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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:KPNA6-TMEM39B (FusionGDB2 ID:43412)

Fusion Gene Summary for KPNA6-TMEM39B

Fusion gene summary

Fusion gene information	Fusion gene name: KPNA6-TMEM39B
	Fusion gene ID: 43412
		Hgene	Tgene
	Gene symbol	KPNA6	TMEM39B
	Gene ID	23633	55116
	Gene name	karyopherin subunit alpha 6	transmembrane protein 39B
	Synonyms	IPOA7	-
	Cytomap	1p35.2	1p35.2
	Type of gene	protein-coding	protein-coding
	Description	importin subunit alpha-7importin alpha 7 subunitimportin-alpha-S2karyopherin alpha 6 (importin alpha 7)	transmembrane protein 39B
	Modification date	20200313	20200320
	UniProtAcc	O60684	.
	Ensembl transtripts involved in fusion gene	ENST00000373625, ENST00000469790, ENST00000537234, ENST00000545542,	ENST00000336294, ENST00000373634, ENST00000427288, ENST00000456834, ENST00000487305,
Fusion gene scores	* DoF score	12 X 6 X 7=504	3 X 5 X 5=75
	# samples	16	6
	** MAII score	log2(16/504*10)=-1.65535182861255 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/75*10)=-0.321928094887362 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: KPNA6 [Title/Abstract] AND TMEM39B [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	KPNA6(32573735)-TMEM39B(32557276), # samples:2 KPNA6(32573735)-TMEM39B(32540552), # samples:2 KPNA6(32573735)-TMEM39B(32566043), # samples:2
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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Fusion gene breakpoints across KPNA6 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across TMEM39B (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	LGG	TCGA-E1-A7Z2-01A	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
ChimerDB4	LGG	TCGA-E1-A7Z2	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
ChimerDB4	OV	TCGA-09-2044-01B	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
ChimerDB4	READ	TCGA-F5-6814-01A	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
ChimerDB4	READ	TCGA-F5-6814	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+

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Fusion Gene ORF analysis for KPNA6-TMEM39B

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-3UTR	ENST00000373625	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
5CDS-3UTR	ENST00000373625	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
5CDS-3UTR	ENST00000373625	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
5CDS-3UTR	ENST00000373625	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
5CDS-3UTR	ENST00000373625	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
5CDS-3UTR	ENST00000373625	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
5CDS-3UTR	ENST00000373625	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
5CDS-3UTR	ENST00000373625	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
5CDS-3UTR	ENST00000373625	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
5CDS-3UTR	ENST00000373625	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
5CDS-3UTR	ENST00000373625	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
5CDS-5UTR	ENST00000373625	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
5CDS-5UTR	ENST00000373625	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
5CDS-5UTR	ENST00000373625	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
5CDS-5UTR	ENST00000373625	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000469790	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000469790	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000469790	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000469790	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000469790	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000469790	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000469790	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000469790	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000469790	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000469790	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000469790	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000537234	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000537234	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000537234	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000537234	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000537234	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000537234	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000537234	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000537234	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000537234	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000537234	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000537234	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000545542	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000545542	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000545542	ENST00000336294	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000545542	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000545542	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000545542	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000545542	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000545542	ENST00000456834	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-3UTR	ENST00000545542	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-3UTR	ENST00000545542	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-3UTR	ENST00000545542	ENST00000487305	KPNA6	chr1	32573735	+	TMEM39B	chr1	32566043	+
intron-5UTR	ENST00000469790	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-5UTR	ENST00000469790	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-5UTR	ENST00000469790	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-5UTR	ENST00000469790	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-5UTR	ENST00000537234	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-5UTR	ENST00000537234	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-5UTR	ENST00000537234	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-5UTR	ENST00000537234	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-5UTR	ENST00000545542	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-5UTR	ENST00000545542	ENST00000373634	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+
intron-5UTR	ENST00000545542	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32557276	+
intron-5UTR	ENST00000545542	ENST00000427288	KPNA6	chr1	32573735	+	TMEM39B	chr1	32540552	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for KPNA6-TMEM39B

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
KPNA6	chr1	32573735	+	TMEM39B	chr1	32540551	+	9.08E-08	0.9999999
KPNA6	chr1	32573735	+	TMEM39B	chr1	32557272	+	5.79E-14	1
KPNA6	chr1	32573735	+	TMEM39B	chr1	32566042	+	1.23E-12	1
KPNA6	chr1	32573735	+	TMEM39B	chr1	32557272	+	5.79E-14	1
KPNA6	chr1	32573735	+	TMEM39B	chr1	32566042	+	1.23E-12	1
KPNA6	chr1	32573735	+	TMEM39B	chr1	32540551	+	9.08E-08	0.9999999
KPNA6	chr1	32573735	+	TMEM39B	chr1	32557272	+	5.79E-14	1
KPNA6	chr1	32573735	+	TMEM39B	chr1	32566042	+	1.23E-12	1
KPNA6	chr1	32573735	+	TMEM39B	chr1	32557272	+	5.79E-14	1
KPNA6	chr1	32573735	+	TMEM39B	chr1	32566042	+	1.23E-12	1

Distribution 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.

Distribution 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 KPNA6-TMEM39B

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:32573735/:32557276)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
KPNA6 O60684	.
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. {ECO:0000269\|PubMed:10523667}.	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}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for KPNA6-TMEM39B

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 KPNA6-TMEM39B

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for KPNA6-TMEM39B

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for KPNA6-TMEM39B

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source