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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:ZCCHC11-NFIA (FusionGDB2 ID:100634)

Fusion Gene Summary for ZCCHC11-NFIA

check button Fusion gene summary
Fusion gene informationFusion gene name: ZCCHC11-NFIA
Fusion gene ID: 100634
HgeneTgene
Gene symbol

ZCCHC11

NFIA

Gene ID

23318

4774

Gene nameterminal uridylyl transferase 4nuclear factor I A
SynonymsPAPD3|TENT3A|ZCCHC11BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L
Cytomap

1p32.3

1p31.3

Type of geneprotein-codingprotein-coding
Descriptionterminal uridylyltransferase 4PAP associated domain containing 3TUTase 4zinc finger CCHC domain-containing protein 11zinc finger CCHC-type containing 11zinc finger, CCHC domain containing 11nuclear factor 1 A-typeCCAAT-box-binding transcription factorTGGCA-binding protein
Modification date2020031320200313
UniProtAcc.

Q12857

Ensembl transtripts involved in fusion geneENST00000257177, ENST00000355809, 
ENST00000371544, ENST00000371541, 
ENST00000371191, ENST00000407417, 
ENST00000371185, ENST00000371187, 
ENST00000371189, ENST00000403491, 
ENST00000479364, ENST00000485903, 
ENST00000357977, ENST00000371184, 
Fusion gene scores* DoF score5 X 4 X 4=8021 X 24 X 8=4032
# samples 528
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/4032*10)=-3.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ZCCHC11 [Title/Abstract] AND NFIA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointZCCHC11(53018603)-NFIA(61824819), # samples:2
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
HgeneZCCHC11

GO:0010526

negative regulation of transposition, RNA-mediated

30122351

HgeneZCCHC11

GO:0010586

miRNA metabolic process

25979828

HgeneZCCHC11

GO:0031054

pre-miRNA processing

25979828

HgeneZCCHC11

GO:0031123

RNA 3'-end processing

19703396

TgeneNFIA

GO:0045944

positive regulation of transcription by RNA polymerase II

17010934


check buttonFusion gene breakpoints across ZCCHC11 (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 NFIA (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
ChimerDB4SARCTCGA-DX-AB3A-01AZCCHC11chr1

53018603

-NFIAchr1

61824819

+


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Fusion Gene ORF analysis for ZCCHC11-NFIA

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-3CDSENST00000257177ENST00000371191ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3CDSENST00000257177ENST00000407417ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3CDSENST00000355809ENST00000371191ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3CDSENST00000355809ENST00000407417ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3CDSENST00000371544ENST00000371191ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3CDSENST00000371544ENST00000407417ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000257177ENST00000371185ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000257177ENST00000371187ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000257177ENST00000371189ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000257177ENST00000403491ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000257177ENST00000479364ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000257177ENST00000485903ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000355809ENST00000371185ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000355809ENST00000371187ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000355809ENST00000371189ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000355809ENST00000403491ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000355809ENST00000479364ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000355809ENST00000485903ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000371544ENST00000371185ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000371544ENST00000371187ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000371544ENST00000371189ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000371544ENST00000403491ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000371544ENST00000479364ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-3UTRENST00000371544ENST00000485903ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-intronENST00000257177ENST00000357977ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-intronENST00000257177ENST00000371184ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-intronENST00000355809ENST00000357977ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-intronENST00000355809ENST00000371184ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-intronENST00000371544ENST00000357977ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
5UTR-intronENST00000371544ENST00000371184ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3CDSENST00000371541ENST00000371191ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3CDSENST00000371541ENST00000407417ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3UTRENST00000371541ENST00000371185ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3UTRENST00000371541ENST00000371187ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3UTRENST00000371541ENST00000371189ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3UTRENST00000371541ENST00000403491ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3UTRENST00000371541ENST00000479364ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-3UTRENST00000371541ENST00000485903ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-intronENST00000371541ENST00000357977ZCCHC11chr1

53018603

-NFIAchr1

61824819

+
intron-intronENST00000371541ENST00000371184ZCCHC11chr1

53018603

-NFIAchr1

61824819

+

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 ZCCHC11-NFIA


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)
ZCCHC11chr153018602-NFIAchr161824818+8.23E-050.99991775
ZCCHC11chr153018602-NFIAchr161824818+8.23E-050.99991775

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 ZCCHC11-NFIA


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/:53018603/:61824819)
- 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

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: 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.

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 ZCCHC11-NFIA


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 ZCCHC11-NFIA


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 ZCCHC11-NFIA


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 ZCCHC11-NFIA


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