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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:PAG1-IKZF1 (FusionGDB2 ID:62350)

Fusion Gene Summary for PAG1-IKZF1

check button Fusion gene summary
Fusion gene informationFusion gene name: PAG1-IKZF1
Fusion gene ID: 62350
HgeneTgene
Gene symbol

PAG1

IKZF1

Gene ID

55824

10320

Gene namephosphoprotein membrane anchor with glycosphingolipid microdomains 1IKAROS family zinc finger 1
SynonymsCBP|PAGCVID13|Hs.54452|IK1|IKAROS|LYF1|LyF-1|PPP1R92|PRO0758|ZNFN1A1
Cytomap

8q21.13

7p12.2

Type of geneprotein-codingprotein-coding
Descriptionphosphoprotein associated with glycosphingolipid-enriched microdomains 1Csk-binding proteinphosphoprotein associated with glycosphingolipid microdomains 1transmembrane adapter protein PAGtransmembrane adaptor protein PAGtransmembrane phosphoprotein CDNA-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)
Modification date2020031320200329
UniProtAcc.

Q13422

Ensembl transtripts involved in fusion geneENST00000220597, ENST00000523463, 
ENST00000359197, ENST00000440768, 
ENST00000331340, ENST00000343574, 
ENST00000346667, ENST00000349824, 
ENST00000357364, ENST00000413698, 
ENST00000438033, ENST00000439701, 
ENST00000492782, 
Fusion gene scores* DoF score8 X 7 X 5=2806 X 5 X 4=120
# samples 86
** MAII scorelog2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PAG1 [Title/Abstract] AND IKZF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPAG1(81982346)-IKZF1(50444230), # 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
HgenePAG1

GO:0035556

intracellular signal transduction

10790433

HgenePAG1

GO:0050863

regulation of T cell activation

10790433


check buttonFusion gene breakpoints across PAG1 (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 IKZF1 (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
ChimerDB4STADTCGA-HU-A4G8PAG1chr8

81982346

-IKZF1chr7

50444230

+


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Fusion Gene ORF analysis for PAG1-IKZF1

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-3CDSENST00000220597ENST00000359197PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-3CDSENST00000220597ENST00000440768PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000331340PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000343574PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000346667PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000349824PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000357364PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000413698PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000438033PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000439701PAG1chr8

81982346

-IKZF1chr7

50444230

+
5UTR-intronENST00000220597ENST00000492782PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-3CDSENST00000523463ENST00000359197PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-3CDSENST00000523463ENST00000440768PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000331340PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000343574PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000346667PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000349824PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000357364PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000413698PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000438033PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000439701PAG1chr8

81982346

-IKZF1chr7

50444230

+
intron-intronENST00000523463ENST00000492782PAG1chr8

81982346

-IKZF1chr7

50444230

+

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 PAG1-IKZF1


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)
PAG1chr881982346-IKZF1chr750444230+0.0012946630.99870527
PAG1chr881982346-IKZF1chr750444230+0.0012946630.99870527

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.
genomic feature of top 1%

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Fusion Protein Features for PAG1-IKZF1


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/:81982346/:50444230)
- 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
.IKZF1

Q13422

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: 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}.

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 PAG1-IKZF1


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 PAG1-IKZF1


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 PAG1-IKZF1


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 PAG1-IKZF1


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