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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:NUP62-ATF5 (FusionGDB2 ID:61074)

Fusion Gene Summary for NUP62-ATF5

check button Fusion gene summary
Fusion gene informationFusion gene name: NUP62-ATF5
Fusion gene ID: 61074
HgeneTgene
Gene symbol

NUP62

ATF5

Gene ID

23636

22809

Gene namenucleoporin 62activating transcription factor 5
SynonymsIBSN|SNDI|p62ATFX|HMFN0395
Cytomap

19q13.33

19q13.33

Type of geneprotein-codingprotein-coding
Descriptionnuclear pore glycoprotein p6262 kDa nucleoporinnucleoporin 62kDnucleoporin 62kDanucleoporin Nup62cyclic AMP-dependent transcription factor ATF-5cAMP-dependent transcription factor ATF-5transcription factor ATFx
Modification date2020032720200313
UniProtAcc.

Q9Y2D1

Ensembl transtripts involved in fusion geneENST00000352066, ENST00000422090, 
ENST00000597029, ENST00000597723, 
ENST00000600583, ENST00000413454, 
ENST00000596217, 		ENST00000423777, 
ENST00000595125, ENST00000600336, 
Fusion gene scores* DoF score10 X 6 X 8=4807 X 8 X 4=224
# samples 148
** MAII scorelog2(14/480*10)=-1.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/224*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NUP62 [Title/Abstract] AND ATF5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNUP62(50432582)-ATF5(50435678), # samples:11
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
HgeneNUP62

GO:0006351

transcription, DNA-templated

10373430

HgeneNUP62

GO:0007166

cell surface receptor signaling pathway

10799545

HgeneNUP62

GO:0008285

negative regulation of cell proliferation

11013214

HgeneNUP62

GO:0043066

negative regulation of apoptotic process

11755531

HgeneNUP62

GO:0043069

negative regulation of programmed cell death

11244088

HgeneNUP62

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

10356400

HgeneNUP62

GO:0045893

positive regulation of transcription, DNA-templated

15625236

TgeneATF5

GO:0006355

regulation of transcription, DNA-templated

20654631

TgeneATF5

GO:0008285

negative regulation of cell proliferation

22528486

TgeneATF5

GO:0045892

negative regulation of transcription, DNA-templated

22528486

TgeneATF5

GO:0045893

positive regulation of transcription, DNA-templated

21212266|25512613

TgeneATF5

GO:0045944

positive regulation of transcription by RNA polymerase II

16300731

TgeneATF5

GO:0046605

regulation of centrosome cycle

26213385

TgeneATF5

GO:1902750

negative regulation of cell cycle G2/M phase transition

22528486


check buttonFusion gene breakpoints across NUP62 (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 ATF5 (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
ChimerDB4ESCATCGA-2H-A9GLNUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4ESCATCGA-IG-A5S3NUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4ESCATCGA-IG-A625NUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4ESCATCGA-L5-A8NNNUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4ESCATCGA-VR-A8EZNUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4LUSCTCGA-96-7544-01ANUP62chr19

50432581

-ATF5chr19

50433987

+
ChimerDB4OVTCGA-25-1871NUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4OVTCGA-29-1695NUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4OVTCGA-29-1774NUP62chr19

50432582

-ATF5chr19

50435678

+
ChimerDB4OVTCGA-59-2354NUP62chr19

50432582

-ATF5chr19

50435678

+


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Fusion Gene ORF analysis for NUP62-ATF5

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
5UTR-3CDSENST00000352066ENST00000423777NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000352066ENST00000595125NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000422090ENST00000423777NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000422090ENST00000595125NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000597029ENST00000423777NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000597029ENST00000595125NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000597723ENST00000423777NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000597723ENST00000595125NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000600583ENST00000423777NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-3CDSENST00000600583ENST00000595125NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-5UTRENST00000352066ENST00000423777NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000352066ENST00000595125NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000352066ENST00000600336NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000422090ENST00000423777NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000422090ENST00000595125NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000422090ENST00000600336NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000597029ENST00000423777NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000597029ENST00000595125NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000597029ENST00000600336NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000597723ENST00000423777NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000597723ENST00000595125NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000597723ENST00000600336NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000600583ENST00000423777NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000600583ENST00000595125NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-5UTRENST00000600583ENST00000600336NUP62chr19

50432581

-ATF5chr19

50433987

+
5UTR-intronENST00000352066ENST00000600336NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-intronENST00000422090ENST00000600336NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-intronENST00000597029ENST00000600336NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-intronENST00000597723ENST00000600336NUP62chr19

50432582

-ATF5chr19

50435678

+
5UTR-intronENST00000600583ENST00000600336NUP62chr19

50432582

-ATF5chr19

50435678

+
intron-3CDSENST00000413454ENST00000423777NUP62chr19

50432582

-ATF5chr19

50435678

+
intron-3CDSENST00000413454ENST00000595125NUP62chr19

50432582

-ATF5chr19

50435678

+
intron-3CDSENST00000596217ENST00000423777NUP62chr19

50432582

-ATF5chr19

50435678

+
intron-3CDSENST00000596217ENST00000595125NUP62chr19

50432582

-ATF5chr19

50435678

+
intron-5UTRENST00000413454ENST00000423777NUP62chr19

50432581

-ATF5chr19

50433987

+
intron-5UTRENST00000413454ENST00000595125NUP62chr19

50432581

-ATF5chr19

50433987

+
intron-5UTRENST00000413454ENST00000600336NUP62chr19

50432581

-ATF5chr19

50433987

+
intron-5UTRENST00000596217ENST00000423777NUP62chr19

50432581

-ATF5chr19

50433987

+
intron-5UTRENST00000596217ENST00000595125NUP62chr19

50432581

-ATF5chr19

50433987

+
intron-5UTRENST00000596217ENST00000600336NUP62chr19

50432581

-ATF5chr19

50433987

+
intron-intronENST00000413454ENST00000600336NUP62chr19

50432582

-ATF5chr19

50435678

+
intron-intronENST00000596217ENST00000600336NUP62chr19

50432582

-ATF5chr19

50435678

+

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 NUP62-ATF5


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)
NUP62chr1950432582-ATF5chr1950435678+0.99959930.000400764
NUP62chr1950432582-ATF5chr1950435678+0.99959930.000400764
NUP62chr1950432582-ATF5chr1950433988+0.0001791190.9998209
NUP62chr1950432582-ATF5chr1950435678+0.99959930.000400764
NUP62chr1950432582-ATF5chr1950435678+0.99959930.000400764
NUP62chr1950432582-ATF5chr1950433988+0.0001791190.9998209

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 NUP62-ATF5


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/:50432582/:50435678)
- 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
.ATF5

Q9Y2D1

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: Transcription factor that either stimulates or represses gene transcription through binding of different DNA regulatory elements such as cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), ATF5-specific response element (ARE) (consensus: 5'-C[CT]TCT[CT]CCTT[AT]-3') but also the amino acid response element (AARE), present in many viral and cellular promoters. Critically involved, often in a cell type-dependent manner, in cell survival, proliferation, and differentiation (PubMed:10373550, PubMed:15358120, PubMed:21212266, PubMed:20654631). Its transcriptional activity is enhanced by CCND3 and slightly inhibited by CDK4 (PubMed:15358120). Important regulator of the cerebral cortex formation, functions in cerebral cortical neuroprogenitor cells to maintain proliferation and to block differentiation into neurons. Must be down-regulated in order for such cells to exit the cycle and differentiate (By similarity). Participates in the pathways by which SHH promotes cerebellar granule neuron progenitor cells proliferation (By similarity). Critical for survival of mature olfactory sensory neurons (OSN), directs expression of OSN-specific genes (By similarity). May be involved in osteogenic differentiation (PubMed:22442021). Promotes cell proliferation and survival by inducing the expression of EGR1 sinergistically with ELK1. Once acetylated by EP300, binds to ARE sequences on target genes promoters, such as BCL2 and EGR1 (PubMed:21791614). Plays an anti-apoptotic role through the transcriptional regulation of BCL2, this function seems to be cell type-dependent (By similarity). Cooperates with NR1I3/CAR in the transcriptional activation of CYP2B6 in liver (PubMed:18332083). In hepatic cells, represses CRE-dependent transcription and inhibits proliferation by blocking at G2/M phase (PubMed:22528486, PubMed:18701499). May act as a negative regulator of IL1B transduction pathway in liver (PubMed:24379400). Upon IL1B stimulus, cooperates with NLK to activate the transactivation activity of C/EBP subfamily members (PubMed:25512613). Besides its function of transcription factor, acts as a cofactor of CEBPB to activate CEBPA and promote adipocyte differentiation (PubMed:24216764). Regulates centrosome dynamics in a cell-cycle- and centriole-age-dependent manner. Forms 9-foci symmetrical ring scaffold around the mother centriole to control centrosome function and the interaction between centrioles and pericentriolar material (PubMed:26213385). {ECO:0000250|UniProtKB:O70191, ECO:0000250|UniProtKB:Q6P788, ECO:0000269|PubMed:10373550, ECO:0000269|PubMed:15358120, ECO:0000269|PubMed:18332083, ECO:0000269|PubMed:18701499, ECO:0000269|PubMed:20654631, ECO:0000269|PubMed:21212266, ECO:0000269|PubMed:21791614, ECO:0000269|PubMed:22442021, ECO:0000269|PubMed:22528486, ECO:0000269|PubMed:24216764, ECO:0000269|PubMed:24379400, ECO:0000269|PubMed:25512613, ECO:0000269|PubMed:26213385}.

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 NUP62-ATF5


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 NUP62-ATF5


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 NUP62-ATF5


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 NUP62-ATF5


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