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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:AGAP3-NOC4L (FusionGDB2 ID:2825)

Fusion Gene Summary for AGAP3-NOC4L

check button Fusion gene summary
Fusion gene informationFusion gene name: AGAP3-NOC4L
Fusion gene ID: 2825
HgeneTgene
Gene symbol

AGAP3

NOC4L

Gene ID

116988

79050

Gene nameArfGAP with GTPase domain, ankyrin repeat and PH domain 3nucleolar complex associated 4 homolog
SynonymsAGAP-3|CENTG3|CRAG|MRIP-1|cnt-g3NET49|NOC4|UTP19
Cytomap

7q36.1

12q24.33

Type of geneprotein-codingprotein-coding
Descriptionarf-GAP with GTPase, ANK repeat and PH domain-containing protein 3CRAM-associated GTPaseCRMP (collapsin response mediator protein) associatedMR1-interacting proteincentaurin-gamma-3nucleolar complex protein 4 homologNOC4 protein homologNOC4-like proteinnucleolar complex-associated protein 4-like protein
Modification date2020031320200313
UniProtAcc

Q96P47

Q9BVI4

Ensembl transtripts involved in fusion geneENST00000397238, ENST00000473312, 
ENST00000479901, ENST00000335367, 
ENST00000463381, ENST00000476375, 
ENST00000538784, ENST00000535343, 
ENST00000330579, 
Fusion gene scores* DoF score15 X 6 X 10=90036 X 4 X 20=2880
# samples 1441
** MAII scorelog2(14/900*10)=-2.68449817427207
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(41/2880*10)=-2.81237299682423
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AGAP3 [Title/Abstract] AND NOC4L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAGAP3(150784159)-NOC4L(132635526), # 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 AGAP3 (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 NOC4L (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
ChimerDB4SKCMTCGA-DA-A1I4-06AAGAP3chr7

150784159

+NOC4Lchr12

132635526

+


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Fusion Gene ORF analysis for AGAP3-NOC4L

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-5UTRENST00000397238ENST00000538784AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
5CDS-5UTRENST00000473312ENST00000538784AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
5CDS-5UTRENST00000479901ENST00000538784AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
5CDS-intronENST00000397238ENST00000535343AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
5CDS-intronENST00000473312ENST00000535343AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
5CDS-intronENST00000479901ENST00000535343AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
In-frameENST00000397238ENST00000330579AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
In-frameENST00000473312ENST00000330579AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
In-frameENST00000479901ENST00000330579AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-3CDSENST00000335367ENST00000330579AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-3CDSENST00000463381ENST00000330579AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-3CDSENST00000476375ENST00000330579AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-5UTRENST00000335367ENST00000538784AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-5UTRENST00000463381ENST00000538784AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-5UTRENST00000476375ENST00000538784AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-intronENST00000335367ENST00000535343AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-intronENST00000463381ENST00000535343AGAP3chr7

150784159

+NOC4Lchr12

132635526

+
intron-intronENST00000476375ENST00000535343AGAP3chr7

150784159

+NOC4Lchr12

132635526

+

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)
ENST00000473312AGAP3chr7150784159+ENST00000330579NOC4Lchr12132635526+10213310980326
ENST00000479901AGAP3chr7150784159+ENST00000330579NOC4Lchr12132635526+10213310980326
ENST00000397238AGAP3chr7150784159+ENST00000330579NOC4Lchr12132635526+10213310980326

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
ENST00000473312ENST00000330579AGAP3chr7150784159+NOC4Lchr12132635526+0.019930880.98006916
ENST00000479901ENST00000330579AGAP3chr7150784159+NOC4Lchr12132635526+0.019930880.98006916
ENST00000397238ENST00000330579AGAP3chr7150784159+NOC4Lchr12132635526+0.019930880.98006916

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Fusion Genomic Features for AGAP3-NOC4L


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)
AGAP3chr7150784159+NOC4Lchr12132635525+2.19E-091
AGAP3chr7150784159+NOC4Lchr12132635525+2.19E-091

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 AGAP3-NOC4L


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/chr7:150784159/chr12:132635526)
- 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
AGAP3

Q96P47

NOC4L

Q9BVI4

FUNCTION: GTPase-activating protein for the ADP ribosylation factor family (Potential). GTPase which may be involved in the degradation of expanded polyglutamine proteins through the ubiquitin-proteasome pathway. {ECO:0000269|PubMed:16461359, ECO:0000305}.

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
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+11898_105110912.0Nucleotide bindingGTP
TgeneNOC4Lchr7:150784159chr12:132635526ENST00000330579815347_367300517.0TransmembraneHelical
TgeneNOC4Lchr7:150784159chr12:132635526ENST00000330579815375_395300517.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118367_605110912.0DomainPH
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118626_746110912.0DomainArf-GAP
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118142_146110912.0Nucleotide bindingGTP
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118198_201110912.0Nucleotide bindingGTP
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+11884_375110912.0RegionNote=Small GTPase-like
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118748_777110912.0RepeatNote=ANK 1
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118785_814110912.0RepeatNote=ANK 2
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118818_847110912.0RepeatNote=ANK 3
HgeneAGAP3chr7:150784159chr12:132635526ENST00000397238+118641_664110912.0Zinc fingerC4-type
TgeneNOC4Lchr7:150784159chr12:132635526ENST00000330579815297_317300517.0TransmembraneHelical


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Fusion Gene Sequence for AGAP3-NOC4L


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.
>2825_2825_1_AGAP3-NOC4L_AGAP3_chr7_150784159_ENST00000397238_NOC4L_chr12_132635526_ENST00000330579_length(transcript)=1021nt_BP=331nt
ATGAACTTCCAGGCGGGCGGGGGGCAGAGCCCGCAGCAGCAGCAGAGCCTGGCGGCTCCGGGGGGCGGCGGCGCTGCCGCGCAGCAGCTC
GTCTGCGGCGGGCAGTTCGGCGGCGCGGGGCCCGGGGCCGGGGGCGGCGGCGGCCCCTCGCAGCAGCTGGCCGGCGGGCCCCCCCAGCAG
TTCGCGCTCTCCAACTCCGCGGCCATCCGGGCCGAGATCCAGCGCTTCGAGTCCGTGCATCCCAATATCTACGCCATCTACGACCTGATC
GAGCGCATCGAGGATTTGGCGCTGCAGAACCAGATCCGGGAGCACGTCATCTCCATCGAGGGGGGGGCCCTCAGCCTCTTGGCCTTGAAC
GGGCTGTTCATCTTGATTCACAAACACAACCTGGAGTACCCTGACTTCTACCGGAAGCTCTACGGCCTCTTGGACCCCTCTGTCTTTCAC
GTCAAGTACCGCGCCCGCTTCTTCCACCTGGCTGACCTCTTCCTGTCCTCCTCCCACCTCCCCGCCTACCTGGTGGCCGCCTTCGCCAAG
CGGCTGGCCCGCCTGGCCCTGACGGCTCCCCCTGAGGCCCTGCTCATGGTCCTGCCTTTCATCTGTAACCTGCTGCGCCGGCACCCTGCC
TGCCGGGTCCTCGTGCACCGTCCACACGGCCCTGAGTTGGACGCCGACCCCTACGACCCTGGAGAGGAGGACCCAGCCCAGAGCCGGGCC
TTGGAGAGCTCCCTGTGGGAGCTTCAGGCCCTCCAGCGCCACTACCACCCTGAGGTGTCCAAAGCCGCCAGCGTCATCAACCAGGCCCTG
TCCATGCCTGAGGTCAGCATCGCGCCACTGCTGGAGCTCACGGCCTACGAGATCTTTGAGCGGGACCTGAAGAAGAAGGGGCCCGAGCCG
GTGCCACTGGAGTTTATCCCAGCCCAGGGCCTGCTGGGACGGCCGGGTGAACTCTGTGCCCAGCACTTCACGCTCAGCTGACCCTGGCCC

>2825_2825_1_AGAP3-NOC4L_AGAP3_chr7_150784159_ENST00000397238_NOC4L_chr12_132635526_ENST00000330579_length(amino acids)=326AA_BP=110
MNFQAGGGQSPQQQQSLAAPGGGGAAAQQLVCGGQFGGAGPGAGGGGGPSQQLAGGPPQQFALSNSAAIRAEIQRFESVHPNIYAIYDLI
ERIEDLALQNQIREHVISIEGGALSLLALNGLFILIHKHNLEYPDFYRKLYGLLDPSVFHVKYRARFFHLADLFLSSSHLPAYLVAAFAK
RLARLALTAPPEALLMVLPFICNLLRRHPACRVLVHRPHGPELDADPYDPGEEDPAQSRALESSLWELQALQRHYHPEVSKAASVINQAL

--------------------------------------------------------------
>2825_2825_2_AGAP3-NOC4L_AGAP3_chr7_150784159_ENST00000473312_NOC4L_chr12_132635526_ENST00000330579_length(transcript)=1021nt_BP=331nt
ATGAACTTCCAGGCGGGCGGGGGGCAGAGCCCGCAGCAGCAGCAGAGCCTGGCGGCTCCGGGGGGCGGCGGCGCTGCCGCGCAGCAGCTC
GTCTGCGGCGGGCAGTTCGGCGGCGCGGGGCCCGGGGCCGGGGGCGGCGGCGGCCCCTCGCAGCAGCTGGCCGGCGGGCCCCCCCAGCAG
TTCGCGCTCTCCAACTCCGCGGCCATCCGGGCCGAGATCCAGCGCTTCGAGTCCGTGCATCCCAATATCTACGCCATCTACGACCTGATC
GAGCGCATCGAGGATTTGGCGCTGCAGAACCAGATCCGGGAGCACGTCATCTCCATCGAGGGGGGGGCCCTCAGCCTCTTGGCCTTGAAC
GGGCTGTTCATCTTGATTCACAAACACAACCTGGAGTACCCTGACTTCTACCGGAAGCTCTACGGCCTCTTGGACCCCTCTGTCTTTCAC
GTCAAGTACCGCGCCCGCTTCTTCCACCTGGCTGACCTCTTCCTGTCCTCCTCCCACCTCCCCGCCTACCTGGTGGCCGCCTTCGCCAAG
CGGCTGGCCCGCCTGGCCCTGACGGCTCCCCCTGAGGCCCTGCTCATGGTCCTGCCTTTCATCTGTAACCTGCTGCGCCGGCACCCTGCC
TGCCGGGTCCTCGTGCACCGTCCACACGGCCCTGAGTTGGACGCCGACCCCTACGACCCTGGAGAGGAGGACCCAGCCCAGAGCCGGGCC
TTGGAGAGCTCCCTGTGGGAGCTTCAGGCCCTCCAGCGCCACTACCACCCTGAGGTGTCCAAAGCCGCCAGCGTCATCAACCAGGCCCTG
TCCATGCCTGAGGTCAGCATCGCGCCACTGCTGGAGCTCACGGCCTACGAGATCTTTGAGCGGGACCTGAAGAAGAAGGGGCCCGAGCCG
GTGCCACTGGAGTTTATCCCAGCCCAGGGCCTGCTGGGACGGCCGGGTGAACTCTGTGCCCAGCACTTCACGCTCAGCTGACCCTGGCCC

>2825_2825_2_AGAP3-NOC4L_AGAP3_chr7_150784159_ENST00000473312_NOC4L_chr12_132635526_ENST00000330579_length(amino acids)=326AA_BP=110
MNFQAGGGQSPQQQQSLAAPGGGGAAAQQLVCGGQFGGAGPGAGGGGGPSQQLAGGPPQQFALSNSAAIRAEIQRFESVHPNIYAIYDLI
ERIEDLALQNQIREHVISIEGGALSLLALNGLFILIHKHNLEYPDFYRKLYGLLDPSVFHVKYRARFFHLADLFLSSSHLPAYLVAAFAK
RLARLALTAPPEALLMVLPFICNLLRRHPACRVLVHRPHGPELDADPYDPGEEDPAQSRALESSLWELQALQRHYHPEVSKAASVINQAL

--------------------------------------------------------------
>2825_2825_3_AGAP3-NOC4L_AGAP3_chr7_150784159_ENST00000479901_NOC4L_chr12_132635526_ENST00000330579_length(transcript)=1021nt_BP=331nt
ATGAACTTCCAGGCGGGCGGGGGGCAGAGCCCGCAGCAGCAGCAGAGCCTGGCGGCTCCGGGGGGCGGCGGCGCTGCCGCGCAGCAGCTC
GTCTGCGGCGGGCAGTTCGGCGGCGCGGGGCCCGGGGCCGGGGGCGGCGGCGGCCCCTCGCAGCAGCTGGCCGGCGGGCCCCCCCAGCAG
TTCGCGCTCTCCAACTCCGCGGCCATCCGGGCCGAGATCCAGCGCTTCGAGTCCGTGCATCCCAATATCTACGCCATCTACGACCTGATC
GAGCGCATCGAGGATTTGGCGCTGCAGAACCAGATCCGGGAGCACGTCATCTCCATCGAGGGGGGGGCCCTCAGCCTCTTGGCCTTGAAC
GGGCTGTTCATCTTGATTCACAAACACAACCTGGAGTACCCTGACTTCTACCGGAAGCTCTACGGCCTCTTGGACCCCTCTGTCTTTCAC
GTCAAGTACCGCGCCCGCTTCTTCCACCTGGCTGACCTCTTCCTGTCCTCCTCCCACCTCCCCGCCTACCTGGTGGCCGCCTTCGCCAAG
CGGCTGGCCCGCCTGGCCCTGACGGCTCCCCCTGAGGCCCTGCTCATGGTCCTGCCTTTCATCTGTAACCTGCTGCGCCGGCACCCTGCC
TGCCGGGTCCTCGTGCACCGTCCACACGGCCCTGAGTTGGACGCCGACCCCTACGACCCTGGAGAGGAGGACCCAGCCCAGAGCCGGGCC
TTGGAGAGCTCCCTGTGGGAGCTTCAGGCCCTCCAGCGCCACTACCACCCTGAGGTGTCCAAAGCCGCCAGCGTCATCAACCAGGCCCTG
TCCATGCCTGAGGTCAGCATCGCGCCACTGCTGGAGCTCACGGCCTACGAGATCTTTGAGCGGGACCTGAAGAAGAAGGGGCCCGAGCCG
GTGCCACTGGAGTTTATCCCAGCCCAGGGCCTGCTGGGACGGCCGGGTGAACTCTGTGCCCAGCACTTCACGCTCAGCTGACCCTGGCCC

>2825_2825_3_AGAP3-NOC4L_AGAP3_chr7_150784159_ENST00000479901_NOC4L_chr12_132635526_ENST00000330579_length(amino acids)=326AA_BP=110
MNFQAGGGQSPQQQQSLAAPGGGGAAAQQLVCGGQFGGAGPGAGGGGGPSQQLAGGPPQQFALSNSAAIRAEIQRFESVHPNIYAIYDLI
ERIEDLALQNQIREHVISIEGGALSLLALNGLFILIHKHNLEYPDFYRKLYGLLDPSVFHVKYRARFFHLADLFLSSSHLPAYLVAAFAK
RLARLALTAPPEALLMVLPFICNLLRRHPACRVLVHRPHGPELDADPYDPGEEDPAQSRALESSLWELQALQRHYHPEVSKAASVINQAL

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

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Fusion Gene PPI Analysis for AGAP3-NOC4L


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 AGAP3-NOC4L


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 AGAP3-NOC4L


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