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	Fusion Gene Summary
	Fusion Gene Breakpoints
	Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Geness
	Fusion Genomic Features
	Fusion Gene ORF Annotations
	Fusion Protein Retained/Non-Retained Functional Features
	Fusion Transcript Sequences
	Fusion Protein Sequences
	Personalized Fusion Protein Sequences
	Fusion Gene Expressed Samples
	Related Drugs

Fusion gene:CXCR4_RARA (FusionGDB2 ID:HG7852TG5914)

Fusion Gene Summary for CXCR4_RARA

Fusion gene summary

Fusion gene information	Fusion gene name: CXCR4_RARA
	Fusion gene ID: hg7852tg5914
		Hgene	Tgene
	Gene symbol	CXCR4	RARA
	Gene ID	7852	5914
	Gene name	C-X-C motif chemokine receptor 4	retinoic acid receptor alpha
	Synonyms	CD184|D2S201E|FB22|HM89|HSY3RR|LAP-3|LAP3|LCR1|LESTR|NPY3R|NPYR|NPYRL|NPYY3R|WHIM|WHIMS|WHIMS1	NR1B1|RAR|RARalpha
	Cytomap	2q22.1	17q21.2
	Type of gene	protein-coding	protein-coding
	Description	C-X-C chemokine receptor type 4CD184 antigenLPS-associated protein 3SDF-1 receptorchemokine (C-X-C motif) receptor 4fusinleukocyte-derived seven transmembrane domain receptorlipopolysaccharide-associated protein 3neuropeptide Y receptor Y3neurope	retinoic acid receptor alphaPML-DDX5-RARA fusionPML-DDX5-RARA fusion proteinRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid receptor, alpha polypeptide
	Modification date	20240416	20240411
	UniProtAcc	P61073	P10276
	Ensembl transtripts involved in fusion gene	ENST00000241393, ENST00000409817,  ENST00000466288,
Fusion gene scores	* DoF score	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 13 X 4 X 6=312	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 17 X 69 X 26=30498
	# samples	18	128
	** MAII score	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) log2(18/312*10)=-0.793549122532573 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) log2(128/30498*10)=-4.57449892128224 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CXCR4 [Title/Abstract] AND RARA [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CXCR4(136875615)-RARA(38504567), # samples:1

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Fusion Gene Breakpoints for CXCR4_RARA

RNA-seq based exon junction arranged fusion gene breakpoints from 8 resources (TCGA, CCLE, cBioPortal, GenBank, ChimerDB, ChimerKB, ChildHoodFusions, and GTEx). For the expressed sample information, go to Fusion Gene Sample section.

DNA-seq based exon junction arranged fusion gene breakpoints from dbVar. For the expressed sample information, go to Fusion Gene Sample section.

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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Genes for CXCR4_RARA

To generate these tumorigenic scenario annotations, we implemented a deduction-first, retrieval-later computational framework. The pipeline first applies rule-guided reasoning across ten core mechanistic categories (M1–M10) derived from fusion gene biology to infer candidate mechanisms, tumorigenic scenarios, targeting points, and targeting backgrounds. To ensure empirical accountability, a governed Python workflow retrieves literature candidates via NCBI E-utilities and Europe PMC using tiered searches. Using JSON Schema-constrained LLM evidence judges (GPT-5.6 Luna and Terra), retrieved articles are evaluated for specificity and confidence without de novo PMID generation. This produces two distinct versions: a strict version restricted to high- or medium-confidence fusion-specific evidence, and an extended version incorporating broader gene-, pathway-, and contextual evidence.

* We have 10 tumorigenic mechanism categories of fusion genes as shown below.

Constitutively Active Kinases, Catalytic Domain Dysregulation, & Transmembrane Ligand Fusions	Aberrant Chimeric Transcription Factor / Fusion Transcription Factor Activity	Epigenetic Reprogramming / Histone Modifier Dysregulation	Chromatin Remodeling Dysregulation	Condensate-Driven Transcriptional Rewiring / LLP	Promoter / Enhancer Hijacking	Dominant-Negative Antagonism	Cell Cycle / Checkpoint Bypass / RNA Processing Dysregulation	Subcellular Mislocalization / Spatial Dysregulation	Nuclear Body / Sub-organellar Architecture Disruption & Differentiation Blockade

* Strict version: Restricted to high- or medium-confidence fusion-specific evidence.

Fusion Gene Name

Mechanism Category

Mechanism PubMed

Tumorigenic Scenarios

Tumorigenic Scenario PubMed

Targeting Points

Targeting PubMed

Mechanism Background

Mechanism Background PubMed

* Extended version: Includes all strict-level fusion evidence plus broader gene-, pathway-, and low-confidence contextual evidence.

Fusion Gene Name

Mechanism Category

Mechanism PubMed

Tumorigenic Scenarios

Tumorigenic Scenario PubMed

Targeting Points

Targeting PubMed

Mechanism Background

Mechanism Background PubMed

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
CXCR4 P61073	RARA P10276

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	CXCR4	GO:0007186	G protein-coupled receptor signaling pathway	10644702
Hgene	CXCR4	GO:0030155	regulation of cell adhesion	19703720
Hgene	CXCR4	GO:0038160	CXCL12-activated CXCR4 signaling pathway	28978524
Hgene	CXCR4	GO:0071345	cellular response to cytokine stimulus	21540189
Tgene	RARA	GO:0030853	negative regulation of granulocyte differentiation	19917671
Tgene	RARA	GO:0032689	negative regulation of type II interferon production	18416830
Tgene	RARA	GO:0032720	negative regulation of tumor necrosis factor production	18416830
Tgene	RARA	GO:0032736	positive regulation of interleukin-13 production	18416830
Tgene	RARA	GO:0032753	positive regulation of interleukin-4 production	18416830
Tgene	RARA	GO:0032754	positive regulation of interleukin-5 production	18416830
Tgene	RARA	GO:0042789	mRNA transcription by RNA polymerase II	1310351
Tgene	RARA	GO:0045630	positive regulation of T-helper 2 cell differentiation	18416830
Tgene	RARA	GO:0045892	negative regulation of DNA-templated transcription	20080953
Tgene	RARA	GO:0045893	positive regulation of DNA-templated transcription	18845237|19850744|20080953
Tgene	RARA	GO:0045944	positive regulation of transcription by RNA polymerase II	9430642|19850744|19917671|21131358
Tgene	RARA	GO:0048384	retinoic acid receptor signaling pathway	2825025|19917671
Tgene	RARA	GO:0071391	cellular response to estrogen stimulus	20080953

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Fusion Genomic Features for CXCR4_RARA

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) of In-frame fusion genes. 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)
CXCR4	chr2	136875615	-	RARA	chr17	38504567	+	2.93e-02	9.71e-01

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) of 5UTR-3CSD fusion genes (N-truncated cases).

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

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) of 5CDS-3UTR fusion genes (C-truncated cases).

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution of six genomic regulatory feature tracks across a ±5 kb window centered on the fusion breakpoints. We input the breakpoint sequences into AlphaGenome and obtained predicted genome tracks at single-base-pair resolution for each modality by running a single forward pass over the reference sequence. Specifically, for each breakpoint, AlphaGenome processed and returned predicted track data across diverse modalities, which were then averaged across all tracks within each output type and visualized across the ±5 kb window. The left panel shows the 5'-gene breakpoint ±5 kb area, and the right panel shows the 3'-gene breakpoint area, with tracks grouped by category: chromatin accessibility (DNase-seq, ATAC-seq), active transcription (RNA-seq, CAGE), and chromatin binding (ChIP-Histone, ChIP-TF).

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Fusion Gene ORF Annotations for CXCR4_RARA

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.

ORFfinder Result Based On The Fusion Transcript Sequences of the In-frame Fusion Genes.

ORFfinder Result Based On The Fusion Transcript Sequences of the 5UTR-3CDS Fusion Genes for N-Truncated Protein Search.

ORFfinder Result Based On The Fusion Transcript Sequences of the 5CDS-3UTR Fusion Genes for C-Truncated Protein Search.

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.

DeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5UTR-3CDS Fusion Genes (Potential N-Truncated Proteins).

DeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5CDS-3UTR Fusion Genes (Potential C-Truncated Proteins).

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Fusion Protein Retained/Non-Retained Functional Features for CXCR4_RARA

Protein Level Annotation from FGviewer * 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 (visualization across fusion protein length).

- In-frame and not-retained protein feature among the 13 regional features.

- Retained PPIs in in-frame fusion.

Partner

Hgene

Hbp

Tgene

Tbp

ENST

UniProt

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Hgene

Hbp

Tgene

Tbp

ENST

UniProt

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Fusion Transcript Sequence for CXCR4_RARA

In-frame Fusion Transcript Sequences.

N-Truncated Transcript (5UTR-3CDS) Sequences

C-Truncated Transcript (5CDS-3UTR) Sequences

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Fusion Protein Sequence for CXCR4_RARA

In-frame Fusion Protein Sequences.

N-Truncated Protein (5UTR-3CDS) Sequences

C-Truncated Protein (5CDS-3UTR) Sequences

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Personalized Fusion Protein Sequence for CXCR4_RARA

TCGA Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

CCLE Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

TCGA All Mutated Fusion Protein Sequences

CCLE All Mutated Fusion Protein Sequences

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Fusion Gene Exprssed Samples for CXCR4_RARA

RNA-seq based fusion gene expressed samples.

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Related Drugs for CXCR4_RARA

PubMed Abstract Search With ['A-B' AND 'drug'], ['A::B' AND 'drug'] * For more details on the Studied, Reported, Approved Drugs targeting this fusion gene, Go to FusionPub.

Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08)