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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:ATP6AP1-OPN1LW (FusionGDB2 ID:HG537TG5956)

Fusion Gene Summary for ATP6AP1-OPN1LW

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP6AP1-OPN1LW
Fusion gene ID: hg537tg5956
HgeneTgene
Gene symbol

ATP6AP1

OPN1LW

Gene ID

537

5956

Gene nameATPase H+ transporting accessory protein 1opsin 1, long wave sensitive
Synonyms16A|ATP6IP1|ATP6S1|Ac45|CF2|VATPS1|XAP-3|XAP3CBBM|CBP|COD5|RCP|ROP
Cytomap('ATP6AP1')('OPN1LW')

Xq28

Xq28

Type of geneprotein-codingprotein-coding
DescriptionV-type proton ATPase subunit S1ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1ATPase, H+ transporting, lysosomal accessory protein 1ATPase, H+ transporting, lysosomal interacting protein 1H-ATPase subunitV-ATPase Ac45 subunitV-Along-wave-sensitive opsin 1cone dystrophy 5 (X-linked)opsin 1 (cone pigments), long-wave-sensitivered cone opsinred cone photoreceptor pigmentred-sensitive opsin
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000369762, ENST00000484908, 
Fusion gene scores* DoF score7 X 5 X 5=1752 X 2 X 2=8
# samples 72
** MAII scorelog2(7/175*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: ATP6AP1 [Title/Abstract] AND OPN1LW [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP6AP1(153657520)-OPN1LW(153421769), # samples:3
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 ATP6AP1 (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 OPN1LW (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
ChimerDB4BLCATCGA-FD-A62P-01AATP6AP1chrX

153657520

-OPN1LWchrX

153421769

+
ChimerDB4BLCATCGA-FD-A62P-01AATP6AP1chrX

153657520

+OPN1LWchrX

153421769

+


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Fusion Gene ORF analysis for ATP6AP1-OPN1LW

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-3UTRENST00000369762ENST00000463296ATP6AP1chrX

153657520

+OPN1LWchrX

153421769

+
In-frameENST00000369762ENST00000369951ATP6AP1chrX

153657520

+OPN1LWchrX

153421769

+
intron-3CDSENST00000484908ENST00000369951ATP6AP1chrX

153657520

+OPN1LWchrX

153421769

+
intron-3UTRENST00000484908ENST00000463296ATP6AP1chrX

153657520

+OPN1LWchrX

153421769

+

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)
ENST00000369762ATP6AP1chrX153657520+ENST00000369951OPN1LWchrX153421769+80634961699212

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
ENST00000369762ENST00000369951ATP6AP1chrX153657520+OPN1LWchrX153421769+0.0045101570.9954899

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Fusion Genomic Features for ATP6AP1-OPN1LW


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)
ATP6AP1chrX153657520+OPN1LWchrX153421768+8.37E-060.99999166
ATP6AP1chrX153657520+OPN1LWchrX153421768+8.37E-060.99999166

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 ATP6AP1-OPN1LW


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/chrX:153657520/chrX:153421769)
- 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
..
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: 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
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136247_268248365.0Topological domainNote=Cytoplasmic
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136293_300248365.0Topological domainNote=Extracellular
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136326_364248365.0Topological domainNote=Cytoplasmic
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136269_292248365.0TransmembraneHelical%3B Name%3D6
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136301_325248365.0TransmembraneHelical%3B Name%3D7

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATP6AP1chrX:153657520chrX:153421769ENST00000369762+21042_41996471.0Topological domainVacuolar
HgeneATP6AP1chrX:153657520chrX:153421769ENST00000369762+210441_47096471.0Topological domainCytoplasmic
HgeneATP6AP1chrX:153657520chrX:153421769ENST00000369762+210420_44096471.0TransmembraneHelical
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136116_129248365.0Topological domainNote=Extracellular
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136150_168248365.0Topological domainNote=Cytoplasmic
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136193_218248365.0Topological domainNote=Extracellular
TgeneOPN1LWchrX:153657520chrX:153421769ENST00000369951361_52248365.0Topological domainNote=Extracellular
TgeneOPN1LWchrX:153657520chrX:153421769ENST000003699513678_89248365.0Topological domainNote=Cytoplasmic
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136130_149248365.0TransmembraneHelical%3B Name%3D3
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136169_192248365.0TransmembraneHelical%3B Name%3D4
TgeneOPN1LWchrX:153657520chrX:153421769ENST0000036995136219_246248365.0TransmembraneHelical%3B Name%3D5
TgeneOPN1LWchrX:153657520chrX:153421769ENST000003699513653_77248365.0TransmembraneHelical%3B Name%3D1
TgeneOPN1LWchrX:153657520chrX:153421769ENST000003699513690_115248365.0TransmembraneHelical%3B Name%3D2


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Fusion Gene Sequence for ATP6AP1-OPN1LW


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.
>8067_8067_1_ATP6AP1-OPN1LW_ATP6AP1_chrX_153657520_ENST00000369762_OPN1LW_chrX_153421769_ENST00000369951_length(transcript)=806nt_BP=349nt
GGGGGCAACGGTCACCTGATCTGCGGCTGTCGAGGCCGCTGAGGCAGTGGAGGCTGAGGCTATGATGGCGGCCATGGCGACGGCTCGAGT
GCGGATGGGGCCGCGATGCGCCCAGGCGCTCTGGCGCATGCCGTGGCTGCCGGTGTTTTTGTCGTTGGCGGCGGCGGCGGCGGCGGCAGC
GGCGGAGCAGCAGGTCCCGCTGGTGCTGTGGTCGAGTGACCGGGACTTGTGGGCTCCTGCGGCCGACACTCATGAAGGCCACATCACCAG
CGACTTGCAGCTCTCTACCTACTTAGATCCCGCCCTGGAGCTGGGTCCCAGGAATGTGCTGCTGTTCCTGCAGGACAAGGTGGCAAAGCA
GCAGAAAGAGTCTGAATCCACCCAGAAGGCAGAGAAGGAAGTGACGCGCATGGTGGTGGTGATGATCTTTGCGTACTGCGTCTGCTGGGG
ACCCTACACCTTCTTCGCATGCTTTGCTGCTGCCAACCCTGGTTACGCCTTCCACCCTTTGATGGCTGCCCTGCCGGCCTACTTTGCCAA
AAGTGCCACTATCTACAACCCCGTTATCTATGTCTTTATGAACCGGCAGTTTCGAAACTGCATCTTGCAGCTTTTCGGGAAGAAGGTTGA
CGATGGCTCTGAACTCTCCAGCGCCTCCAAAACGGAGGTCTCATCTGTGTCCTCGGTATCGCCTGCATGAGGTCTGCCTCCTACCCATCC

>8067_8067_1_ATP6AP1-OPN1LW_ATP6AP1_chrX_153657520_ENST00000369762_OPN1LW_chrX_153421769_ENST00000369951_length(amino acids)=212AA_BP=96
MMAAMATARVRMGPRCAQALWRMPWLPVFLSLAAAAAAAAAEQQVPLVLWSSDRDLWAPAADTHEGHITSDLQLSTYLDPALELGPRNVL
LFLQDKVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNC

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

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Fusion Gene PPI Analysis for ATP6AP1-OPN1LW


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


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 ATP6AP1-OPN1LW


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 ATP6AP1-OPN1LW


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATP6AP1C0024301Lymphoma, Follicular1CTD_human
HgeneATP6AP1C0079745Lymphoma, Large-Cell, Follicular1CTD_human
HgeneATP6AP1C0079758Lymphoma, Mixed-Cell, Follicular1CTD_human
HgeneATP6AP1C0079765Lymphoma, Small Cleaved-Cell, Follicular1CTD_human
HgeneATP6AP1C1956130Lymphoma, Follicular, Grade 11CTD_human
HgeneATP6AP1C1956131Lymphoma, Follicular, Grade 31CTD_human
HgeneATP6AP1C1956132Lymphoma, Follicular, Grade 21CTD_human
HgeneATP6AP1C4310819IMMUNODEFICIENCY 471CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0339537Cone monochromatism4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC2931753Achromatopsia incomplete, X-linked1ORPHANET
TgeneC3159311BORNHOLM EYE DISEASE1ORPHANET
TgeneC3489532Cone-Rod Dystrophy 21ORPHANET
TgeneC3887980Protanomaly1CTD_human;UNIPROT