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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:CXCR4-PTP4A1 (FusionGDB2 ID:HG7852TG7803)

Fusion Gene Summary for CXCR4-PTP4A1

check button Fusion gene summary
Fusion gene informationFusion gene name: CXCR4-PTP4A1
Fusion gene ID: hg7852tg7803
HgeneTgene
Gene symbol

CXCR4

PTP4A1

Gene ID

7852

7803

Gene nameC-X-C motif chemokine receptor 4protein tyrosine phosphatase 4A1
SynonymsCD184|D2S201E|FB22|HM89|HSY3RR|LAP-3|LAP3|LCR1|LESTR|NPY3R|NPYR|NPYRL|NPYY3R|WHIM|WHIMSHH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1
Cytomap('CXCR4')('PTP4A1')

2q22.1

6q12

Type of geneprotein-codingprotein-coding
DescriptionC-X-C chemokine receptor type 4CD184 antigenLPS-associated protein 3SDF-1 receptorchemokine (C-X-C motif) receptor 4chemokine receptorfusinleukocyte-derived seven transmembrane domain receptorlipopolysaccharide-associated protein 3neuropeptide Y protein tyrosine phosphatase type IVA 1PVT1/PTP4A1 fusionphosphatase of regenerating liver 1protein tyrosine phosphatase type IVA protein 1protein tyrosine phosphatase type IVA, member 1protein-tyrosine phosphatase of regenerating liver 1
Modification date2020031320200320
UniProtAcc

P61073

.
Ensembl transtripts involved in fusion geneENST00000241393, ENST00000409817, 
ENST00000466288, 
Fusion gene scores* DoF score12 X 4 X 4=19215 X 5 X 5=375
# samples 1411
** MAII scorelog2(14/192*10)=-0.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/375*10)=-1.76938707185858
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CXCR4 [Title/Abstract] AND PTP4A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCXCR4(136875616)-PTP4A1(64286341), # 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
HgeneCXCR4

GO:0007186

G protein-coupled receptor signaling pathway

10644702

HgeneCXCR4

GO:0030155

regulation of cell adhesion

19703720

HgeneCXCR4

GO:0038160

CXCL12-activated CXCR4 signaling pathway

28978524

HgeneCXCR4

GO:0071345

cellular response to cytokine stimulus

21540189



check button Fusion gene information
* 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
ChimerDB4Non-CancerERR315406CXCR4chr2

136875616

-PTP4A1chr6

64286341

+


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Fusion Gene ORF analysis for CXCR4-PTP4A1

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
5CDS-3UTRENST00000241393ENST00000473334CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
5CDS-5UTRENST00000241393ENST00000370650CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
5CDS-5UTRENST00000241393ENST00000370651CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
5CDS-5UTRENST00000241393ENST00000578299CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-3UTRENST00000409817ENST00000473334CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-3UTRENST00000466288ENST00000473334CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-5UTRENST00000409817ENST00000370650CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-5UTRENST00000409817ENST00000370651CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-5UTRENST00000409817ENST00000578299CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-5UTRENST00000466288ENST00000370650CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-5UTRENST00000466288ENST00000370651CXCR4chr2

136875616

-PTP4A1chr6

64286341

+
intron-5UTRENST00000466288ENST00000578299CXCR4chr2

136875616

-PTP4A1chr6

64286341

+

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 CXCR4-PTP4A1


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)
CXCR4chr2136875615-PTP4A1chr664286340+0.0005587110.9994413
CXCR4chr2136875615-PTP4A1chr664286340+0.0005587110.9994413


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%

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Fusion Protein Features for CXCR4-PTP4A1


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/:136875616/:64286341)
- 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
CXCR4

P61073

.
FUNCTION: Receptor for the C-X-C chemokine CXCL12/SDF-1 that transduces a signal by increasing intracellular calcium ion levels and enhancing MAPK1/MAPK3 activation (PubMed:10452968, PubMed:28978524, PubMed:18799424, PubMed:24912431). Involved in the AKT signaling cascade (PubMed:24912431). Plays a role in regulation of cell migration, e.g. during wound healing (PubMed:28978524). Acts as a receptor for extracellular ubiquitin; leading to enhanced intracellular calcium ions and reduced cellular cAMP levels (PubMed:20228059). Binds bacterial lipopolysaccharide (LPS) et mediates LPS-induced inflammatory response, including TNF secretion by monocytes (PubMed:11276205). Involved in hematopoiesis and in cardiac ventricular septum formation. Also plays an essential role in vascularization of the gastrointestinal tract, probably by regulating vascular branching and/or remodeling processes in endothelial cells. Involved in cerebellar development. In the CNS, could mediate hippocampal-neuron survival (By similarity). {ECO:0000250|UniProtKB:P70658, ECO:0000269|PubMed:10074102, ECO:0000269|PubMed:10452968, ECO:0000269|PubMed:10644702, ECO:0000269|PubMed:10825158, ECO:0000269|PubMed:11276205, ECO:0000269|PubMed:17197449, ECO:0000269|PubMed:18799424, ECO:0000269|PubMed:20048153, ECO:0000269|PubMed:20228059, ECO:0000269|PubMed:20505072, ECO:0000269|PubMed:24912431, ECO:0000269|PubMed:28978524, ECO:0000269|PubMed:8752280, ECO:0000269|PubMed:8752281}.; FUNCTION: (Microbial infection) Acts as a coreceptor (CD4 being the primary receptor) for human immunodeficiency virus-1/HIV-1 X4 isolates and as a primary receptor for some HIV-2 isolates. Promotes Env-mediated fusion of the virus (PubMed:8849450, PubMed:8929542, PubMed:9427609, PubMed:10074122, PubMed:10756055). {ECO:0000269|PubMed:10074122, ECO:0000269|PubMed:10756055, ECO:0000269|PubMed:8849450, ECO:0000269|PubMed:8929542, ECO:0000269|PubMed:9427609}.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


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Fusion Gene Sequence for CXCR4-PTP4A1


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 CXCR4-PTP4A1


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 CXCR4-PTP4A1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCXCR4P61073DB00452FramycetinAntagonistSmall moleculeApproved
HgeneCXCR4P61073DB06809PlerixaforAntagonistSmall moleculeApproved
HgeneCXCR4P61073DB12698IbalizumabAntagonistBiotechApproved|Investigational

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Related Diseases for CXCR4-PTP4A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCXCR4C0472817WHIM syndrome3CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneCXCR4C0027627Neoplasm Metastasis2CTD_human
HgeneCXCR4C0087031Juvenile-Onset Still Disease2CTD_human
HgeneCXCR4C0340970Congenital neutropenia2GENOMICS_ENGLAND
HgeneCXCR4C3495559Juvenile arthritis2CTD_human
HgeneCXCR4C3714758Juvenile psoriatic arthritis2CTD_human
HgeneCXCR4C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative2CTD_human
HgeneCXCR4C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive2CTD_human
HgeneCXCR4C0003873Rheumatoid Arthritis1CTD_human
HgeneCXCR4C0006142Malignant neoplasm of breast1CTD_human
HgeneCXCR4C0007621Neoplastic Cell Transformation1CTD_human
HgeneCXCR4C0027626Neoplasm Invasiveness1CTD_human
HgeneCXCR4C0027719Nephrosclerosis1CTD_human
HgeneCXCR4C0027796Neuralgia1CTD_human
HgeneCXCR4C0038870Neuralgia, Supraorbital1CTD_human
HgeneCXCR4C0042656Neuralgia, Vidian1CTD_human
HgeneCXCR4C0234247Neuralgia, Atypical1CTD_human
HgeneCXCR4C0234249Neuralgia, Stump1CTD_human
HgeneCXCR4C0423711Neuralgia, Perineal1CTD_human
HgeneCXCR4C0423712Neuralgia, Iliohypogastric Nerve1CTD_human
HgeneCXCR4C0678222Breast Carcinoma1CTD_human
HgeneCXCR4C0751371Neuralgia, Ilioinguinal1CTD_human
HgeneCXCR4C0751372Nerve Pain1CTD_human
HgeneCXCR4C0751373Paroxysmal Nerve Pain1CTD_human
HgeneCXCR4C1257931Mammary Neoplasms, Human1CTD_human
HgeneCXCR4C1458155Mammary Neoplasms1CTD_human
HgeneCXCR4C1834176MYELOKATHEXIS, ISOLATED1GENOMICS_ENGLAND
HgeneCXCR4C4704874Mammary Carcinoma, Human1CTD_human
TgeneC0001973Alcoholic Intoxication, Chronic2PSYGENET