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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:IKZF1-RPRD1A (FusionGDB2 ID:39225)

Fusion Gene Summary for IKZF1-RPRD1A

check button Fusion gene summary
Fusion gene informationFusion gene name: IKZF1-RPRD1A
Fusion gene ID: 39225
HgeneTgene
Gene symbol

IKZF1

RPRD1A

Gene ID

10320

55197

Gene nameIKAROS family zinc finger 1regulation of nuclear pre-mRNA domain containing 1A
SynonymsCVID13|Hs.54452|IK1|IKAROS|LYF1|LyF-1|PPP1R92|PRO0758|ZNFN1A1HsT3101|P15RS
Cytomap

7p12.2

18q12.2

Type of geneprotein-codingprotein-coding
DescriptionDNA-binding protein IkarosCLL-associated antigen KW-6ikaros family zinc finger protein 1lymphoid transcription factor LyF-1protein phosphatase 1, regulatory subunit 92zinc finger protein, subfamily 1A, 1 (Ikaros)regulation of nuclear pre-mRNA domain-containing protein 1ACDKN2B-related proteinCyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)cyclin-dependent kinase 2B-inhibitor-related proteinp15INK4B-related protein
Modification date2020032920200313
UniProtAcc

Q13422

.
Ensembl transtripts involved in fusion geneENST00000440768, ENST00000359197, 
ENST00000343574, ENST00000331340, 
ENST00000349824, ENST00000357364, 
ENST00000346667, ENST00000438033, 
ENST00000439701, ENST00000413698, 
ENST00000492782, 		ENST00000590898, 
ENST00000399022, ENST00000337059, 
ENST00000357384, ENST00000588737, 
ENST00000319040, ENST00000588459, 
Fusion gene scores* DoF score8 X 7 X 6=33610 X 9 X 5=450
# samples 812
** MAII scorelog2(8/336*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/450*10)=-1.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: IKZF1 [Title/Abstract] AND RPRD1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointIKZF1(50344518)-RPRD1A(33573263), # 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

check buttonFusion gene breakpoints across IKZF1 (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 RPRD1A (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
ChimerDB4Non-Cancer135NIKZF1chr7

50344518

+RPRD1Achr18

33573263

-


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Fusion Gene ORF analysis for IKZF1-RPRD1A

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-3CDSENST00000440768ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000440768ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000440768ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000440768ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000440768ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000440768ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000440768ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000359197ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000359197ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000359197ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000359197ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000359197ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000359197ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000359197ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000343574ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000343574ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000343574ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000343574ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000343574ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000343574ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000343574ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000331340ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000331340ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000331340ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000331340ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000331340ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000331340ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000331340ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000349824ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000349824ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000349824ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000349824ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000349824ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000349824ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000349824ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000357364ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000357364ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000357364ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000357364ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000357364ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000357364ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000357364ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000346667ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000346667ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000346667ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000346667ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000346667ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000346667ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000346667ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000438033ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000438033ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000438033ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000438033ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000438033ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-intronENST00000438033ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-intronENST00000438033ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000439701ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000439701ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000439701ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000439701ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000439701ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-intronENST00000439701ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-intronENST00000439701ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000413698ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000413698ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000413698ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000413698ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-3CDSENST00000413698ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000413698ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
5UTR-intronENST00000413698ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000492782ENST00000590898IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000492782ENST00000399022IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000492782ENST00000337059IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000492782ENST00000357384IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-3CDSENST00000492782ENST00000588737IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-intronENST00000492782ENST00000319040IKZF1chr7

50344518

+RPRD1Achr18

33573263

-
intron-intronENST00000492782ENST00000588459IKZF1chr7

50344518

+RPRD1Achr18

33573263

-

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 IKZF1-RPRD1A


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 IKZF1-RPRD1A


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
IKZF1

Q13422

.
FUNCTION: Transcription regulator of hematopoietic cell differentiation (PubMed:17934067). Binds gamma-satellite DNA (PubMed:17135265, PubMed:19141594). Plays a role in the development of lymphocytes, B- and T-cells. Binds and activates the enhancer (delta-A element) of the CD3-delta gene. Repressor of the TDT (fikzfterminal deoxynucleotidyltransferase) gene during thymocyte differentiation. Regulates transcription through association with both HDAC-dependent and HDAC-independent complexes. Targets the 2 chromatin-remodeling complexes, NuRD and BAF (SWI/SNF), in a single complex (PYR complex), to the beta-globin locus in adult erythrocytes. Increases normal apoptosis in adult erythroid cells. Confers early temporal competence to retinal progenitor cells (RPCs) (By similarity). Function is isoform-specific and is modulated by dominant-negative inactive isoforms (PubMed:17135265, PubMed:17934067). {ECO:0000250|UniProtKB:Q03267, ECO:0000269|PubMed:10204490, ECO:0000269|PubMed:17135265, ECO:0000269|PubMed:17934067, ECO:0000269|PubMed:19141594}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 IKZF1-RPRD1A


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 IKZF1-RPRD1A


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 IKZF1-RPRD1A


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 IKZF1-RPRD1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneIKZF1C0006413Burkitt Lymphoma4ORPHANET
HgeneIKZF1C1292769Precursor B-cell lymphoblastic leukemia4ORPHANET
HgeneIKZF1C4225173IMMUNODEFICIENCY, COMMON VARIABLE, 132GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneIKZF1C0009324Ulcerative Colitis1CTD_human
HgeneIKZF1C0023452Childhood Acute Lymphoblastic Leukemia1CTD_human;GENOMICS_ENGLAND
HgeneIKZF1C0023453L2 Acute Lymphoblastic Leukemia1CTD_human
HgeneIKZF1C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
HgeneIKZF1C0024141Lupus Erythematosus, Systemic1CTD_human
HgeneIKZF1C0024299Lymphoma1CTD_human
HgeneIKZF1C0038325Stevens-Johnson Syndrome1ORPHANET
HgeneIKZF1C0242380Libman-Sacks Disease1CTD_human
HgeneIKZF1C1846546Recurrent sinopulmonary infections1GENOMICS_ENGLAND
HgeneIKZF1C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CGI;CTD_human
HgeneIKZF1C2930967Gastro-enteropancreatic neuroendocrine tumor1CTD_human