Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:HOXB3-PTPRA (FusionGDB2 ID:HG3213TG5786)

Fusion Gene Summary for HOXB3-PTPRA

check button Fusion gene summary
Fusion gene informationFusion gene name: HOXB3-PTPRA
Fusion gene ID: hg3213tg5786
HgeneTgene
Gene symbol

HOXB3

PTPRA

Gene ID

3213

5786

Gene namehomeobox B3protein tyrosine phosphatase receptor type A
SynonymsHOX2|HOX2G|Hox-2.7HEPTP|HLPR|HPTPA|HPTPalpha|LRP|PTPA|PTPRL2|R-PTP-alpha|RPTPA
Cytomap('HOXB3')('PTPRA')

17q21.32

20p13

Type of geneprotein-codingprotein-coding
Descriptionhomeobox protein Hox-B3homeo box 2Ghomeobox protein Hox-2.7homeobox protein Hox-2Greceptor-type tyrosine-protein phosphatase alphaLeukocyte common antigen-related peptide (protein tyrosine phosphate)PTPLCA-related phosphatasePTPase-alphaprotein tyrosine phosphatase, receptor type, alpha polypeptideprotein-tyrosine phosphatase alph
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000460160, ENST00000472863, 
ENST00000476342, ENST00000498678, 
ENST00000311626, ENST00000465120, 
ENST00000470495, ENST00000485909, 
ENST00000489475, ENST00000490677, 
ENST00000552000, 
Fusion gene scores* DoF score9 X 6 X 6=3249 X 9 X 2=162
# samples 109
** MAII scorelog2(10/324*10)=-1.6959938131099
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/162*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HOXB3 [Title/Abstract] AND PTPRA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHOXB3(46667485)-PTPRA(2903853), # 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
HgeneHOXB3

GO:0045944

positive regulation of transcription by RNA polymerase II

9556594



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
ChiTaRS5.0N/ADA748390HOXB3chr17

46667485

-PTPRAchr20

2903853

+


Top

Fusion Gene ORF analysis for HOXB3-PTPRA

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-5UTRENST00000460160ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000460160ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000460160ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000460160ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000460160ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000460160ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000460160ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000472863ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000472863ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000472863ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000472863ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000472863ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000472863ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000472863ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000476342ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000476342ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000476342ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000476342ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000476342ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000476342ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000476342ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000498678ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000498678ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000498678ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000498678ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000498678ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000498678ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
5UTR-5UTRENST00000498678ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000311626ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000311626ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000311626ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000311626ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000311626ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000311626ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000311626ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000465120ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000465120ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000465120ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000465120ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000465120ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000465120ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000465120ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000470495ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000470495ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000470495ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000470495ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000470495ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000470495ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000470495ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000485909ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000485909ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000485909ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000485909ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000485909ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000485909ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000485909ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000489475ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000489475ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000489475ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000489475ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000489475ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000489475ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000489475ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000490677ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000490677ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000490677ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000490677ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000490677ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000490677ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000490677ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000552000ENST00000216877HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000552000ENST00000318266HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000552000ENST00000356147HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000552000ENST00000358719HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000552000ENST00000380393HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000552000ENST00000399903HOXB3chr17

46667485

-PTPRAchr20

2903853

+
intron-5UTRENST00000552000ENST00000425918HOXB3chr17

46667485

-PTPRAchr20

2903853

+

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

Top

Fusion Genomic Features for HOXB3-PTPRA


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)
HOXB3chr1746667486-PTPRAchr202903852+0.0055630070.994437
HOXB3chr1746667486-PTPRAchr202903852+0.0055630070.994437


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.
genomic feature of top 1%

Top

Fusion Protein Features for HOXB3-PTPRA


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/:46667485/:2903853)
- 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
..
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}.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}.

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


Top

Fusion Gene Sequence for HOXB3-PTPRA


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.

Top

Fusion Gene PPI Analysis for HOXB3-PTPRA


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


Top

Related Drugs for HOXB3-PTPRA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for HOXB3-PTPRA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHOXB3C0019284Diaphragmatic Hernia1CTD_human
TgeneC0036341Schizophrenia2PSYGENET
TgeneC0151744Myocardial Ischemia1CTD_human