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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:NFIA-CBFA2T3 (FusionGDB2 ID:58862)

Fusion Gene Summary for NFIA-CBFA2T3

check button Fusion gene summary
Fusion gene informationFusion gene name: NFIA-CBFA2T3
Fusion gene ID: 58862
HgeneTgene
Gene symbol

NFIA

CBFA2T3

Gene ID

4774

863

Gene namenuclear factor I ACBFA2/RUNX1 partner transcriptional co-repressor 3
SynonymsBRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-LETO2|MTG16|MTGR2|RUNX1T3|ZMYND4
Cytomap

1p31.3

16q24.3

Type of geneprotein-codingprotein-coding
Descriptionnuclear factor 1 A-typeCCAAT-box-binding transcription factorTGGCA-binding proteinprotein CBFA2T3CBFA2/RUNX1 translocation partner 3MTG8-related gene 2MTG8-related protein 2core-binding factor, runt domain, alpha subunit 2; translocated to, 3myeloid translocation gene 8 and 16bmyeloid translocation gene on chromosome 16 proteinz
Modification date2020031320200313
UniProtAcc

Q12857

O75081

Ensembl transtripts involved in fusion geneENST00000357977, ENST00000371184, 
ENST00000371185, ENST00000371187, 
ENST00000371189, ENST00000371191, 
ENST00000403491, ENST00000407417, 
ENST00000479364, ENST00000485903, 
ENST00000268679, ENST00000327483, 
ENST00000360302, ENST00000436887, 
ENST00000448839, 
Fusion gene scores* DoF score21 X 22 X 8=36966 X 6 X 4=144
# samples 256
** MAII scorelog2(25/3696*10)=-3.88596475675397
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NFIA [Title/Abstract] AND CBFA2T3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint
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
HgeneNFIA

GO:0045944

positive regulation of transcription by RNA polymerase II

17010934

TgeneCBFA2T3

GO:0001666

response to hypoxia

23840896

TgeneCBFA2T3

GO:0008285

negative regulation of cell proliferation

23840896

TgeneCBFA2T3

GO:0030851

granulocyte differentiation

15231665

TgeneCBFA2T3

GO:0045820

negative regulation of glycolytic process

23840896

TgeneCBFA2T3

GO:0045892

negative regulation of transcription, DNA-templated

23840896|25974097

TgeneCBFA2T3

GO:1903715

regulation of aerobic respiration

23840896


check buttonFusion gene breakpoints across NFIA (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 CBFA2T3 (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
ChimerKB4..NFIAchr1

61818121

+CBFA2T3chr16

61818121

-


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Fusion Gene ORF analysis for NFIA-CBFA2T3

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
intron-intronENST00000357977ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000357977ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000357977ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000357977ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000357977ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371184ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371184ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371184ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371184ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371184ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371185ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371185ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371185ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371185ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371185ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371187ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371187ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371187ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371187ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371187ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371189ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371189ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371189ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371189ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371189ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371191ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371191ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371191ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371191ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000371191ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000403491ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000403491ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000403491ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000403491ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000403491ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000407417ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000407417ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000407417ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000407417ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000407417ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000479364ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000479364ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000479364ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000479364ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000479364ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000485903ENST00000268679NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000485903ENST00000327483NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000485903ENST00000360302NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000485903ENST00000436887NFIAchr1

61818121

+CBFA2T3chr16

61818121

-
intron-intronENST00000485903ENST00000448839NFIAchr1

61818121

+CBFA2T3chr16

61818121

-

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 NFIA-CBFA2T3


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 NFIA-CBFA2T3


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/:/:)
- 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
NFIA

Q12857

CBFA2T3

O75081

FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.FUNCTION: Transcriptional corepressor which facilitates transcriptional repression via its association with DNA-binding transcription factors and recruitment of other corepressors and histone-modifying enzymes (PubMed:12559562, PubMed:15203199). Can repress the expression of MMP7 in a ZBTB33-dependent manner (PubMed:23251453). Reduces the protein levels and stability of the transcriptinal regulator HIF1A; interacts with EGLN1 and promotes the HIF1A prolyl hydroxylation-dependent ubiquitination and proteasomal degradation pathway (PubMed:25974097). Contributes to inhibition of glycolysis and stimulation of mitochondrial respiration by down-regulating the expression of glycolytic genes including PFKFB3, PFKFB4, PDK1, PFKP, LDHA and HK1 which are direct targets of HIF1A (PubMed:23840896, PubMed:25974097). Regulates the proliferation and the differentiation of erythroid progenitors by repressing the expression of TAL1 target genes (By similarity). Plays a role in granulocyte differentiation (PubMed:15231665). {ECO:0000250|UniProtKB:O54972, ECO:0000269|PubMed:12183414, ECO:0000269|PubMed:15231665, ECO:0000269|PubMed:16966434, ECO:0000269|PubMed:23251453, ECO:0000269|PubMed:23840896, ECO:0000269|PubMed:25974097, ECO:0000303|PubMed:12559562, ECO:0000303|PubMed:15203199}.; FUNCTION: Isoform 2 functions as an A-kinase-anchoring protein (PubMed:11823486). {ECO:0000269|PubMed:11823486}.

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 NFIA-CBFA2T3


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 NFIA-CBFA2T3


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 NFIA-CBFA2T3


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 NFIA-CBFA2T3


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