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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:ELAVL2-CFTR (FusionGDB2 ID:26141)

Fusion Gene Summary for ELAVL2-CFTR

check button Fusion gene summary
Fusion gene informationFusion gene name: ELAVL2-CFTR
Fusion gene ID: 26141
HgeneTgene
Gene symbol

ELAVL2

CFTR

Gene ID

1993

1080

Gene nameELAV like RNA binding protein 2CF transmembrane conductance regulator
SynonymsHEL-N1|HELN1|HUBABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1
Cytomap

9p21.3

7q31.2

Type of geneprotein-codingprotein-coding
DescriptionELAV-like protein 2ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)ELAV like neuron-specific RNA binding protein 2ELAV-like neuronal protein 1 isoform Hel-N2hu-antigen Bnervous system-specific RNA-binding protein Hel-N1cystic fibrosis transmembrane conductance regulatorcAMP-dependent chloride channelchannel conductance-controlling ATPasecystic fibrosis transmembrane conductance regulatingcystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-f
Modification date2020031320200329
UniProtAcc

Q12926

P13569

Ensembl transtripts involved in fusion geneENST00000380117, ENST00000397312, 
ENST00000462649, ENST00000544538, 
ENST00000223951, ENST00000380110, 
ENST00000003084, ENST00000454343, 
ENST00000608965, 
Fusion gene scores* DoF score1 X 2 X 1=213 X 15 X 10=1950
# samples 113
** MAII scorelog2(1/2*10)=2.32192809488736log2(13/1950*10)=-3.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ELAVL2 [Title/Abstract] AND CFTR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointELAVL2(23825804)-CFTR(117304742), # 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
TgeneCFTR

GO:0015701

bicarbonate transport

15010471|19019741

TgeneCFTR

GO:0034976

response to endoplasmic reticulum stress

21884936|28067262

TgeneCFTR

GO:1902476

chloride transmembrane transport

11524016|11707463|19019741

TgeneCFTR

GO:1902943

positive regulation of voltage-gated chloride channel activity

22006324

TgeneCFTR

GO:1904322

cellular response to forskolin

15010471|19621064


check buttonFusion gene breakpoints across ELAVL2 (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 CFTR (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
ChimerDB4PRADTCGA-YL-A8HM-01AELAVL2chr9

23821603

-CFTRchr7

117304742

+
ChimerDB4PRADTCGA-YL-A8HM-01AELAVL2chr9

23825804

-CFTRchr7

117304742

+
ChimerDB4PRADTCGA-YL-A8HMELAVL2chr9

23825804

-CFTRchr7

117304742

+


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Fusion Gene ORF analysis for ELAVL2-CFTR

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-3CDSENST00000380117ENST00000003084ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-3CDSENST00000380117ENST00000454343ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-3CDSENST00000397312ENST00000003084ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-3CDSENST00000397312ENST00000454343ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-3CDSENST00000462649ENST00000003084ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-3CDSENST00000462649ENST00000454343ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-3CDSENST00000544538ENST00000003084ELAVL2chr9

23821603

-CFTRchr7

117304742

+
5UTR-3CDSENST00000544538ENST00000454343ELAVL2chr9

23821603

-CFTRchr7

117304742

+
5UTR-intronENST00000380117ENST00000608965ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-intronENST00000397312ENST00000608965ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-intronENST00000462649ENST00000608965ELAVL2chr9

23825804

-CFTRchr7

117304742

+
5UTR-intronENST00000544538ENST00000608965ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000223951ENST00000003084ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000223951ENST00000003084ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-3CDSENST00000223951ENST00000454343ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000223951ENST00000454343ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-3CDSENST00000380110ENST00000003084ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000380110ENST00000003084ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-3CDSENST00000380110ENST00000454343ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000380110ENST00000454343ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-3CDSENST00000380117ENST00000003084ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000380117ENST00000454343ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000397312ENST00000003084ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000397312ENST00000454343ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000462649ENST00000003084ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000462649ENST00000454343ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-3CDSENST00000544538ENST00000003084ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-3CDSENST00000544538ENST00000454343ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-intronENST00000223951ENST00000608965ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-intronENST00000223951ENST00000608965ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-intronENST00000380110ENST00000608965ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-intronENST00000380110ENST00000608965ELAVL2chr9

23825804

-CFTRchr7

117304742

+
intron-intronENST00000380117ENST00000608965ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-intronENST00000397312ENST00000608965ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-intronENST00000462649ENST00000608965ELAVL2chr9

23821603

-CFTRchr7

117304742

+
intron-intronENST00000544538ENST00000608965ELAVL2chr9

23825804

-CFTRchr7

117304742

+

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 ELAVL2-CFTR


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)
ELAVL2chr923825803-CFTRchr7117304741+0.97648910.02351086
ELAVL2chr923825803-CFTRchr7117304741+0.97648910.02351086
ELAVL2chr923821602-CFTRchr7117304741+4.40E-050.999956
ELAVL2chr923825803-CFTRchr7117304741+0.97648910.02351086
ELAVL2chr923825803-CFTRchr7117304741+0.97648910.02351086
ELAVL2chr923821602-CFTRchr7117304741+4.40E-050.999956

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 ELAVL2-CFTR


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/:23825804/:117304742)
- 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
ELAVL2

Q12926

CFTR

P13569

FUNCTION: RNA-binding protein that binds to the 3' untranslated region (3'UTR) of target mRNAs (By similarity). Seems to recognize a GAAA motif (By similarity). Can bind to its own 3'UTR, the FOS 3'UTR and the ID 3'UTR (By similarity). {ECO:0000250|UniProtKB:Q60899}.FUNCTION: Epithelial ion channel that plays an important role in the regulation of epithelial ion and water transport and fluid homeostasis (PubMed:26823428). Mediates the transport of chloride ions across the cell membrane (PubMed:10792060, PubMed:11524016, PubMed:11707463, PubMed:12519745, PubMed:15010471, PubMed:12588899, PubMed:17036051, PubMed:19398555, PubMed:19621064, PubMed:22178883, PubMed:25330774, PubMed:1712898, PubMed:8910473, PubMed:9804160, PubMed:12529365, PubMed:17182731, PubMed:26846474, PubMed:28087700). Channel activity is coupled to ATP hydrolysis (PubMed:8910473). The ion channel is also permeable to HCO(3-); selectivity depends on the extracellular chloride concentration (PubMed:15010471, PubMed:19019741). Exerts its function also by modulating the activity of other ion channels and transporters (PubMed:12403779, PubMed:22178883, PubMed:22121115, PubMed:27941075). Plays an important role in airway fluid homeostasis (PubMed:16645176, PubMed:19621064, PubMed:26823428). Contributes to the regulation of the pH and the ion content of the airway surface fluid layer and thereby plays an important role in defense against pathogens (PubMed:14668433, PubMed:16645176, PubMed:26823428). Modulates the activity of the epithelial sodium channel (ENaC) complex, in part by regulating the cell surface expression of the ENaC complex (PubMed:17434346, PubMed:27941075, PubMed:17182731). Inhibits the activity of the ENaC channel containing subunits SCNN1A, SCNN1B and SCNN1G (PubMed:17182731). Inhibits the activity of the ENaC channel containing subunits SCNN1D, SCNN1B and SCNN1G, but not of the ENaC channel containing subunits SCNN1A, SCNN1B and SCNN1G (PubMed:27941075). May regulate bicarbonate secretion and salvage in epithelial cells by regulating the transporter SLC4A7 (PubMed:12403779). Can inhibit the chloride channel activity of ANO1 (PubMed:22178883). Plays a role in the chloride and bicarbonate homeostasis during sperm epididymal maturation and capacitation (PubMed:19923167, PubMed:27714810). {ECO:0000269|PubMed:10792060, ECO:0000269|PubMed:11524016, ECO:0000269|PubMed:11707463, ECO:0000269|PubMed:12403779, ECO:0000269|PubMed:12519745, ECO:0000269|PubMed:12529365, ECO:0000269|PubMed:12588899, ECO:0000269|PubMed:14668433, ECO:0000269|PubMed:15010471, ECO:0000269|PubMed:16645176, ECO:0000269|PubMed:17036051, ECO:0000269|PubMed:1712898, ECO:0000269|PubMed:17182731, ECO:0000269|PubMed:19019741, ECO:0000269|PubMed:19398555, ECO:0000269|PubMed:19621064, ECO:0000269|PubMed:22178883, ECO:0000269|PubMed:25330774, ECO:0000269|PubMed:26627831, ECO:0000269|PubMed:26823428, ECO:0000269|PubMed:26846474, ECO:0000269|PubMed:27714810, ECO:0000269|PubMed:27941075, ECO:0000269|PubMed:28087700, ECO:0000269|PubMed:8910473, ECO:0000269|PubMed:9804160, ECO:0000305|PubMed:19923167}.

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 ELAVL2-CFTR


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 ELAVL2-CFTR


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 ELAVL2-CFTR


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 ELAVL2-CFTR


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