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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-ELAVL4 (FusionGDB2 ID:99950)

Fusion Gene Summary for ZCCHC11-ELAVL4

check button Fusion gene summary
Fusion gene informationFusion gene name: ZCCHC11-ELAVL4
Fusion gene ID: 99950
HgeneTgene
Gene symbol

ZCCHC11

ELAVL4

Gene ID

23318

1996

Gene nameterminal uridylyl transferase 4ELAV like RNA binding protein 4
SynonymsPAPD3|TENT3A|ZCCHC11HUD|PNEM
Cytomap

1p32.3

1p33-p32.3

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 11ELAV-like protein 4ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)ELAV like neuron-specific RNA binding protein 4Hu antigen Dparaneoplastic encephalomyelitis antigen HuD
Modification date2020031320200320
UniProtAcc.

P26378

Ensembl transtripts involved in fusion geneENST00000257177, ENST00000371544, 
ENST00000371541, ENST00000355809, 
ENST00000448907, ENST00000371827, 
ENST00000357083, ENST00000371824, 
ENST00000371823, ENST00000371821, 
ENST00000371819, ENST00000492299, 
Fusion gene scores* DoF score5 X 4 X 4=804 X 3 X 2=24
# samples 54
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ZCCHC11 [Title/Abstract] AND ELAVL4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointZCCHC11(53018603)-ELAVL4(50642761), # 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
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


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 ELAVL4 (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
ChimerDB4BRCATCGA-D8-A1JA-01AZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+


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Fusion Gene ORF analysis for ZCCHC11-ELAVL4

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-3CDSENST00000257177ENST00000448907ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000257177ENST00000371827ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000257177ENST00000357083ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000257177ENST00000371824ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000257177ENST00000371823ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000257177ENST00000371821ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000257177ENST00000371819ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3UTRENST00000257177ENST00000492299ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000371544ENST00000448907ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000371544ENST00000371827ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000371544ENST00000357083ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000371544ENST00000371824ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000371544ENST00000371823ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000371544ENST00000371821ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000371544ENST00000371819ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3UTRENST00000371544ENST00000492299ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3CDSENST00000371541ENST00000448907ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3CDSENST00000371541ENST00000371827ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3CDSENST00000371541ENST00000357083ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3CDSENST00000371541ENST00000371824ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3CDSENST00000371541ENST00000371823ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3CDSENST00000371541ENST00000371821ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3CDSENST00000371541ENST00000371819ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
intron-3UTRENST00000371541ENST00000492299ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000355809ENST00000448907ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000355809ENST00000371827ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000355809ENST00000357083ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000355809ENST00000371824ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000355809ENST00000371823ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000355809ENST00000371821ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3CDSENST00000355809ENST00000371819ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+
5UTR-3UTRENST00000355809ENST00000492299ZCCHC11chr1

53018603

-ELAVL4chr1

50642761

+

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-ELAVL4


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-ELAVL4chr150642760+8.55E-060.9999914
ZCCHC11chr153018602-ELAVL4chr150642760+8.55E-060.9999914

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 ZCCHC11-ELAVL4


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
.ELAVL4

P26378

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.FUNCTION: RNA-binding protein that is involved in the post-transcriptional regulation of mRNAs (PubMed:7898713, PubMed:10710437, PubMed:12034726, PubMed:12468554, PubMed:17035636, PubMed:17234598). Plays a role in the regulation of mRNA stability, alternative splicing and translation (PubMed:7898713, PubMed:10710437, PubMed:12034726, PubMed:12468554, PubMed:17035636, PubMed:17234598). Binds to AU-rich element (ARE) sequences in the 3' untranslated region (UTR) of target mRNAs, including GAP43, VEGF, FOS, CDKN1A and ACHE mRNA (PubMed:7898713, PubMed:10710437, PubMed:12034726, PubMed:12468554). Many of the target mRNAs are coding for RNA-binding proteins, transcription factors and proteins involved in RNA processing and/or neuronal development and function (By similarity). By binding to the mRNA 3'UTR, decreases mRNA deadenylation and thereby contributes to the stabilization of mRNA molecules and their protection from decay (PubMed:12034726). Also binds to the polyadenylated (poly(A)) tail in the 3'UTR of mRNA, thereby increasing its affinity for mRNA binding (PubMed:12034726). Mainly plays a role in neuron-specific RNA processing by stabilization of mRNAs such as GAP43, ACHE and mRNAs of other neuronal proteins, thereby contributing to the differentiation of neural progenitor cells, nervous system development, learning and memory mechanisms (PubMed:12034726, PubMed:12468554, PubMed:17234598, PubMed:18218628). Involved in the negative regulation of the proliferative activity of neuronal stem cells and in the positive regulation of neuronal differentiation of neural progenitor cells (By similarity). Promotes neuronal differentiation of neural stem/progenitor cells in the adult subventricular zone of the hippocampus by binding to and stabilizing SATB1 mRNA (By similarity). Binds and stabilizes MSI1 mRNA in neural stem cells (By similarity). Exhibits increased binding to ACHE mRNA during neuronal differentiation, thereby stabilizing ACHE mRNA and enhancing its expression (PubMed:12468554, PubMed:17234598). Protects CDKN1A mRNA from decay by binding to its 3'-UTR (By similarity). May bind to APP and BACE1 mRNAS and the BACE1AS lncRNA and enhance their stabilization (PubMed:24857657). Plays a role in neurite outgrowth and in the establishment and maturation of dendritic arbors, thereby contributing to neocortical and hippocampal circuitry function (By similarity). Stabilizes GAP43 mRNA and protects it from decay during postembryonic development in the brain (PubMed:12034726). By promoting the stabilization of GAP43 mRNA, plays a role in NGF-mediated neurite outgrowth (By similarity). Binds to BDNF long 3'UTR mRNA, thereby leading to its stabilization and increased dendritic translation after activation of PKC (By similarity). By increasing translation of BDNF after nerve injury, may contribute to nerve regeneration (By similarity). Acts as a stabilizing factor by binding to the 3'UTR of NOVA1 mRNA, thereby increasing its translation and enhancing its functional activity in neuron-specific splicing (PubMed:18218628). Stimulates translation of mRNA in a poly(A)- and cap-dependent manner, possibly by associating with the EIF4F cap-binding complex (By similarity). May also negatively regulate translation by binding to the 5'UTR of Ins2 mRNA, thereby repressing its translation (By similarity). Upon glucose stimulation, Ins2 mRNA is released from ELAVL4 and translational inhibition is abolished (By similarity). Also plays a role in the regulation of alternative splicing (PubMed:17035636). May regulate alternative splicing of CALCA pre-mRNA into Calcitonin and Calcitonin gene-related peptide 1 (CGRP) by competing with splicing regulator TIAR for binding to U-rich intronic sequences of CALCA pre-mRNA (PubMed:17035636). {ECO:0000250|UniProtKB:O09032, ECO:0000250|UniProtKB:Q61701, ECO:0000269|PubMed:10710437, ECO:0000269|PubMed:12034726, ECO:0000269|PubMed:12468554, ECO:0000269|PubMed:17035636, ECO:0000269|PubMed:17234598, ECO:0000269|PubMed:18218628, ECO:0000269|PubMed:24857657, ECO:0000269|PubMed:7898713}.

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-ELAVL4


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-ELAVL4


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-ELAVL4


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-ELAVL4


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