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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:HMBOX1-INTS9 (FusionGDB2 ID:36763)

Fusion Gene Summary for HMBOX1-INTS9

check button Fusion gene summary
Fusion gene informationFusion gene name: HMBOX1-INTS9
Fusion gene ID: 36763
HgeneTgene
Gene symbol

HMBOX1

INTS9

Gene ID

79618

55756

Gene namehomeobox containing 1integrator complex subunit 9
SynonymsHNF1LA|HOT1|PBHNF|TAH1CPSF2L|INT9|RC74
Cytomap

8p21.1-p12

8p21.1

Type of geneprotein-codingprotein-coding
Descriptionhomeobox-containing protein 1homeobox telomere-binding protein 1homeobox-containing protein PBHNFtelomere-associated homeobox-containing protein 1integrator complex subunit 9protein related to CPSF subunits of 74 kDa
Modification date2020031320200313
UniProtAcc

Q6NT76

Q9NV88

Ensembl transtripts involved in fusion geneENST00000287701, ENST00000397358, 
ENST00000403668, ENST00000444075, 
ENST00000519047, ENST00000523613, 
ENST00000558662, ENST00000355231, 
ENST00000517386, ENST00000524238, 
ENST00000416984, ENST00000521022, 
ENST00000521777, ENST00000397363, 
ENST00000521070, 
Fusion gene scores* DoF score15 X 13 X 8=156011 X 10 X 5=550
# samples 1611
** MAII scorelog2(16/1560*10)=-3.28540221886225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/550*10)=-2.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMBOX1 [Title/Abstract] AND INTS9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHMBOX1(28748195)-INTS9(28717080), # samples:1
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
HgeneHMBOX1

GO:0000122

negative regulation of transcription by RNA polymerase II

21839858

HgeneHMBOX1

GO:0032212

positive regulation of telomere maintenance via telomerase

23685356

HgeneHMBOX1

GO:0045892

negative regulation of transcription, DNA-templated

19757162

HgeneHMBOX1

GO:0051972

regulation of telomerase activity

23685356

HgeneHMBOX1

GO:0051973

positive regulation of telomerase activity

23685356

TgeneINTS9

GO:0016180

snRNA processing

16239144


check buttonFusion 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.

check buttonFusion gene breakpoints across INTS9 (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
ChimerDB4BLCATCGA-G2-A3IBHMBOX1chr8

28748195

+INTS9chr8

28717080

-


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Fusion Gene ORF analysis for HMBOX1-INTS9

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-3CDSENST00000287701ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000287701ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000397358ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000397358ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000403668ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000403668ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000444075ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000444075ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000519047ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000519047ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000523613ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000523613ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000558662ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-3CDSENST00000558662ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-5UTRENST00000287701ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-5UTRENST00000397358ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-5UTRENST00000403668ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-5UTRENST00000444075ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-5UTRENST00000519047ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-5UTRENST00000523613ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-5UTRENST00000558662ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000287701ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000287701ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000397358ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000397358ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000403668ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000403668ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000444075ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000444075ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000519047ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000519047ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000523613ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000523613ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000558662ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
5UTR-intronENST00000558662ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-3CDSENST00000355231ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-3CDSENST00000355231ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-3CDSENST00000517386ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-3CDSENST00000517386ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-3CDSENST00000524238ENST00000416984HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-3CDSENST00000524238ENST00000521022HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-5UTRENST00000355231ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-5UTRENST00000517386ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-5UTRENST00000524238ENST00000521777HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-intronENST00000355231ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-intronENST00000355231ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-intronENST00000517386ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-intronENST00000517386ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-intronENST00000524238ENST00000397363HMBOX1chr8

28748195

+INTS9chr8

28717080

-
intron-intronENST00000524238ENST00000521070HMBOX1chr8

28748195

+INTS9chr8

28717080

-

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 HMBOX1-INTS9


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)

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 HMBOX1-INTS9


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/:28748195/:28717080)
- 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
HMBOX1

Q6NT76

INTS9

Q9NV88

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: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.

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 HMBOX1-INTS9


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 HMBOX1-INTS9


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 HMBOX1-INTS9


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 HMBOX1-INTS9


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