule assembly. May have a protective role against oxidative stress in mitochondria. {ECO:0000269|PubMed:1279700, ECO:0000269|PubMed:1376003, ECO:0000269|PubMed:19945390, ECO:0000269|PubMed:21730050, ECO:0000269|PubMed:2378870}.

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
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822120_1424181036.0Topological domainLumenal
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822164_2994181036.0Topological domainCytoplasmic
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-8221_984181036.0Topological domainCytoplasmic
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822320_3314181036.0Topological domainLumenal
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822143_1634181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822300_3194181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822332_3494181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-82299_1194181036.0TransmembraneHelical
TgeneFKBP4chr19:36049894chr12:2908253ENST00000001008310270_303171460.0RepeatNote=TPR 1
TgeneFKBP4chr19:36049894chr12:2908253ENST00000001008310319_352171460.0RepeatNote=TPR 2
TgeneFKBP4chr19:36049894chr12:2908253ENST00000001008310353_386171460.0RepeatNote=TPR 3

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-8221019_10354181036.0Topological domainCytoplasmic
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822350_7834181036.0Topological domainCytoplasmic
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822804_8134181036.0Topological domainLumenal
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822835_8544181036.0Topological domainCytoplasmic
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822878_9294181036.0Topological domainLumenal
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822950_9634181036.0Topological domainCytoplasmic
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822983_9974181036.0Topological domainLumenal
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822784_8034181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822814_8344181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822855_8774181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822930_9494181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822964_9824181036.0TransmembraneHelical
HgeneATP4Achr19:36049894chr12:2908253ENST00000262623-822998_10184181036.0TransmembraneHelical
TgeneFKBP4chr19:36049894chr12:2908253ENST00000001008310167_253171460.0DomainPPIase FKBP-type 2
TgeneFKBP4chr19:36049894chr12:2908253ENST0000000100831050_138171460.0DomainPPIase FKBP-type 1


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Fusion Gene Sequence for ATP4A-FKBP4


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.
>7909_7909_1_ATP4A-FKBP4_ATP4A_chr19_36049894_ENST00000262623_FKBP4_chr12_2908253_ENST00000001008_length(transcript)=2850nt_BP=1284nt
GTTGGGTGGGAGCACAGGCACCGGGCACCATGGGGAAGGCCGAGAACTATGAGCTCTACTCGGTGGAGCTGGGTCCTGGCCCTGGCGGGG
ACATGGCTGCCAAGATGAGCAAGAAGAAGAAGGCGGGTGGCGGGGGTGGCAAGAGGAAGGAGAAGCTGGAGAACATGAAGAAGGAGATGG
AGATTAACGACCACCAGCTGTCAGTGGCGGAGCTGGAACAGAAATACCAGACCAGTGCCACCAAGGGCCTCTCTGCGAGCCTGGCTGCTG
AGCTGCTGCTGCGGGATGGGCCCAACGCACTGCGGCCACCACGGGGCACCCCAGAGTACGTCAAGTTCGCGAGGCAGCTGGCCGGGGGCC
TGCAGTGCCTCATGTGGGTTGCCGCCGCCATCTGCCTCATCGCCTTTGCCATCCAGGCTAGTGAGGGGGACCTCACCACCGACGACAATC
TGTACCTGGCAATCGCTCTCATTGCTGTGGTTGTCGTCACCGGCTGCTTTGGCTACTACCAGGAATTCAAGAGCACCAACATCATCGCCA
GCTTTAAGAACCTTGTGCCACAGCAAGCCACTGTCATCCGCGATGGAGACAAATTCCAGATCAACGCTGACCAACTGGTGGTGGGCGACC
TGGTGGAGATGAAAGGTGGGGACAGAGTGCCCGCCGACATCCGCATCCTGGCGGCCCAGGGCTGCAAGGTGGACAACTCCTCGCTGACAG
GGGAGTCTGAGCCACAGACCCGCTCACCCGAGTGCACGCACGAGAGCCCTCTGGAGACCCGCAACATCGCCTTCTTCTCCACCATGTGCC
TTGAGGGCACCGTGCAGGGCCTGGTGGTGAACACGGGCGACCGCACCATCATTGGGCGCATCGCATCGCTGGCGTCGGGGGTGGAAAACG
AGAAGACACCCATCGCTATCGAGATCGAGCATTTTGTGGACATCATCGCGGGCCTGGCCATTCTCTTCGGTGCCACATTTTTTATTGTGG
CCATGTGCATTGGCTACACCTTCCTGCGGGCCATGGTCTTCTTCATGGCCATCGTGGTGGCCTATGTGCCTGAGGGGCTGCTGGCCACTG
TCACAGTCTGCCTGTCCCTGACAGCCAAGCGCCTGGCCAGTAAGAACTGCGTGGTCAAGAACCTGGAGGCGGTGGAGACATTGGGCTCCA
CTTCGGTGATCTGCTCGGACAAGACAGGGACTCTCACTCAGAACCGCATGACTGTGTCCCATCTGTGGTTTGACAACCACATCCACACAG
CTGACACCACGGAAGACCAGTCAGTTGCACTGGAAGGGTACTACAAGGACAAGCTCTTTGACCAGCGGGAGCTCCGCTTTGAGATTGGCG
AGGGGGAGAACCTGGATCTGCCTTATGGTCTGGAGAGGGCCATTCAGCGCATGGAGAAAGGAGAACATTCCATCGTGTACCTCAAGCCCA
GCTATGCTTTTGGCAGTGTTGGGAAGGAAAAGTTCCAAATCCCACCAAATGCTGAGCTGAAATATGAATTACACCTCAAGAGTTTTGAAA
AGGCCAAGGAGTCTTGGGAGATGAATTCAGAAGAGAAGCTGGAACAGAGCACCATAGTGAAAGAGCGGGGCACTGTGTACTTCAAGGAAG
GTAAATACAAGCAAGCTTTACTACAGTATAAGAAGATCGTGTCTTGGCTGGAATATGAGTCTAGTTTTTCCAATGAGGAAGCACAGAAAG
CACAGGCCCTTCGACTGGCCTCTCACCTCAACCTGGCCATGTGTCATCTGAAACTACAGGCCTTCTCTGCTGCCATTGAAAGCTGTAACA
AGGCCCTAGAACTGGACAGCAACAACGAGAAGGGCCTCTTCCGCCGGGGAGAGGCCCACCTGGCCGTGAATGACTTTGAACTGGCACGGG
CTGATTTCCAGAAGGTCCTGCAGCTCTACCCCAACAACAAAGCCGCCAAGACCCAGCTGGCTGTGTGCCAGCAGCGGATCCGAAGGCAGC
TTGCCCGGGAGAAGAAGCTCTATGCCAATATGTTTGAGAGGCTGGCTGAGGAGGAGAACAAGGCCAAGGCAGAGGCTTCCTCAGGAGACC
ATCCCACTGACACAGAGATGAAGGAGGAGCAGAAGAGCAACACGGCAGGGAGCCAGTCTCAGGTGGAGACAGAAGCATAGCCCCTCTCCA
CCAGCCCTACTCCTGCGGCTGCCTGCCCCCCAGTCTCCCCACTCCACCCTGTTAGTTTTGTAAAAACTGAAGAATTTTGAGTGAATTAGA
CCTTTATTTTTCTATCTGGTTGGATGGTGGCTTTAGGGGAAGGGGGAAAGGTGTAGGCTGGGGGATTGAGGTGGGGAATCATTTTAGCTG
GTGTCAGCCCCTCTTCCCTTCCTCCATTGCACATGAACATATGTCCATCCATATATATTCATCAGAATGTTAATTTATTTTGCTCCCTCT
GTTAGGTCCATTTTCTAAGGGTAGAAGAGGCAAGTGGTAGGGATGAGGTCTGATAAGAACCCAGGGTGGAGAGGGAGACTCCTGGGCAGC
CGTTTTCCTCATCCTTTCCCTCTCCCAGTCCATTTCCAAATGTGGCCTCCATGTGGGTGCTAGGGACATGGGAAAAACCACTGCTATGCC
ATTTCTTCTCTCTGTTCCCTTCCTCACCCCCGACGGTGTGGCTGATGATGTCTTCTGGTGTCATGGTGACCACCCCCTGTTCCCTGTTCT
GGTATTTCCCCTGTCAGTTTCCCCTCTCGGCCAGGTTGTGTCCCAAAATCCCCTCAGCCTCTTCTCTGCACGTTGCTGAAGGTCCAGGCT

>7909_7909_1_ATP4A-FKBP4_ATP4A_chr19_36049894_ENST00000262623_FKBP4_chr12_2908253_ENST00000001008_length(amino acids)=706AA_BP=418
MGKAENYELYSVELGPGPGGDMAAKMSKKKKAGGGGGKRKEKLENMKKEMEINDHQLSVAELEQKYQTSATKGLSASLAAELLLRDGPNA
LRPPRGTPEYVKFARQLAGGLQCLMWVAAAICLIAFAIQASEGDLTTDDNLYLAIALIAVVVVTGCFGYYQEFKSTNIIASFKNLVPQQA
TVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILAAQGCKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTVQGLVV
NTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATVTVCLSLTAK
RLASKNCVVKNLEAVETLGSTSVICSDKTGTLTQNRMTVSHLWFDNHIHTADTTEDQSVALEGYYKDKLFDQRELRFEIGEGENLDLPYG
LERAIQRMEKGEHSIVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQY
KKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLFRRGEAHLAVNDFELARADFQKVLQLY

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

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Fusion Gene PPI Analysis for ATP4A-FKBP4


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
TgeneFKBP4chr19:36049894chr12:2908253ENST00000001008310267_400171.33333333333334460.0tubulin


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 ATP4A-FKBP4


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 ATP4A-FKBP4


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