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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:ELF1-FGFR1OP2 (FusionGDB2 ID:26153)

Fusion Gene Summary for ELF1-FGFR1OP2

check button Fusion gene summary
Fusion gene informationFusion gene name: ELF1-FGFR1OP2
Fusion gene ID: 26153
HgeneTgene
Gene symbol

ELF1

FGFR1OP2

Gene ID

84337

26127

Gene nameelongation factor 1 homologFGFR1 oncogene partner 2
SynonymsELF1HSPC123-like|WIT3.0
Cytomap

19p13.2

12p11.23

Type of geneprotein-codingprotein-coding
Descriptiontranscription elongation factor 1 homologELF1 homolog, elongation factor 1elongation factor 1 homolog (ELF1, S. cerevisiae)FGFR1 oncogene partner 2fibroblast growth factor receptor 1 oncogene partner 2wound inducible transcript 3.0
Modification date2020031320200313
UniProtAcc.

Q9NVK5

Ensembl transtripts involved in fusion geneENST00000239882, ENST00000442101, 
ENST00000498824, 		ENST00000327214, 
ENST00000546072, ENST00000229395, 
Fusion gene scores* DoF score18 X 11 X 6=11886 X 5 X 4=120
# samples 176
** MAII scorelog2(17/1188*10)=-2.80492818466306
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ELF1 [Title/Abstract] AND FGFR1OP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointELF1(41556118)-FGFR1OP2(27116274), # 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

check buttonFusion gene breakpoints across ELF1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across FGFR1OP2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4ESCATCGA-IG-A4QTELF1chr13

41556118

-FGFR1OP2chr12

27116274

+


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Fusion Gene ORF analysis for ELF1-FGFR1OP2

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
5CDS-intronENST00000239882ENST00000327214ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
5CDS-intronENST00000239882ENST00000546072ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
5CDS-intronENST00000442101ENST00000327214ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
5CDS-intronENST00000442101ENST00000546072ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
5UTR-3CDSENST00000498824ENST00000229395ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
5UTR-intronENST00000498824ENST00000327214ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
5UTR-intronENST00000498824ENST00000546072ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
In-frameENST00000239882ENST00000229395ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+
In-frameENST00000442101ENST00000229395ELF1chr13

41556118

-FGFR1OP2chr12

27116274

+

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)
ENST00000442101ELF1chr1341556118-ENST00000229395FGFR1OP2chr1227116274+2372300696280138
ENST00000239882ELF1chr1341556118-ENST00000229395FGFR1OP2chr1227116274+2459387783367138

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
ENST00000442101ENST00000229395ELF1chr1341556118-FGFR1OP2chr1227116274+0.0259079170.97409207
ENST00000239882ENST00000229395ELF1chr1341556118-FGFR1OP2chr1227116274+0.0311510880.96884894

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Fusion Genomic Features for ELF1-FGFR1OP2


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)
ELF1chr1341556118-FGFR1OP2chr1227116274+1.33E-101
ELF1chr1341556118-FGFR1OP2chr1227116274+1.33E-101

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.
genomic feature

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 ELF1-FGFR1OP2


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/chr13:41556118/chr12:27116274)
- 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
.FGFR1OP2

Q9NVK5

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: May be involved in wound healing pathway. {ECO:0000250}.

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
TgeneFGFR1OP2chr13:41556118chr12:27116274ENST0000032721436160_223132216.0Coiled coilOntology_term=ECO:0000255
TgeneFGFR1OP2chr13:41556118chr12:27116274ENST0000054607205160_2230173.0Coiled coilOntology_term=ECO:0000255
TgeneFGFR1OP2chr13:41556118chr12:27116274ENST00000546072055_1040173.0Coiled coilOntology_term=ECO:0000255

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneELF1chr13:41556118chr12:27116274ENST00000239882-2975_8024620.0Compositional biasNote=Poly-Asp
HgeneELF1chr13:41556118chr12:27116274ENST00000442101-1875_8024596.0Compositional biasNote=Poly-Asp
HgeneELF1chr13:41556118chr12:27116274ENST00000239882-29208_29024620.0DNA bindingETS
HgeneELF1chr13:41556118chr12:27116274ENST00000442101-18208_29024596.0DNA bindingETS
TgeneFGFR1OP2chr13:41556118chr12:27116274ENST0000022939547160_223170254.0Coiled coilOntology_term=ECO:0000255
TgeneFGFR1OP2chr13:41556118chr12:27116274ENST00000229395475_104170254.0Coiled coilOntology_term=ECO:0000255
TgeneFGFR1OP2chr13:41556118chr12:27116274ENST00000327214365_104132216.0Coiled coilOntology_term=ECO:0000255


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Fusion Gene Sequence for ELF1-FGFR1OP2


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.
>26153_26153_1_ELF1-FGFR1OP2_ELF1_chr13_41556118_ENST00000239882_FGFR1OP2_chr12_27116274_ENST00000229395_length(transcript)=2459nt_BP=387nt
TCTACAGGAGCCATTTTAACAGCTAAAACTTGTCGGATTGCTTTTTATTTTCAAGCTCAAAAGACGATAGAGAAAGAATACTTGAAGGCC
AAGAAGCTTGAGAGAAGAAAAATTTCAGAAAAATTGTCTCAATTTGACTAGAATATCAATGAACCAGGAAAACTGAAGCACCTTCCCTAA
AGAAAACTTGGGTATACAATTACTCCACAGACAGAGCTGAGGGTTTTTTACCCAAATCAGTCACTGGATTTTGCTGCCTGATACGTGAAT
CTTCTTGGAATTTTTCTCATGTGGATCTAAGGGGAATGCTTTATTATGGCTGCTGTTGTCCAACAGAACGACCTAGTATTTGAATTTGCT
AGTAACGTCATGGAGGATGAACGACAGGAACTGCAAGCACATGTTGACCAGATAACTGAAATGGCAGCAGTAATGAGGAAAGCCATTGAA
ATTGACGAGCAACAGGGTTGCAAGGAACAAGAACGAATATTTCAACTTGAACAAGAAAACAAAGGCTTGAGAGAGATCCTTCAAATAACT
CGAGAATCATTTTTGAACCTAAGGAAAGATGATGCGTCGGAAAGTACTTCTTTGTCAGCATTAGTGACCAACAGTGATTTGAGTCTGAGG
AAGAGCTGAAGAGTTTCTGAGTCTGTGAGCTTCTTACATGGCTCCAAATGGTCAAATAAGTGAATGAATGAATGGACAGAAAATTCAATC
CTTTATTTTTTTCTCTGTAAATATGTACAGTGCACGGGCTATGAGATAGCAACAAAAAATGCATAGTTAATGGTCATAGACTTTATTCCA
AAACATAATTGGAAAATAGAAACTGAGCCATTGCCAAATGGTAAAGAAATGAAAAGTTTTCACAGTGACTACTGAATATACCAAGAGCTT
TTGGCAGTACTGCTGGCTTTCTGGGTGATTAATTAGGTAAACTTGAATATTCCCAGTAAATGTTTGAGAATGCATAAAATTATACCAATT
TAAAAATATAAATTTTTGCCACTGTTTTGTGAACGGAGGATTTGTACGCTAAATTTCATCCTTATTTGGCGTCAAAGTTGATGCAAAGTT
TATGTACCATGAGACTTCTAGTGATTGCCTACTTTCACATTTATTTAAATTTTTGTGAAAGAAAATACAGTTTTAAAGGCTATAGGAATG
TGTTATATGTACCTTAAACAGATAATTTAATTTTAGCAATTTATCATAACTGATACTTAGCTAACAATTGTCCATAACTTGTTTAAGTGT
AAGAAATACCATTTCAGGAATGAAAAAGAAGGAATACTACTTTCTAAGAAAGAAGATCTTATAATAGACATATTTAGTAGGTTAAACTAC
TCCTTTGAAAGAATAAGTTTTGGTTCAAAGTCAATAATGAAGACGAGATTTGTTTTTCTCTTCTCTGGCTGATTTTTAAGGATATTATGT
AGTTCATTTAGTTAACAGAATTGAAATGTTTGATATGGCAAGATAGGTATGGTAATTTCAAAGTGAATTGGGAATTCCTCTGGCTCATAG
AACCCTTTTTTTTTTCCTTTAAGTATTCTTGAGATACAAAAAAAAAAAGTAAATACAATTTCAAAAAAAAAGTTCCGGATCTGTTTTTAA
GCTCCATCTGGTCCTCATAACCTGCAAGATTTTTCTTAAAACCTTTCAGCTGAAAGTGGGGGTAAAGGTGGAGTAATCTGTGGATTTGTT
TCTGTTGTCTTTTAAAATGTCAAATATATAATATGTAATTTTTTTAAAAACCACCAGATACAGAAATGTGCTTTAACATCAGTTGAAACC
TAAATTTTCTTATGTTGTGGTGATTGTATTAAAAAGGGATAAAAGAAGAGTGTCAAACATGGTTAAATATATTGTACTCATTTATGTTGA
ATACGTATTAAAATTAAGACAAATGGAAAATTATACTTTGAGTATATAATTTGTTAAATATTACTTTATATGGTAATTTTATGTATAATT
TCATATATTGGTAAAATTCAAAACTACACTTGAGAATTTTTTTATCTTAAGTTTGGGGTGAATGGGGTGGATGAGACTGATTGAATAGAA
AAGGGCTAATGGCCCAAACATTATATAGATTTCTTTTTTTCAGTCAGAGGCCTTATTTGATATTTTATAAATAAATGACAGTTTTTATTT
TTAAACTTTTTATTGTTTTTGGGAAAGTATTCCTTAATTTAATGACACATTCATTCAGATACTTCTTATCCCTGCTAATAAAGGAAATCT
ATTTCAAGCTACACCATTGAGATTAAGTCTGAGGCAGTTCATTGAGGCAGCTCTACTATAAAAGCTTACTTGATAAATAATTATTTTTGT
AAACAAGTTGGGTTAACTTATTCTTCGTCTTTTTGCTTGGATATGAATTTAAGGTCTTCATGTTTAAAGACATTTACTTTGTTATTTAGT

>26153_26153_1_ELF1-FGFR1OP2_ELF1_chr13_41556118_ENST00000239882_FGFR1OP2_chr12_27116274_ENST00000229395_length(amino acids)=138AA_BP=0
MHFLLLSHSPCTVHIYREKNKGLNFLSIHSFTYLTIWSHVRSSQTQKLFSSSSDSNHCWSLMLTKKYFPTHHLSLGSKMILELFEGSLSS

--------------------------------------------------------------
>26153_26153_2_ELF1-FGFR1OP2_ELF1_chr13_41556118_ENST00000442101_FGFR1OP2_chr12_27116274_ENST00000229395_length(transcript)=2372nt_BP=300nt
GCCAAGAAGCTTGAGAGAAGAAAAATTTCAGAAAAATTGTCTCAATTTGACTAGAATATCAATGAACCAGGAAAACTGAAGCACCTTCCC
TAAAGAAAACTTGGGTATACAATTACTCCACAGACAGAGCTGAGGGTTTTTTACCCAAATCAGTCACTGGATTTTGCTGCCTGATACGTG
AATCTTCTTGGAATTTTTCTCATGTGGATCTAAGGGGAATGCTTTATTATGGCTGCTGTTGTCCAACAGAACGACCTAGTATTTGAATTT
GCTAGTAACGTCATGGAGGATGAACGACAGGAACTGCAAGCACATGTTGACCAGATAACTGAAATGGCAGCAGTAATGAGGAAAGCCATT
GAAATTGACGAGCAACAGGGTTGCAAGGAACAAGAACGAATATTTCAACTTGAACAAGAAAACAAAGGCTTGAGAGAGATCCTTCAAATA
ACTCGAGAATCATTTTTGAACCTAAGGAAAGATGATGCGTCGGAAAGTACTTCTTTGTCAGCATTAGTGACCAACAGTGATTTGAGTCTG
AGGAAGAGCTGAAGAGTTTCTGAGTCTGTGAGCTTCTTACATGGCTCCAAATGGTCAAATAAGTGAATGAATGAATGGACAGAAAATTCA
ATCCTTTATTTTTTTCTCTGTAAATATGTACAGTGCACGGGCTATGAGATAGCAACAAAAAATGCATAGTTAATGGTCATAGACTTTATT
CCAAAACATAATTGGAAAATAGAAACTGAGCCATTGCCAAATGGTAAAGAAATGAAAAGTTTTCACAGTGACTACTGAATATACCAAGAG
CTTTTGGCAGTACTGCTGGCTTTCTGGGTGATTAATTAGGTAAACTTGAATATTCCCAGTAAATGTTTGAGAATGCATAAAATTATACCA
ATTTAAAAATATAAATTTTTGCCACTGTTTTGTGAACGGAGGATTTGTACGCTAAATTTCATCCTTATTTGGCGTCAAAGTTGATGCAAA
GTTTATGTACCATGAGACTTCTAGTGATTGCCTACTTTCACATTTATTTAAATTTTTGTGAAAGAAAATACAGTTTTAAAGGCTATAGGA
ATGTGTTATATGTACCTTAAACAGATAATTTAATTTTAGCAATTTATCATAACTGATACTTAGCTAACAATTGTCCATAACTTGTTTAAG
TGTAAGAAATACCATTTCAGGAATGAAAAAGAAGGAATACTACTTTCTAAGAAAGAAGATCTTATAATAGACATATTTAGTAGGTTAAAC
TACTCCTTTGAAAGAATAAGTTTTGGTTCAAAGTCAATAATGAAGACGAGATTTGTTTTTCTCTTCTCTGGCTGATTTTTAAGGATATTA
TGTAGTTCATTTAGTTAACAGAATTGAAATGTTTGATATGGCAAGATAGGTATGGTAATTTCAAAGTGAATTGGGAATTCCTCTGGCTCA
TAGAACCCTTTTTTTTTTCCTTTAAGTATTCTTGAGATACAAAAAAAAAAAGTAAATACAATTTCAAAAAAAAAGTTCCGGATCTGTTTT
TAAGCTCCATCTGGTCCTCATAACCTGCAAGATTTTTCTTAAAACCTTTCAGCTGAAAGTGGGGGTAAAGGTGGAGTAATCTGTGGATTT
GTTTCTGTTGTCTTTTAAAATGTCAAATATATAATATGTAATTTTTTTAAAAACCACCAGATACAGAAATGTGCTTTAACATCAGTTGAA
ACCTAAATTTTCTTATGTTGTGGTGATTGTATTAAAAAGGGATAAAAGAAGAGTGTCAAACATGGTTAAATATATTGTACTCATTTATGT
TGAATACGTATTAAAATTAAGACAAATGGAAAATTATACTTTGAGTATATAATTTGTTAAATATTACTTTATATGGTAATTTTATGTATA
ATTTCATATATTGGTAAAATTCAAAACTACACTTGAGAATTTTTTTATCTTAAGTTTGGGGTGAATGGGGTGGATGAGACTGATTGAATA
GAAAAGGGCTAATGGCCCAAACATTATATAGATTTCTTTTTTTCAGTCAGAGGCCTTATTTGATATTTTATAAATAAATGACAGTTTTTA
TTTTTAAACTTTTTATTGTTTTTGGGAAAGTATTCCTTAATTTAATGACACATTCATTCAGATACTTCTTATCCCTGCTAATAAAGGAAA
TCTATTTCAAGCTACACCATTGAGATTAAGTCTGAGGCAGTTCATTGAGGCAGCTCTACTATAAAAGCTTACTTGATAAATAATTATTTT
TGTAAACAAGTTGGGTTAACTTATTCTTCGTCTTTTTGCTTGGATATGAATTTAAGGTCTTCATGTTTAAAGACATTTACTTTGTTATTT

>26153_26153_2_ELF1-FGFR1OP2_ELF1_chr13_41556118_ENST00000442101_FGFR1OP2_chr12_27116274_ENST00000229395_length(amino acids)=138AA_BP=0
MHFLLLSHSPCTVHIYREKNKGLNFLSIHSFTYLTIWSHVRSSQTQKLFSSSSDSNHCWSLMLTKKYFPTHHLSLGSKMILELFEGSLSS

--------------------------------------------------------------

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Fusion Gene PPI Analysis for ELF1-FGFR1OP2


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 ELF1-FGFR1OP2


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 ELF1-FGFR1OP2


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