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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:NAT10-CAPRIN1 (FusionGDB2 ID:57306)

Fusion Gene Summary for NAT10-CAPRIN1

check button Fusion gene summary
Fusion gene informationFusion gene name: NAT10-CAPRIN1
Fusion gene ID: 57306
HgeneTgene
Gene symbol

NAT10

CAPRIN1

Gene ID

55226

4076

Gene nameN-acetyltransferase 10cell cycle associated protein 1
SynonymsALP|Kre33|NET43GPIAP1|GPIP137|GRIP137|M11S1|RNG105|p137GPI
Cytomap

11p13

11p13

Type of geneprotein-codingprotein-coding
DescriptionRNA cytidine acetyltransferase18S rRNA cytosine acetyltransferaseN-acetyltransferase 10 (GCN5-related)N-acetyltransferase-like proteincaprin-1GPI-anchored membrane protein 1GPI-anchored protein p137GPI-p137RNA granule protein 105activation/proliferation-associated protein 1caprin 1cytoplasmic activation- and proliferation-associated protein 1cytoplasmic activation/proliferation-
Modification date2020031320200313
UniProtAcc

Q9H0A0

Q14444

Ensembl transtripts involved in fusion geneENST00000257829, ENST00000527971, 
ENST00000531159, ENST00000532555, 
ENST00000533657, ENST00000341394, 
ENST00000389645, ENST00000529307, 
ENST00000530820, ENST00000532820, 
Fusion gene scores* DoF score4 X 5 X 4=8011 X 12 X 6=792
# samples 514
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/792*10)=-2.50007360313464
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NAT10 [Title/Abstract] AND CAPRIN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNAT10(34127339)-CAPRIN1(34118026), # samples:4
Anticipated loss of major functional domain due to fusion event.NAT10-CAPRIN1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
NAT10-CAPRIN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
NAT10-CAPRIN1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneNAT10

GO:0045727

positive regulation of translation

30449621


check buttonFusion gene breakpoints across NAT10 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CAPRIN1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BRCATCGA-AN-A0XU-01ANAT10chr11

34127339

+CAPRIN1chr11

34118026

+
ChimerDB4BRCATCGA-AN-A0XU-01ANAT10chr11

34130380

-CAPRIN1chr11

34118026

+
ChimerDB4BRCATCGA-AN-A0XU-01ANAT10chr11

34130380

+CAPRIN1chr11

34118026

+
ChimerDB4OVTCGA-13-1501-01ANAT10chr11

34127339

-CAPRIN1chr11

34118026

+
ChimerDB4OVTCGA-13-1501-01ANAT10chr11

34127339

+CAPRIN1chr11

34118026

+


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Fusion Gene ORF analysis for NAT10-CAPRIN1

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-3UTRENST00000257829ENST00000533657NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
5CDS-3UTRENST00000527971ENST00000533657NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000257829ENST00000341394NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000257829ENST00000389645NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000257829ENST00000529307NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000257829ENST00000530820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000257829ENST00000532820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000531159ENST00000341394NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000531159ENST00000389645NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000531159ENST00000529307NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000531159ENST00000530820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3CDSENST00000531159ENST00000532820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3UTRENST00000257829ENST00000533657NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
5UTR-3UTRENST00000531159ENST00000533657NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000257829ENST00000341394NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000257829ENST00000389645NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000257829ENST00000529307NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000257829ENST00000530820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000257829ENST00000532820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000527971ENST00000341394NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000527971ENST00000389645NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000527971ENST00000529307NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000527971ENST00000530820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
Frame-shiftENST00000527971ENST00000532820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000527971ENST00000341394NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000527971ENST00000389645NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000527971ENST00000529307NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000527971ENST00000530820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000527971ENST00000532820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000531159ENST00000341394NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000531159ENST00000389645NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000531159ENST00000529307NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000531159ENST00000530820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000531159ENST00000532820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000341394NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000341394NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000389645NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000389645NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000529307NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000529307NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000530820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000530820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000532820NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3CDSENST00000532555ENST00000532820NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3UTRENST00000527971ENST00000533657NAT10chr11

34127339

+CAPRIN1chr11

34118026

+
intron-3UTRENST00000531159ENST00000533657NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3UTRENST00000532555ENST00000533657NAT10chr11

34130380

+CAPRIN1chr11

34118026

+
intron-3UTRENST00000532555ENST00000533657NAT10chr11

34127339

+CAPRIN1chr11

34118026

+

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)

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

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Fusion Genomic Features for NAT10-CAPRIN1


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)
NAT10chr1134130380+CAPRIN1chr1134118025+0.0001015990.99989843
NAT10chr1134127339+CAPRIN1chr1134118025+7.68E-050.9999232
NAT10chr1134127339+CAPRIN1chr1134118025+7.68E-050.9999232
NAT10chr1134130380+CAPRIN1chr1134118025+0.0001015990.99989843
NAT10chr1134127339+CAPRIN1chr1134118025+7.68E-050.9999232
NAT10chr1134127339+CAPRIN1chr1134118025+7.68E-050.9999232

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.

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 NAT10-CAPRIN1


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/:34127339/:34118026)
- 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
NAT10

Q9H0A0

CAPRIN1

Q14444

FUNCTION: RNA cytidine acetyltransferase that catalyzes the formation of N(4)-acetylcytidine (ac4C) modification on mRNAs, 18S rRNA and tRNAs (PubMed:25411247, PubMed:25653167, PubMed:30449621). Catalyzes ac4C modification of a broad range of mRNAs, enhancing mRNA stability and translation (PubMed:30449621). mRNA ac4C modification is frequently present within wobble cytidine sites and promotes translation efficiency (PubMed:30449621). Mediates the formation of ac4C at position 1842 in 18S rRNA (PubMed:25411247). May also catalyze the formation of ac4C at position 1337 in 18S rRNA (By similarity). Required for early nucleolar cleavages of precursor rRNA at sites A0, A1 and A2 during 18S rRNA synthesis (PubMed:25411247, PubMed:25653167). Catalyzes the formation of ac4C in serine and leucine tRNAs (By similarity). Requires the tRNA-binding adapter protein THUMPD1 for full tRNA acetyltransferase activity but not for 18S rRNA acetylation (PubMed:25653167). In addition to RNA acetyltransferase activity, also able to acetylate lysine residues of proteins, such as histones, microtubules, p53/TP53 and MDM2, in vitro (PubMed:14592445, PubMed:17631499, PubMed:19303003, PubMed:26882543, PubMed:27993683, PubMed:30165671). The relevance of the protein lysine acetyltransferase activity is however unsure in vivo (PubMed:30449621). Activates telomerase activity by stimulating the transcription of TERT, and may also regulate telomerase function by affecting the balance of telomerase subunit assembly, disassembly, and localization (PubMed:14592445, PubMed:18082603). Involved in the regulation of centrosome duplication by acetylating CENATAC during mitosis, promoting SASS6 proteasome degradation (PubMed:31722219). {ECO:0000250|UniProtKB:P53914, ECO:0000269|PubMed:14592445, ECO:0000269|PubMed:17631499, ECO:0000269|PubMed:18082603, ECO:0000269|PubMed:19303003, ECO:0000269|PubMed:25411247, ECO:0000269|PubMed:25653167, ECO:0000269|PubMed:26882543, ECO:0000269|PubMed:27993683, ECO:0000269|PubMed:30165671, ECO:0000269|PubMed:30449621, ECO:0000269|PubMed:31722219}.FUNCTION: May regulate the transport and translation of mRNAs of proteins involved in synaptic plasticity in neurons and cell proliferation and migration in multiple cell types. Binds directly and selectively to MYC and CCND2 RNAs. In neuronal cells, directly binds to several mRNAs associated with RNA granules, including BDNF, CAMK2A, CREB1, MAP2, NTRK2 mRNAs, as well as to GRIN1 and KPNB1 mRNAs, but not to rRNAs. {ECO:0000269|PubMed:17210633}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for NAT10-CAPRIN1


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.

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Fusion Gene PPI Analysis for NAT10-CAPRIN1


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 NAT10-CAPRIN1


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 NAT10-CAPRIN1


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