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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:C12orf49-ERF (FusionGDB2 ID:HG79794TG2077)

Fusion Gene Summary for C12orf49-ERF

check button Fusion gene summary
Fusion gene informationFusion gene name: C12orf49-ERF
Fusion gene ID: hg79794tg2077
HgeneTgene
Gene symbol

C12orf49

ERF

Gene ID

79794

2077

Gene namechromosome 12 open reading frame 49ETS2 repressor factor
Synonyms-CHYTS|CRS4|PE-2|PE2
Cytomap('C12orf49')('ERF')

12q24.22

19q13.2

Type of geneprotein-codingprotein-coding
DescriptionUPF0454 protein C12orf49ETS domain-containing transcription factor ERF
Modification date2020031320200313
UniProtAcc.

P50548

Ensembl transtripts involved in fusion geneENST00000261318, ENST00000536380, 
ENST00000548356, 
Fusion gene scores* DoF score8 X 4 X 2=644 X 3 X 3=36
# samples 64
** MAII scorelog2(6/64*10)=-0.0931094043914815
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: C12orf49 [Title/Abstract] AND ERF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC12orf49(117173841)-ERF(42751724), # 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
TgeneERF

GO:0000122

negative regulation of transcription by RNA polymerase II

7588608



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


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Fusion Gene ORF analysis for C12orf49-ERF

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

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 C12orf49-ERF


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)


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Fusion Protein Features for C12orf49-ERF


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/:117173841/:42751724)
- 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
.ERF

P50548

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: Potent transcriptional repressor that binds to the H1 element of the Ets2 promoter. May regulate other genes involved in cellular proliferation. Required for extraembryonic ectoderm differentiation, ectoplacental cone cavity closure, and chorioallantoic attachment (By similarity). May be important for regulating trophoblast stem cell differentiation (By similarity). {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

- 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 C12orf49-ERF


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 C12orf49-ERF


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 C12orf49-ERF


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 C12orf49-ERF


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3806917CRANIOSYNOSTOSIS 42GENOMICS_ENGLAND;UNIPROT
TgeneC4310679CHITAYAT SYNDROME2CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0003803Arnold Chiari Malformation1CTD_human
TgeneC0010278Craniosynostosis1CTD_human
TgeneC0023012Language Delay1CTD_human
TgeneC0023014Language Development Disorders1CTD_human
TgeneC0030044Acrocephaly1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0221356Brachycephaly1CTD_human
TgeneC0241210Speech Delay1CTD_human
TgeneC0265534Scaphycephaly1CTD_human;ORPHANET
TgeneC0265535Trigonocephaly1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0454655Semantic-Pragmatic Disorder1CTD_human
TgeneC0555206Chiari malformation type II1CTD_human
TgeneC0750929Arnold-Chiari Malformation, Type I1CTD_human
TgeneC0750931Arnold-Chiari Malformation, Type III1CTD_human
TgeneC0750932Arnold-Chiari Malformation, Type IV1CTD_human
TgeneC0751257Auditory Processing Disorder, Central1CTD_human
TgeneC1833340Synostotic Posterior Plagiocephaly1CTD_human
TgeneC1860050Cloverleaf skull1ORPHANET
TgeneC1860819Metopic synostosis1CTD_human
TgeneC2931150Synostotic Anterior Plagiocephaly1CTD_human
TgeneC2931196Craniofacial dysostosis type 11ORPHANET
TgeneC3839609Complex craniosynostosis1GENOMICS_ENGLAND
TgeneC4551902Craniosynostosis, Type 11CTD_human
TgeneC4707866Familial lambdoid synostosis1ORPHANET