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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:ELP3-FZD3 (FusionGDB2 ID:HG55140TG7976)

Fusion Gene Summary for ELP3-FZD3

check button Fusion gene summary
Fusion gene informationFusion gene name: ELP3-FZD3
Fusion gene ID: hg55140tg7976
HgeneTgene
Gene symbol

ELP3

FZD3

Gene ID

55140

7976

Gene nameelongator acetyltransferase complex subunit 3frizzled class receptor 3
SynonymsKAT9Fz-3
Cytomap('ELP3')('FZD3')

8p21.1

8p21.1

Type of geneprotein-codingprotein-coding
Descriptionelongator complex protein 3elongation protein 3 homologprotein lysine acetyltransferase ELP3tRNA uridine(34) acetyltransferasefrizzled-3frizzled 3, seven transmembrane spanning receptorfrizzled family receptor 3frizzled homolog 3
Modification date2020032220200313
UniProtAcc

Q9H9T3

Q9NPG1

Ensembl transtripts involved in fusion geneENST00000523760, ENST00000256398, 
ENST00000380353, ENST00000524103, 
ENST00000537665, ENST00000542181, 
ENST00000521015, 
Fusion gene scores* DoF score3 X 3 X 3=274 X 5 X 3=60
# samples 35
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ELP3 [Title/Abstract] AND FZD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointELP3(27950750)-FZD3(28378155), # samples:2
Anticipated loss of major functional domain due to fusion event.ELP3-FZD3 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
ELP3-FZD3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ELP3-FZD3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ELP3-FZD3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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
HgeneELP3

GO:0006357

regulation of transcription by RNA polymerase II

11818576

TgeneFZD3

GO:0060070

canonical Wnt signaling pathway

20802536



check button Fusion gene information
* 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
ChimerDB4PRADTCGA-YL-A8SO-01BELP3chr8

27950750

+FZD3chr8

28378155

+
ChimerDB4PRADTCGA-YL-A8SOELP3chr8

27950750

+FZD3chr8

28378155

+


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Fusion Gene ORF analysis for ELP3-FZD3

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
3UTR-3CDSENST00000523760ENST00000240093ELP3chr8

27950750

+FZD3chr8

28378155

+
3UTR-3CDSENST00000523760ENST00000537916ELP3chr8

27950750

+FZD3chr8

28378155

+
3UTR-intronENST00000523760ENST00000517911ELP3chr8

27950750

+FZD3chr8

28378155

+
5CDS-intronENST00000256398ENST00000517911ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000380353ENST00000240093ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000380353ENST00000537916ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000524103ENST00000240093ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000524103ENST00000537916ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000537665ENST00000240093ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000537665ENST00000537916ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000542181ENST00000240093ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-3CDSENST00000542181ENST00000537916ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-intronENST00000380353ENST00000517911ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-intronENST00000524103ENST00000517911ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-intronENST00000537665ENST00000517911ELP3chr8

27950750

+FZD3chr8

28378155

+
5UTR-intronENST00000542181ENST00000517911ELP3chr8

27950750

+FZD3chr8

28378155

+
Frame-shiftENST00000256398ENST00000240093ELP3chr8

27950750

+FZD3chr8

28378155

+
Frame-shiftENST00000256398ENST00000537916ELP3chr8

27950750

+FZD3chr8

28378155

+
intron-3CDSENST00000521015ENST00000240093ELP3chr8

27950750

+FZD3chr8

28378155

+
intron-3CDSENST00000521015ENST00000537916ELP3chr8

27950750

+FZD3chr8

28378155

+
intron-intronENST00000521015ENST00000517911ELP3chr8

27950750

+FZD3chr8

28378155

+

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 ELP3-FZD3


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)
ELP3chr827950750+FZD3chr828378154+0.0081919070.9918081
ELP3chr827950750+FZD3chr828378154+0.0081919070.9918081
ELP3chr827950750+FZD3chr828378154+0.0081919070.9918081
ELP3chr827950750+FZD3chr828378154+0.0081919070.9918081


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 ELP3-FZD3


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/:27950750/:28378155)
- 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
ELP3

Q9H9T3

FZD3

Q9NPG1

FUNCTION: Catalytic tRNA acetyltransferase subunit of the RNA polymerase II elongator complex, which is a component of the RNA polymerase II (Pol II) holoenzyme and is involved in transcriptional elongation (PubMed:11714725, PubMed:11818576, PubMed:15902492, PubMed:16713582). The elongator complex is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine) (PubMed:29415125). In the elongator complex, acts as a tRNA uridine(34) acetyltransferase by mediating formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (By similarity). May also act as a protein lysine acetyltransferase by mediating acetylation of target proteins; such activity is however unclear in vivo and recent evidences suggest that ELP3 primarily acts as a tRNA acetyltransferase (PubMed:29415125). Involved in neurogenesis: regulates the migration and branching of projection neurons in the developing cerebral cortex, through a process depending on alpha-tubulin acetylation (PubMed:19185337). Required for acetylation of GJA1 in the developing cerebral cortex (By similarity). {ECO:0000250|UniProtKB:D5VRB9, ECO:0000250|UniProtKB:Q9CZX0, ECO:0000269|PubMed:11714725, ECO:0000269|PubMed:11818576, ECO:0000269|PubMed:15902492, ECO:0000269|PubMed:16713582, ECO:0000269|PubMed:19185337, ECO:0000269|PubMed:29415125}.FUNCTION: Receptor for Wnt proteins. Most of frizzled receptors are coupled to the beta-catenin canonical signaling pathway, which leads to the activation of disheveled proteins, inhibition of GSK-3 kinase, nuclear accumulation of beta-catenin and activation of Wnt target genes. A second signaling pathway involving PKC and calcium fluxes has been seen for some family members, but it is not yet clear if it represents a distinct pathway or if it can be integrated in the canonical pathway, as PKC seems to be required for Wnt-mediated inactivation of GSK-3 kinase. Both pathways seem to involve interactions with G-proteins. Activation by Wnt5A stimulates PKC activity via a G-protein-dependent mechanism. Involved in transduction and intercellular transmission of polarity information during tissue morphogenesis and/or in differentiated tissues. Plays a role in controlling early axon growth and guidance processes necessary for the formation of a subset of central and peripheral major fiber tracts. Required for the development of major fiber tracts in the central nervous system, including: the anterior commissure, the corpus callosum, the thalamocortical, corticothalamic and nigrostriatal tracts, the corticospinal tract, the fasciculus retroflexus, the mammillothalamic tract, the medial lemniscus, and ascending fiber tracts from the spinal cord to the brain. In the peripheral nervous system, controls axon growth in distinct populations of cranial and spinal motor neurons, including the facial branchimotor nerve, the hypoglossal nerve, the phrenic nerve, and motor nerves innervating dorsal limbs. Involved in the migration of cranial neural crest cells. May also be implicated in the transmission of sensory information from the trunk and limbs to the brain. Controls commissural sensory axons guidance after midline crossing along the anterior-posterior axis in the developing spinal cord in a Wnt-dependent signaling pathway. Together with FZD6, is involved in the neural tube closure and plays a role in the regulation of the establishment of planar cell polarity (PCP), particularly in the orientation of asymmetric bundles of stereocilia on the apical faces of a subset of auditory and vestibular sensory cells located in the inner ear. Promotes neurogenesis by maintaining sympathetic neuroblasts within the cell cycle in a beta-catenin-dependent manner (By similarity). {ECO:0000250|UniProtKB:Q61086}.

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 ELP3-FZD3


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 ELP3-FZD3


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 ELP3-FZD3


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 ELP3-FZD3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneELP3C0006142Malignant neoplasm of breast1CTD_human
HgeneELP3C0027626Neoplasm Invasiveness1CTD_human
HgeneELP3C0027627Neoplasm Metastasis1CTD_human
HgeneELP3C0678222Breast Carcinoma1CTD_human
HgeneELP3C1257931Mammary Neoplasms, Human1CTD_human
HgeneELP3C1458155Mammary Neoplasms1CTD_human
HgeneELP3C4704874Mammary Carcinoma, Human1CTD_human
TgeneC0036341Schizophrenia5PSYGENET
TgeneC0019569Hirschsprung Disease1GENOMICS_ENGLAND