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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:ATP11B-NIT2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ATP11B-NIT2
FusionPDB ID: 7738
FusionGDB2.0 ID: 7738
HgeneTgene
Gene symbol

ATP11B

NIT2

Gene ID

23200

56954

Gene nameATPase phospholipid transporting 11B (putative)nitrilase family member 2
SynonymsATPIF|ATPIRHEL-S-8a
Cytomap

3q26.33

3q12.2

Type of geneprotein-codingprotein-coding
Descriptionprobable phospholipid-transporting ATPase IFATPase IRATPase, class VI, type 11BP4-ATPase flippase complex alpha subunit ATP11Btruncated ATPase 11B proteinomega-amidase NIT2Nit protein 2epididymis secretory sperm binding protein Li 8anitrilase homolog 2
Modification date2020031320200313
UniProtAcc

Q9Y2G3

Q9NQR4

Ensembl transtripts involved in fusion geneENST idsENST00000482794, ENST00000323116, 
ENST00000493826, 		ENST00000394140, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score20 X 15 X 10=30005 X 5 X 5=125
# samples 226
** MAII scorelog2(22/3000*10)=-3.76938707185858
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/125*10)=-1.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ATP11B [Title/Abstract] AND NIT2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATP11B(182566345)-NIT2(100071247), # samples:1
Anticipated loss of major functional domain due to fusion event.ATP11B-NIT2 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.
ATP11B-NIT2 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.
ATP11B-NIT2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ATP11B-NIT2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ATP11B-NIT2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ATP11B-NIT2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted 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
TgeneNIT2

GO:0006107

oxaloacetate metabolic process

22674578

TgeneNIT2

GO:0006528

asparagine metabolic process

22674578

TgeneNIT2

GO:0006541

glutamine metabolic process

22674578


check buttonFusion gene breakpoints across ATP11B (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 NIT2 (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
ChimerDB4LUSCTCGA-60-2726ATP11Bchr3

182566345

+NIT2chr3

100071247

+


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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)
ENST00000323116ATP11Bchr3182566345+ENST00000394140NIT2chr3100071247+295611112061357383

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
ENST00000323116ENST00000394140ATP11Bchr3182566345+NIT2chr3100071247+0.0005750150.99942505

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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

>7738_7738_1_ATP11B-NIT2_ATP11B_chr3_182566345_ENST00000323116_NIT2_chr3_100071247_ENST00000394140_length(amino acids)=383AA_BP=302
MQPRGPRAPRDPDGDDGGMWRWIRQQLGFDPPHQSDTRTIYVANRFPQNGLYTPQKFIDNRIISSKYTVWNFVPKNLFEQFRRVANFYFL
IIFLVQLMIDTPTSPVTSGLPLFFVITVTAIKQGYEDWLRHNSDNEVNGAPVYVVRSGGLVKTRSKNIRVGDIVRIAKDEIFPADLVLLS
SDRLDGSCHVTTASLDGETNLKTHVAVPETALLQTVANLDTLVAVIECQQPEADLYRFMGRMIITQQMEEIVRPLGPESLLLRGARLKNT
KEIFGVAVYTGMETKMALNYKSKSQKRSAVEKAVDNQVYVATASPARDDKASYVAWGHSTVVNPWGEVLAKAGTEEAIVYSDIDLKKLAE

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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/chr3:182566345/chr3:100071247)
- 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
ATP11B

Q9Y2G3

NIT2

Q9NQR4

FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids, phosphatidylserines (PS) and phosphatidylethanolamines (PE), from the outer to the inner leaflet of intracellular membranes (PubMed:30018401). May contribute to the maintenance of membrane lipid asymmetry in endosome compartment (PubMed:30018401). {ECO:0000269|PubMed:30018401}.FUNCTION: Has omega-amidase activity (PubMed:22674578, PubMed:19595734). The role of omega-amidase is to remove potentially toxic intermediates by converting 2-oxoglutaramate and 2-oxosuccinamate to biologically useful 2-oxoglutarate and oxaloacetate, respectively (PubMed:19595734). {ECO:0000269|PubMed:19595734, ECO:0000269|PubMed:22674578}.

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
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+10301_55283.66666666666671178.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+103078_82283.66666666666671178.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+103056_77283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+103083_104283.66666666666671178.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+10301021_1025283.66666666666671178.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+10301048_1065283.66666666666671178.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030105_289283.66666666666671178.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+10301091_1177283.66666666666671178.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030312_341283.66666666666671178.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030360_876283.66666666666671178.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030899_910283.66666666666671178.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030931_960283.66666666666671178.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030983_997283.66666666666671178.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+161021_10250196.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+161048_10650196.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16105_2890196.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+161091_11770196.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+161_550196.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16312_3410196.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16360_8760196.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+1678_820196.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16899_9100196.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16931_9600196.0Topological domainCytoplasmic
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16983_9970196.0Topological domainExtracellular
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+10301026_1047283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+10301066_1090283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030290_311283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030342_359283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030877_898283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030911_930283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030961_982283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000323116+1030998_1020283.66666666666671178.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+161026_10470196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+161066_10900196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16290_3110196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16342_3590196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+1656_770196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+1683_1040196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16877_8980196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16911_9300196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16961_9820196.0TransmembraneHelical
HgeneATP11Bchr3:182566345chr3:100071247ENST00000493826+16998_10200196.0TransmembraneHelical
TgeneNIT2chr3:182566345chr3:100071247ENST000003941406104_248194.66666666666666277.0DomainCN hydrolase


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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
ATP11B
NIT2


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 ATP11B-NIT2


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 ATP11B-NIT2


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