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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:HMBOX1-KANK2 (FusionGDB2 ID:36764)

Fusion Gene Summary for HMBOX1-KANK2

Fusion gene summary

Fusion gene information	Fusion gene name: HMBOX1-KANK2
	Fusion gene ID: 36764
		Hgene	Tgene
	Gene symbol	HMBOX1	KANK2
	Gene ID	79618	25959
	Gene name	homeobox containing 1	KN motif and ankyrin repeat domains 2
	Synonyms	HNF1LA\|HOT1\|PBHNF\|TAH1	ANKRD25\|MXRA3\|NPHS16\|PPKWH\|SIP
	Cytomap	8p21.1-p12	19p13.2
	Type of gene	protein-coding	protein-coding
	Description	homeobox-containing protein 1homeobox telomere-binding protein 1homeobox-containing protein PBHNFtelomere-associated homeobox-containing protein 1	KN motif and ankyrin repeat domain-containing protein 2SRC-interacting proteinSRC1-interacting proteinankyrin repeat domain-containing protein 25kidney ankyrin repeat-containing protein 2matrix-remodeling-associated protein 3
	Modification date	20200313	20200313
	UniProtAcc	Q6NT76	Q63ZY3
	Ensembl transtripts involved in fusion gene	ENST00000287701, ENST00000355231, ENST00000397358, ENST00000403668, ENST00000444075, ENST00000517386, ENST00000519047, ENST00000523613, ENST00000524238, ENST00000558662,	ENST00000355150, ENST00000432929, ENST00000586659, ENST00000587317, ENST00000589359, ENST00000589894,
Fusion gene scores	* DoF score	15 X 13 X 8=1560	4 X 3 X 3=36
	# samples	16	4
	** MAII score	log2(16/1560*10)=-3.28540221886225 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/36*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: HMBOX1 [Title/Abstract] AND KANK2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	HMBOX1(28834553)-KANK2(11274948), # 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
Hgene	HMBOX1	GO:0000122	negative regulation of transcription by RNA polymerase II	21839858
Hgene	HMBOX1	GO:0032212	positive regulation of telomere maintenance via telomerase	23685356
Hgene	HMBOX1	GO:0045892	negative regulation of transcription, DNA-templated	19757162
Hgene	HMBOX1	GO:0051972	regulation of telomerase activity	23685356
Hgene	HMBOX1	GO:0051973	positive regulation of telomerase activity	23685356
Tgene	KANK2	GO:0000122	negative regulation of transcription by RNA polymerase II	17476305
Tgene	KANK2	GO:0008285	negative regulation of cell proliferation	17476305
Tgene	KANK2	GO:0033147	negative regulation of intracellular estrogen receptor signaling pathway	17476305
Tgene	KANK2	GO:0043069	negative regulation of programmed cell death	22371500
Tgene	KANK2	GO:2000134	negative regulation of G1/S transition of mitotic cell cycle	17476305

Fusion gene breakpoints across HMBOX1 (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 KANK2 (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
ChiTaRS5.0	N/A	BI492948	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
ChiTaRS5.0	N/A	BI496579	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+

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Fusion Gene ORF analysis for HMBOX1-KANK2

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
intron-intron	ENST00000287701	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000287701	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000287701	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000287701	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000287701	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000287701	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000355231	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000355231	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000355231	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000355231	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000355231	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000355231	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000397358	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000397358	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000397358	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000397358	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000397358	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000397358	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000403668	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000403668	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000403668	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000403668	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000403668	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000403668	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000444075	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000444075	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000444075	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000444075	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000444075	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000444075	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000517386	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000517386	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000517386	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000517386	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000517386	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000517386	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000519047	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000519047	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000519047	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000519047	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000519047	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000519047	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000523613	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000523613	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000523613	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000523613	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000523613	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000523613	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000524238	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000524238	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000524238	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000524238	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000524238	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000524238	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000558662	ENST00000355150	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000558662	ENST00000432929	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000558662	ENST00000586659	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000558662	ENST00000587317	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000558662	ENST00000589359	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+
intron-intron	ENST00000558662	ENST00000589894	HMBOX1	chr8	28834553	+	KANK2	chr19	11274948	+

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 HMBOX1-KANK2

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 HMBOX1-KANK2

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:28834553/:11274948)
- 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
HMBOX1 Q6NT76	KANK2 Q63ZY3
FUNCTION: Binds directly to 5'-TTAGGG-3' repeats in telomeric DNA (PubMed:23813958, PubMed:23685356). Associates with the telomerase complex at sites of active telomere processing and positively regulates telomere elongation (PubMed:23685356). Important for TERT binding to chromatin, indicating a role in recruitment of the telomerase complex to telomeres (By similarity). Also plays a role in the alternative lengthening of telomeres (ALT) pathway in telomerase-negative cells where it promotes formation and/or maintenance of ALT-associated promyelocytic leukemia bodies (APBs) (PubMed:23813958). Enhances formation of telomere C-circles in ALT cells, suggesting a possible role in telomere recombination (PubMed:23813958). Might also be involved in the DNA damage response at telomeres (PubMed:23813958). {ECO:0000250\|UniProtKB:Q8BJA3, ECO:0000269\|PubMed:23685356, ECO:0000269\|PubMed:23813958}.	FUNCTION: Involved in transcription regulation by sequestering in the cytoplasm nuclear receptor coactivators such as NCOA1, NCOA2 and NCOA3 (PubMed:17476305). Involved in regulation of caspase-independent apoptosis by sequestering the proapoptotic factor AIFM1 in mitochondria (PubMed:22371500). Pro-apoptotic stimuli can induce its proteasomal degradation allowing the translocation of AIFM1 to the nucleus to induce apoptosis (PubMed:22371500). Involved in the negative control of vitamin D receptor signaling pathway (PubMed:24671081). Involved in actin stress fibers formation through its interaction with ARHGDIA and the regulation of the Rho signaling pathway (PubMed:17996375, PubMed:25961457). May thereby play a role in cell adhesion and migration, regulating for instance podocytes migration during development of the kidney (PubMed:25961457). Through the Rho signaling pathway may also regulate cell proliferation (By similarity). {ECO:0000250\|UniProtKB:Q8BX02, ECO:0000269\|PubMed:17476305, ECO:0000269\|PubMed:17996375, ECO:0000269\|PubMed:22371500, ECO:0000269\|PubMed:24671081, ECO:0000269\|PubMed:25961457}.

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 HMBOX1-KANK2

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 HMBOX1-KANK2

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 HMBOX1-KANK2

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 HMBOX1-KANK2

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source