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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:OS9-KPNA2 (FusionGDB2 ID:61335)

Fusion Gene Summary for OS9-KPNA2

check button Fusion gene summary
Fusion gene informationFusion gene name: OS9-KPNA2
Fusion gene ID: 61335
HgeneTgene
Gene symbol

OS9

KPNA2

Gene ID

10956

3838

Gene nameOS9 endoplasmic reticulum lectinkaryopherin subunit alpha 2
SynonymsERLEC2|OS-9IPOA1|QIP2|RCH1|SRP1-alpha|SRP1alpha
Cytomap

12q13.3-q14.1

17q24.2

Type of geneprotein-codingprotein-coding
Descriptionprotein OS-9amplified in osteosarcoma 9endoplasmic reticulum lectin 2erlectin 2osteosarcoma amplified 9, endoplasmic reticulum associated proteinosteosarcoma amplified 9, endoplasmic reticulum lectinimportin subunit alpha-1RAG cohort protein 1importin subunit alpha-2importin-alpha-P1karyopherin alpha 2 (RAG cohort 1, importin alpha 1)pendulin
Modification date2020031320200327
UniProtAcc.

P52292

Ensembl transtripts involved in fusion geneENST00000552285, ENST00000315970, 
ENST00000439210, ENST00000389146, 
ENST00000413095, ENST00000551035, 
ENST00000435406, ENST00000257966, 
ENST00000389142, 		ENST00000330459, 
ENST00000537025, ENST00000582898, 
Fusion gene scores* DoF score23 X 16 X 8=29441 X 1 X 1=1
# samples 251
** MAII scorelog2(25/2944*10)=-3.55777767139493
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context

PubMed: OS9 [Title/Abstract] AND KPNA2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointOS9(58114046)-KPNA2(66038200), # samples:1
Anticipated loss of major functional domain due to fusion event.OS9-KPNA2 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
HgeneOS9

GO:0006621

protein retention in ER lumen

18417469

HgeneOS9

GO:0034976

response to endoplasmic reticulum stress

19084021

TgeneKPNA2

GO:0006607

NLS-bearing protein import into nucleus

17324944

TgeneKPNA2

GO:0099527

postsynapse to nucleus signaling pathway

15603742


check buttonFusion gene breakpoints across OS9 (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 KPNA2 (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
ChimerDB4OVTCGA-30-1866OS9chr12

58114046

+KPNA2chr17

66038200

+


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Fusion Gene ORF analysis for OS9-KPNA2

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
intron-3CDSENST00000552285ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000552285ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-intronENST00000552285ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
Frame-shiftENST00000315970ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
Frame-shiftENST00000315970ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
5CDS-intronENST00000315970ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000439210ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000439210ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-intronENST00000439210ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
Frame-shiftENST00000389146ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
Frame-shiftENST00000389146ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
5CDS-intronENST00000389146ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000413095ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000413095ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-intronENST00000413095ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000551035ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000551035ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-intronENST00000551035ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000435406ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000435406ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-intronENST00000435406ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000257966ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000257966ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-intronENST00000257966ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000389142ENST00000330459OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-3CDSENST00000389142ENST00000537025OS9chr12

58114046

+KPNA2chr17

66038200

+
intron-intronENST00000389142ENST00000582898OS9chr12

58114046

+KPNA2chr17

66038200

+

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 OS9-KPNA2


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)
OS9chr1258114046+KPNA2chr1766038200+1.31E-060.9999987
OS9chr1258114046+KPNA2chr1766038200+1.31E-060.9999987

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.

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Fusion Protein Features for OS9-KPNA2


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.KPNA2

P52292

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus.

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 OS9-KPNA2


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 OS9-KPNA2


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 OS9-KPNA2


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 OS9-KPNA2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneKPNA2C0152013Adenocarcinoma of lung (disorder)1CTD_human