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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:GNL3-MANF (FusionGDB2 ID:33796)

Fusion Gene Summary for GNL3-MANF

check button Fusion gene summary
Fusion gene informationFusion gene name: GNL3-MANF
Fusion gene ID: 33796
HgeneTgene
Gene symbol

GNL3

MANF

Gene ID

26354

7873

Gene nameG protein nucleolar 3mesencephalic astrocyte derived neurotrophic factor
SynonymsC77032|E2IG3|NNP47|NSARMET|ARP
Cytomap

3p21.1

3p21.2

Type of geneprotein-codingprotein-coding
Descriptionguanine nucleotide-binding protein-like 3E2-induced gene 3 proteinestradiol-induced nucleotide binding proteinguanine nucleotide binding protein-like 3 (nucleolar)novel nucleolar protein 47nucleolar GTP-binding protein 3nucleosteminmesencephalic astrocyte-derived neurotrophic factorarginine-rich, mutated in early stage tumors
Modification date2020032720200313
UniProtAcc

Q9BVP2

P55145

Ensembl transtripts involved in fusion geneENST00000418458, ENST00000394799, 
ENST00000460073, 
ENST00000470900, 
ENST00000528157, 
Fusion gene scores* DoF score10 X 11 X 5=5504 X 5 X 2=40
# samples 125
** MAII scorelog2(12/550*10)=-2.1963972128035
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/40*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: GNL3 [Title/Abstract] AND MANF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGNL3(52720121)-MANF(51423639), # 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
HgeneGNL3

GO:0017145

stem cell division

25522312


check buttonFusion gene breakpoints across GNL3 (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 MANF (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
ChimerDB4LUSCTCGA-33-AASB-01AGNL3chr3

52720121

-MANFchr3

51423639

+
ChimerDB4LUSCTCGA-33-AASB-01AGNL3chr3

52720121

+MANFchr3

51423639

+
ChimerDB4LUSCTCGA-33-AASBGNL3chr3

52720121

+MANFchr3

51423638

+
ChimerDB4LUSCTCGA-33-AASBGNL3chr3

52720121

+MANFchr3

51423639

+


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Fusion Gene ORF analysis for GNL3-MANF

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-3UTRENST00000418458ENST00000470900GNL3chr3

52720121

+MANFchr3

51423639

+
5CDS-3UTRENST00000418458ENST00000470900GNL3chr3

52720121

+MANFchr3

51423638

+
5UTR-3CDSENST00000394799ENST00000528157GNL3chr3

52720121

+MANFchr3

51423639

+
5UTR-3CDSENST00000394799ENST00000528157GNL3chr3

52720121

+MANFchr3

51423638

+
5UTR-3UTRENST00000394799ENST00000470900GNL3chr3

52720121

+MANFchr3

51423639

+
5UTR-3UTRENST00000394799ENST00000470900GNL3chr3

52720121

+MANFchr3

51423638

+
In-frameENST00000418458ENST00000528157GNL3chr3

52720121

+MANFchr3

51423639

+
In-frameENST00000418458ENST00000528157GNL3chr3

52720121

+MANFchr3

51423638

+
intron-3CDSENST00000460073ENST00000528157GNL3chr3

52720121

+MANFchr3

51423639

+
intron-3CDSENST00000460073ENST00000528157GNL3chr3

52720121

+MANFchr3

51423638

+
intron-3UTRENST00000460073ENST00000470900GNL3chr3

52720121

+MANFchr3

51423639

+
intron-3UTRENST00000460073ENST00000470900GNL3chr3

52720121

+MANFchr3

51423638

+

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)
ENST00000418458GNL3chr352720121+ENST00000528157MANFchr351423639+949186173640155
ENST00000418458GNL3chr352720121+ENST00000528157MANFchr351423638+949186173640155

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
ENST00000418458ENST00000528157GNL3chr352720121+MANFchr351423639+0.0046901540.9953099
ENST00000418458ENST00000528157GNL3chr352720121+MANFchr351423638+0.0046901540.9953099

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Fusion Genomic Features for GNL3-MANF


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)
GNL3chr352720121+MANFchr351423638+0.034078540.9659215
GNL3chr352720121+MANFchr351423638+0.034078540.9659215
GNL3chr352720121+MANFchr351423638+0.034078540.9659215
GNL3chr352720121+MANFchr351423638+0.034078540.9659215

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 GNL3-MANF


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/chr3:52720121/chr3:51423639)
- 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
GNL3

Q9BVP2

MANF

P55145

FUNCTION: May be required to maintain the proliferative capacity of stem cells. Stabilizes MDM2 by preventing its ubiquitination, and hence proteasomal degradation (By similarity). {ECO:0000250, ECO:0000269|PubMed:12464630, ECO:0000269|PubMed:16012751}.FUNCTION: Selectively promotes the survival of dopaminergic neurons of the ventral mid-brain (PubMed:12794311). Modulates GABAergic transmission to the dopaminergic neurons of the substantia nigra (By similarity). Enhances spontaneous, as well as evoked, GABAergic inhibitory postsynaptic currents in dopaminergic neurons (By similarity). Inhibits cell proliferation and endoplasmic reticulum (ER) stress-induced cell death (PubMed:18561914, PubMed:22637475, PubMed:29497057). Retained in the ER/sarcoplasmic reticulum (SR) through association with the endoplasmic reticulum chaperone protein HSPA5 under normal conditions (PubMed:22637475). Up-regulated and secreted by the ER/SR in response to ER stress and hypoxia (PubMed:22637475). Following secretion by the ER/SR, directly binds to 3-O-sulfogalactosylceramide, a lipid sulfatide in the outer cell membrane of target cells (PubMed:29497057). Sulfatide binding promotes its cellular uptake by endocytosis, and is required for its role in alleviating ER stress and cell toxicity under hypoxic and ER stress conditions (PubMed:29497057). {ECO:0000250|UniProtKB:P0C5H9, ECO:0000269|PubMed:12794311, ECO:0000269|PubMed:18561914, ECO:0000269|PubMed:22637475, ECO:0000269|PubMed:29497057}.

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
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+11556_950538.0Coiled coilOntology_term=ECO:0000255
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+11556_954550.0Coiled coilOntology_term=ECO:0000255
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+11556_950538.0Coiled coilOntology_term=ECO:0000255
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+11556_954550.0Coiled coilOntology_term=ECO:0000255
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+115131_3120538.0DomainCP-type G
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+115131_3124550.0DomainCP-type G
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+115131_3120538.0DomainCP-type G
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+115131_3124550.0DomainCP-type G
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+115178_1810538.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+115261_2680538.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+115305_3080538.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+115178_1814550.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+115261_2684550.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+115305_3084550.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+115178_1810538.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+115261_2680538.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+115305_3080538.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+115178_1814550.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+115261_2684550.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+115305_3084550.0Nucleotide bindingGTP
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+115282_4560538.0RegionIntermediate
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+1152_460538.0RegionBasic
HgeneGNL3chr3:52720121chr3:51423638ENST00000394799+115465_5430538.0RegionAcidic
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+115282_4564550.0RegionIntermediate
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+1152_464550.0RegionBasic
HgeneGNL3chr3:52720121chr3:51423638ENST00000418458+115465_5434550.0RegionAcidic
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+115282_4560538.0RegionIntermediate
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+1152_460538.0RegionBasic
HgeneGNL3chr3:52720121chr3:51423639ENST00000394799+115465_5430538.0RegionAcidic
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+115282_4564550.0RegionIntermediate
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+1152_464550.0RegionBasic
HgeneGNL3chr3:52720121chr3:51423639ENST00000418458+115465_5434550.0RegionAcidic


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Fusion Gene Sequence for GNL3-MANF


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.
>33796_33796_1_GNL3-MANF_GNL3_chr3_52720121_ENST00000418458_MANF_chr3_51423638_ENST00000528157_length(transcript)=949nt_BP=186nt
GCGGCCGCCAAGCGATCCCTGCTCCGCGCGACACTGCGTGCCCGCGCACGCAGAGAGGCGGTGACGCACTTTACGGCGGCAGCGTAAGTG
CGTGACGCTCGTCAGTGGCTTCAGTTCACACGTGGCGCCAGCGGAGGCAGGTTGATGTGTTTGTGCTTCCTTCTACAGCCAATATGAAAA
GGCCTATTTGTATTTCTTATCTGGGAAGATTTTACCAGGACCTCAAAGACAGAGATGTCACATTCTCACCAGCCACTATTGAAAACGAAC
TTATAAAGTTCTGCCGGGAAGCAAGAGGCAAAGAGAATCGGTTGTGCTACTATATCGGGGCCACAGATGATGCAGCCACCAAAATCATCA
ATGAGGTATCAAAGCCTCTGGCCCACCACATCCCTGTGGAGAAGATCTGTGAGAAGCTTAAGAAGAAGGACAGCCAGATATGTGAGCTTA
AGTATGACAAGCAGATCGACCTGAGCACAGTGGACCTGAAGAAGCTCCGAGTTAAAGAGCTGAAGAAGATTCTGGATGACTGGGGGGAGA
CATGCAAAGGCTGTGCAGAAAAGTCTGACTACATCCGGAAGATAAATGAACTGATGCCTAAATATGCCCCCAAGGCAGCCAGTGCACGGA
CCGATTTGTAGTCTGCTCAATCTCTGTTGCACCTGAGGGGGAAAAAACAGTTCAACTGCTTACTCCCAAAACAGCCTTTTTGTAATTTAT
TTTTTAAGTGGGCTCCTGACAATACTGTATCAGATGTGAAGCCTGGAGCTTTCCTGATGATGCTGGCCCTACAGTACCCCCATGAGGGGA
TTCCCTTCCTTCTGTTGCTGGTGTACTCTAGGACTTCAAAGTGTGTCTGGGATTTTTTTATTAAAGAAAAAAAATTTCTAGCTGTCCTTG

>33796_33796_1_GNL3-MANF_GNL3_chr3_52720121_ENST00000418458_MANF_chr3_51423638_ENST00000528157_length(amino acids)=155AA_BP=3
MKRPICISYLGRFYQDLKDRDVTFSPATIENELIKFCREARGKENRLCYYIGATDDAATKIINEVSKPLAHHIPVEKICEKLKKKDSQIC

--------------------------------------------------------------
>33796_33796_2_GNL3-MANF_GNL3_chr3_52720121_ENST00000418458_MANF_chr3_51423639_ENST00000528157_length(transcript)=949nt_BP=186nt
GCGGCCGCCAAGCGATCCCTGCTCCGCGCGACACTGCGTGCCCGCGCACGCAGAGAGGCGGTGACGCACTTTACGGCGGCAGCGTAAGTG
CGTGACGCTCGTCAGTGGCTTCAGTTCACACGTGGCGCCAGCGGAGGCAGGTTGATGTGTTTGTGCTTCCTTCTACAGCCAATATGAAAA
GGCCTATTTGTATTTCTTATCTGGGAAGATTTTACCAGGACCTCAAAGACAGAGATGTCACATTCTCACCAGCCACTATTGAAAACGAAC
TTATAAAGTTCTGCCGGGAAGCAAGAGGCAAAGAGAATCGGTTGTGCTACTATATCGGGGCCACAGATGATGCAGCCACCAAAATCATCA
ATGAGGTATCAAAGCCTCTGGCCCACCACATCCCTGTGGAGAAGATCTGTGAGAAGCTTAAGAAGAAGGACAGCCAGATATGTGAGCTTA
AGTATGACAAGCAGATCGACCTGAGCACAGTGGACCTGAAGAAGCTCCGAGTTAAAGAGCTGAAGAAGATTCTGGATGACTGGGGGGAGA
CATGCAAAGGCTGTGCAGAAAAGTCTGACTACATCCGGAAGATAAATGAACTGATGCCTAAATATGCCCCCAAGGCAGCCAGTGCACGGA
CCGATTTGTAGTCTGCTCAATCTCTGTTGCACCTGAGGGGGAAAAAACAGTTCAACTGCTTACTCCCAAAACAGCCTTTTTGTAATTTAT
TTTTTAAGTGGGCTCCTGACAATACTGTATCAGATGTGAAGCCTGGAGCTTTCCTGATGATGCTGGCCCTACAGTACCCCCATGAGGGGA
TTCCCTTCCTTCTGTTGCTGGTGTACTCTAGGACTTCAAAGTGTGTCTGGGATTTTTTTATTAAAGAAAAAAAATTTCTAGCTGTCCTTG

>33796_33796_2_GNL3-MANF_GNL3_chr3_52720121_ENST00000418458_MANF_chr3_51423639_ENST00000528157_length(amino acids)=155AA_BP=3
MKRPICISYLGRFYQDLKDRDVTFSPATIENELIKFCREARGKENRLCYYIGATDDAATKIINEVSKPLAHHIPVEKICEKLKKKDSQIC

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

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Fusion Gene PPI Analysis for GNL3-MANF


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 GNL3-MANF


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 GNL3-MANF


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