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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:NKAIN3-TOX (FusionGDB2 ID:59255)

Fusion Gene Summary for NKAIN3-TOX

Fusion gene summary

Fusion gene information	Fusion gene name: NKAIN3-TOX
	Fusion gene ID: 59255
		Hgene	Tgene
	Gene symbol	NKAIN3	TOX
	Gene ID	286183	9760
	Gene name	sodium/potassium transporting ATPase interacting 3	thymocyte selection associated high mobility group box
	Synonyms	FAM77D\|NKAIN3-IT1\|UG0898H09	TOX1
	Cytomap	8q12.3	8q12.1
	Type of gene	protein-coding	protein-coding
	Description	sodium/potassium-transporting ATPase subunit beta-1-interacting protein 3NKAIN3 intronic transcriptNa(+)/K(+)-transporting ATPase subunit beta-1-interacting protein 3Na+/K+ transporting ATPase interacting 3family with sequence similarity 77, member D	thymocyte selection-associated high mobility group box protein TOXthymus high mobility group box protein TOX
	Modification date	20200313	20200313
	UniProtAcc	Q8N8D7	TOX4
	Ensembl transtripts involved in fusion gene	ENST00000519049, ENST00000328472, ENST00000523211,	ENST00000361421,
Fusion gene scores	* DoF score	11 X 10 X 4=440	8 X 5 X 6=240
	# samples	11	8
	** MAII score	log2(11/440*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(8/240*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: NKAIN3 [Title/Abstract] AND TOX [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	NKAIN3(63161686)-TOX(59720828), # 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 NKAIN3 (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 TOX (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	SKCM	TCGA-WE-AAA3-06A	NKAIN3	chr8	63161686	-	TOX	chr8	59720828	-
ChimerDB4	SKCM	TCGA-WE-AAA3-06A	NKAIN3	chr8	63161686	+	TOX	chr8	59720828	-

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Fusion Gene ORF analysis for NKAIN3-TOX

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
3UTR-3CDS	ENST00000519049	ENST00000361421	NKAIN3	chr8	63161686	+	TOX	chr8	59720828	-
In-frame	ENST00000328472	ENST00000361421	NKAIN3	chr8	63161686	+	TOX	chr8	59720828	-
In-frame	ENST00000523211	ENST00000361421	NKAIN3	chr8	63161686	+	TOX	chr8	59720828	-

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)

ENST00000523211

NKAIN3

chr8

63161686

ENST00000361421

TOX

chr8

59720828

2704

186

347

116

ENST00000328472

NKAIN3

chr8

63161686

ENST00000361421

TOX

chr8

59720828

2572

242

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
ENST00000523211	ENST00000361421	NKAIN3	chr8	63161686	+	TOX	chr8	59720828	-	0.15285105	0.84714895
ENST00000328472	ENST00000361421	NKAIN3	chr8	63161686	+	TOX	chr8	59720828	-	0.64629877	0.35370123

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Fusion Genomic Features for NKAIN3-TOX

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)

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 NKAIN3-TOX

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:63161686/chr8:59720828)
- 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
NKAIN3 Q8N8D7	TOX TOX4
	621

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

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000328472

152_172

198.0

Transmembrane

Helical

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000328472

2_22

198.0

Transmembrane

Helical

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000328472

35_55

198.0

Transmembrane

Helical

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000328472

62_82

198.0

Transmembrane

Helical

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000523211

152_172

276.6666666666667

Transmembrane

Helical

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000523211

2_22

276.6666666666667

Transmembrane

Helical

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000523211

35_55

276.6666666666667

Transmembrane

Helical

Hgene

NKAIN3

chr8:63161686

chr8:59720828

ENST00000523211

62_82

276.6666666666667

Transmembrane

Helical

Tgene

TOX

chr8:63161686

chr8:59720828

ENST00000361421

417_420

464

527.0

Compositional bias

Note=Poly-Pro

Tgene

TOX

chr8:63161686

chr8:59720828

ENST00000361421

261_329

464

527.0

DNA binding

HMG box

Tgene

TOX

chr8:63161686

chr8:59720828

ENST00000361421

237_256

464

527.0

Motif

Nuclear localization signal

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Fusion Gene Sequence for NKAIN3-TOX

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.

>59255_59255_1_NKAIN3-TOX_NKAIN3_chr8_63161686_ENST00000328472_TOX_chr8_59720828_ENST00000361421_length(transcript)=2572nt_BP=54nt
ATGGGCTGCTGCACCGGACGCTGCTCGCTCATCTGCCTCTGCGCGCTGCAGTTGGGATTTACTCTTCAACCCGACTATCAGACTATTATC
AATCCTACATCTACAGCTGCACAAGTTGTCACCCAGGCAATGGAGTATGTGCGTTCGGGGTGCAGAAATCCTCCCCCACAACCGGTGGAC
TGGAATAACGACTACTGCAGTAGTGGGGGCATGCAGAGGGACAAAGCACTGTACCTTACTTGAGAATCTGAACACCTCTTCTTTCCACTG
AGGAATTCAGGGAAGTGTTTTCACCATGGATTGCTTTGTACAGTCAAGGCAGTTCTCCATTTTATTAGAAAATACAAGTTGCTAAGCACT
TAGGACCATTTGAGCTTGTGGGTCACCCACTCTGGAAGAAATAGTCATGCTTCTTTATTATTTTTTTAATCCTTTATGGACATTGTTTTT
CTTCTTCCCTGAAGGAAATTTGGACCATTCAGATTTTATGTTGGTTTTTTGCTGTGAAGTGCTGCGCTCTAGTAACTGCCTTAGCAACTG
TAGATGTCTCGGATAAAAGTCCTGGATTTTCCATTGGTTTTCATAATGGGTGTTTATATGAAACTACTAAAGACTTTTTAAATGGCTTGA
TGTAGCAGTCATAGCAAGTTTGTAAATAGCATCTATGTTACACTCTCCTAGAGTATAAAATGTGAATGTTTTTGTAGCTAAATTGTAATT
GAAACTGGCTCATTCCAGTTTATTGATTTCACAATAGGGGTTAAATTGGCAAACATTCATATTTTTACTTCATTTTTAAAACAACTGACT
GATAGTTCTATATTTTCAAAATATTTGAAAATAAAAAGTATTCCCAAGTGATTTTAATTTAAAAACAAATTGGCTTTGTCTCATTGATCA
GACAAAAAGAAACTAGTATTAAGGGAAGCGCAAACACATTTATTTTGTACTGCAGAAAAATTGCTTTTTTGTATCACTTTTTGTGTAATG
GTTAGTAAATGTCATTTAAGTCCTTTTATGTATAAAACTGCCAAATGCTTACCTGGTATTTTATTAGATGCAGAAACAGATTGGAAACAG
CTAAATTACAACTTTTACATATGGCTCTGTCTTATTGTTTCTTCATACTGTGTCTGTATTTAATCTTTTTTTATGGAACCTGTTGCGCCT
ATTTATGAAATAATAAATATAGGTGTTTGTAAGTAAATTTGTTAGTATTTGAAAGAGGTTTCTTTGATGTTTTAACTTTTGCTGGCAAAA
AAAAATTCACGCTTGGTGTGAATACTTTATTATTTAGTTTTTACAGTAACATGAATAAAGCCAAACCTGCTTTTCATTTAGCAGCAAATT
AAAGTAACCAGTCCTTATTTCTGCATTTCTTTGGTTGATGCAAACAAAAAACTATTATATTTAAGAACTTTATTTCTTCATACGACATAA
CAGAATTGCCCTCCAAGTCACACAAGCTCCAAGACTAAACAAACAGACAGGTCCTCTGTCTTAAAAAGGTTACTTCTTGGTTCTCAGCTG
GTTCTAGTCAATTCTGAACCACCACCCCCCGCCCCCCGCAAAAAAGTAAAAGTCAAACCAAACTTCCTCAAGCTGCATGCTTTTCACAAA
ATCCAGAAAGCATTTAAGAATTGAACTAGGGGCTGGAAGAAGTGAAAGGGAAGCATCTAAAAATGAAAGGTGAGTAACCAGATAGCAAAA
GAAAAGGGAAAGCCATCCAAATTTGAAAGCTGTTGATAGAAATTGAGATTCTTGCTGTCTTTTGTGCCTCTACAAGCTACTACTCATTCC
AGAATTCCTGGGTCTTCCAAGAGGATTCTTAAGGTACCAGAGATTTGCTAGGGAACCAAAAGTGCTTGAGAATCTGCCTGAGGGCTTGCA
TAGCTTTCACATTAAAAAAAGAAAAAGCTAGCAGATTTACTCCTTTTTAGGGGATCATATCAAGAAAGTTAGTCTGGTTGGAAACCAAGA
GAATGGCTGATGTCTCTTTCTTGGAATATGTGAAATAAATTTAGCAGTTTAACTAAATACAAATATATGCATTGTGTAATCCACTCAGAA
TTAAACAGACAAAAGGTATGCTTGCTTTGGAATGATTTTAGGCATTGTACAACCTTGAATCACTTGAGCATGTAATAACTAATAAATAAT
GCAGATCCATGTGATTATTAAAATGACTGTAGCTGAGAGCTCTAATTTTCCTGTCTTGAAACTGTATAAGAACTCATGTGATTAAGTTCA
CAGTTTATTGTTTGTCTGTTTAGTATTTTAGAAATATACCAGCACTACTAATTAACTAATGTCTTTTATTTATTATATTATGATAAAGTA
AAAATTTCACTTGCATTAAGTCTAAACTGAGAAGGTAATTACTGGGAGGAGAATGAGCAGCTTTGACTTTGACAGGCGGTTTGTGCAGGA
AAGCACAGTGCCGTGTTGTTTACAGCTTTTCTAGAGCAGCTGTGCGACCAGGGTAGAGAGTGTTGAAATTCAATACCAAATACAGTAAAA

>59255_59255_1_NKAIN3-TOX_NKAIN3_chr8_63161686_ENST00000328472_TOX_chr8_59720828_ENST00000361421_length(amino acids)=80AA_BP=6

--------------------------------------------------------------
>59255_59255_2_NKAIN3-TOX_NKAIN3_chr8_63161686_ENST00000523211_TOX_chr8_59720828_ENST00000361421_length(transcript)=2704nt_BP=186nt
AGCCGCGAGCGGCGGCCGCGGGGCCGAGGAGCCTGGGCCGGGCCGGGCGGGGACTACTCCGGAGTCAGGAGGCAGCAGCGGCGGAGGACG
AGGATCTCTGGCAGTCAGCGCCGCTCGGACGCCGCCGGCACCATGGGCTGCTGCACCGGACGCTGCTCGCTCATCTGCCTCTGCGCGCTG
CAGTTGGGATTTACTCTTCAACCCGACTATCAGACTATTATCAATCCTACATCTACAGCTGCACAAGTTGTCACCCAGGCAATGGAGTAT
GTGCGTTCGGGGTGCAGAAATCCTCCCCCACAACCGGTGGACTGGAATAACGACTACTGCAGTAGTGGGGGCATGCAGAGGGACAAAGCA
CTGTACCTTACTTGAGAATCTGAACACCTCTTCTTTCCACTGAGGAATTCAGGGAAGTGTTTTCACCATGGATTGCTTTGTACAGTCAAG
GCAGTTCTCCATTTTATTAGAAAATACAAGTTGCTAAGCACTTAGGACCATTTGAGCTTGTGGGTCACCCACTCTGGAAGAAATAGTCAT
GCTTCTTTATTATTTTTTTAATCCTTTATGGACATTGTTTTTCTTCTTCCCTGAAGGAAATTTGGACCATTCAGATTTTATGTTGGTTTT
TTGCTGTGAAGTGCTGCGCTCTAGTAACTGCCTTAGCAACTGTAGATGTCTCGGATAAAAGTCCTGGATTTTCCATTGGTTTTCATAATG
GGTGTTTATATGAAACTACTAAAGACTTTTTAAATGGCTTGATGTAGCAGTCATAGCAAGTTTGTAAATAGCATCTATGTTACACTCTCC
TAGAGTATAAAATGTGAATGTTTTTGTAGCTAAATTGTAATTGAAACTGGCTCATTCCAGTTTATTGATTTCACAATAGGGGTTAAATTG
GCAAACATTCATATTTTTACTTCATTTTTAAAACAACTGACTGATAGTTCTATATTTTCAAAATATTTGAAAATAAAAAGTATTCCCAAG
TGATTTTAATTTAAAAACAAATTGGCTTTGTCTCATTGATCAGACAAAAAGAAACTAGTATTAAGGGAAGCGCAAACACATTTATTTTGT
ACTGCAGAAAAATTGCTTTTTTGTATCACTTTTTGTGTAATGGTTAGTAAATGTCATTTAAGTCCTTTTATGTATAAAACTGCCAAATGC
TTACCTGGTATTTTATTAGATGCAGAAACAGATTGGAAACAGCTAAATTACAACTTTTACATATGGCTCTGTCTTATTGTTTCTTCATAC
TGTGTCTGTATTTAATCTTTTTTTATGGAACCTGTTGCGCCTATTTATGAAATAATAAATATAGGTGTTTGTAAGTAAATTTGTTAGTAT
TTGAAAGAGGTTTCTTTGATGTTTTAACTTTTGCTGGCAAAAAAAAATTCACGCTTGGTGTGAATACTTTATTATTTAGTTTTTACAGTA
ACATGAATAAAGCCAAACCTGCTTTTCATTTAGCAGCAAATTAAAGTAACCAGTCCTTATTTCTGCATTTCTTTGGTTGATGCAAACAAA
AAACTATTATATTTAAGAACTTTATTTCTTCATACGACATAACAGAATTGCCCTCCAAGTCACACAAGCTCCAAGACTAAACAAACAGAC
AGGTCCTCTGTCTTAAAAAGGTTACTTCTTGGTTCTCAGCTGGTTCTAGTCAATTCTGAACCACCACCCCCCGCCCCCCGCAAAAAAGTA
AAAGTCAAACCAAACTTCCTCAAGCTGCATGCTTTTCACAAAATCCAGAAAGCATTTAAGAATTGAACTAGGGGCTGGAAGAAGTGAAAG
GGAAGCATCTAAAAATGAAAGGTGAGTAACCAGATAGCAAAAGAAAAGGGAAAGCCATCCAAATTTGAAAGCTGTTGATAGAAATTGAGA
TTCTTGCTGTCTTTTGTGCCTCTACAAGCTACTACTCATTCCAGAATTCCTGGGTCTTCCAAGAGGATTCTTAAGGTACCAGAGATTTGC
TAGGGAACCAAAAGTGCTTGAGAATCTGCCTGAGGGCTTGCATAGCTTTCACATTAAAAAAAGAAAAAGCTAGCAGATTTACTCCTTTTT
AGGGGATCATATCAAGAAAGTTAGTCTGGTTGGAAACCAAGAGAATGGCTGATGTCTCTTTCTTGGAATATGTGAAATAAATTTAGCAGT
TTAACTAAATACAAATATATGCATTGTGTAATCCACTCAGAATTAAACAGACAAAAGGTATGCTTGCTTTGGAATGATTTTAGGCATTGT
ACAACCTTGAATCACTTGAGCATGTAATAACTAATAAATAATGCAGATCCATGTGATTATTAAAATGACTGTAGCTGAGAGCTCTAATTT
TCCTGTCTTGAAACTGTATAAGAACTCATGTGATTAAGTTCACAGTTTATTGTTTGTCTGTTTAGTATTTTAGAAATATACCAGCACTAC
TAATTAACTAATGTCTTTTATTTATTATATTATGATAAAGTAAAAATTTCACTTGCATTAAGTCTAAACTGAGAAGGTAATTACTGGGAG
GAGAATGAGCAGCTTTGACTTTGACAGGCGGTTTGTGCAGGAAAGCACAGTGCCGTGTTGTTTACAGCTTTTCTAGAGCAGCTGTGCGAC
CAGGGTAGAGAGTGTTGAAATTCAATACCAAATACAGTAAAAACAAATGTAAATAAAAGAAAACACATCATCAATAAAACTGTTATTATG

>59255_59255_2_NKAIN3-TOX_NKAIN3_chr8_63161686_ENST00000523211_TOX_chr8_59720828_ENST00000361421_length(amino acids)=116AA_BP=3
MHAPTTAVVVIPVHRLWGRISAPRTHILHCLGDNLCSCRCRIDNSLIVGLKSKSQLQRAEADERAASGAAAHGAGGVRAALTARDPRPPP

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

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Fusion Gene PPI Analysis for NKAIN3-TOX

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 NKAIN3-TOX

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 NKAIN3-TOX

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source