FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

leaf

Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

leaf

Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

leaf

Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:DNMT1-EMR1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: DNMT1-EMR1
FusionPDB ID: 23694
FusionGDB2.0 ID: 23694
HgeneTgene
Gene symbol

DNMT1

EMR1

Gene ID

1786

2015

Gene nameDNA methyltransferase 1adhesion G protein-coupled receptor E1
SynonymsADCADN|AIM|CXXC9|DNMT|HSN1E|MCMT|m.HsaIEMR1|TM7LN3
Cytomap

19p13.2

19p13.3-p13.2

Type of geneprotein-codingprotein-coding
DescriptionDNA (cytosine-5)-methyltransferase 1CXXC-type zinc finger protein 9DNA (cytosine-5-)-methyltransferase 1DNA MTase HsaIDNA methyltransferase HsaIadhesion G protein-coupled receptor E1EGF-like module receptor 1EGF-like module-containing mucin-like hormone receptor-like 1EMR1 hormone receptoregf-like module containing, mucin-like, hormone receptor-like 1egf-like module containing, mucin-like, h
Modification date2020031320200313
UniProtAcc

P26358

Main function of 5'-partner protein: FUNCTION: Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). Promotes tumor growth (PubMed:24623306). {ECO:0000269|PubMed:16357870, ECO:0000269|PubMed:18413740, ECO:0000269|PubMed:18754681, ECO:0000269|PubMed:24623306}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000340748, ENST00000359526, 
ENST00000540357, ENST00000589538, 
ENST00000601198, ENST00000250572, 
ENST00000312053, ENST00000381404, 
ENST00000381407, ENST00000450315, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 12 X 11=18482 X 2 X 2=8
# samples 172
** MAII scorelog2(17/1848*10)=-3.44235810527836
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Fusion gene context

PubMed: DNMT1 [Title/Abstract] AND EMR1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: DNMT1 [Title/Abstract] AND EMR1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)DNMT1(10266529)-EMR1(6890492), # samples:1
Anticipated loss of major functional domain due to fusion event.DNMT1-EMR1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
DNMT1-EMR1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
DNMT1-EMR1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
DNMT1-EMR1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneDNMT1

GO:0010216

maintenance of DNA methylation

18754681|21745816



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/chr19:10266529/chr19:6890492)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across DNMT1 (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 EMR1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000340748DNMT1chr1910266529-ENST00000250572EMR1chr196890492+4545168016914114807
ENST00000340748DNMT1chr1910266529-ENST00000381407EMR1chr196890492+4298168016913886731
ENST00000340748DNMT1chr1910266529-ENST00000312053EMR1chr196890492+4740168016914309872
ENST00000340748DNMT1chr1910266529-ENST00000450315EMR1chr196890492+4184168016913778695
ENST00000340748DNMT1chr1910266529-ENST00000381404EMR1chr196890492+4675168016914252853
ENST00000540357DNMT1chr1910266529-ENST00000250572EMR1chr196890492+4489162416354058807
ENST00000540357DNMT1chr1910266529-ENST00000381407EMR1chr196890492+4242162416353830731
ENST00000540357DNMT1chr1910266529-ENST00000312053EMR1chr196890492+4684162416354253872
ENST00000540357DNMT1chr1910266529-ENST00000450315EMR1chr196890492+4128162416353722695
ENST00000540357DNMT1chr1910266529-ENST00000381404EMR1chr196890492+4619162416354196853
ENST00000359526DNMT1chr1910266529-ENST00000250572EMR1chr196890492+4537167216834106807
ENST00000359526DNMT1chr1910266529-ENST00000381407EMR1chr196890492+4290167216833878731
ENST00000359526DNMT1chr1910266529-ENST00000312053EMR1chr196890492+4732167216834301872
ENST00000359526DNMT1chr1910266529-ENST00000450315EMR1chr196890492+4176167216833770695
ENST00000359526DNMT1chr1910266529-ENST00000381404EMR1chr196890492+4667167216834244853

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
ENST00000340748ENST00000250572DNMT1chr1910266529-EMR1chr196890492+0.0030035850.9969964
ENST00000340748ENST00000381407DNMT1chr1910266529-EMR1chr196890492+0.0047923320.9952076
ENST00000340748ENST00000312053DNMT1chr1910266529-EMR1chr196890492+0.0042401070.9957599
ENST00000340748ENST00000450315DNMT1chr1910266529-EMR1chr196890492+0.0041155990.99588436
ENST00000340748ENST00000381404DNMT1chr1910266529-EMR1chr196890492+0.0022909940.99770904
ENST00000540357ENST00000250572DNMT1chr1910266529-EMR1chr196890492+0.0030860110.996914
ENST00000540357ENST00000381407DNMT1chr1910266529-EMR1chr196890492+0.0050122340.99498785
ENST00000540357ENST00000312053DNMT1chr1910266529-EMR1chr196890492+0.0041040550.995896
ENST00000540357ENST00000450315DNMT1chr1910266529-EMR1chr196890492+0.0042603570.9957397
ENST00000540357ENST00000381404DNMT1chr1910266529-EMR1chr196890492+0.0022647920.99773514
ENST00000359526ENST00000250572DNMT1chr1910266529-EMR1chr196890492+0.0031441380.99685585
ENST00000359526ENST00000381407DNMT1chr1910266529-EMR1chr196890492+0.005139340.9948606
ENST00000359526ENST00000312053DNMT1chr1910266529-EMR1chr196890492+0.0043795830.9956204
ENST00000359526ENST00000450315DNMT1chr1910266529-EMR1chr196890492+0.0043764930.9956235
ENST00000359526ENST00000381404DNMT1chr1910266529-EMR1chr196890492+0.0024116050.9975884

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

Top

Fusion Protein Breakpoint Sequences for DNMT1-EMR1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
DNMT1chr1910266529EMR1chr196890492162459GFLSSNGQNHFKDPGVRCKDINECLT
DNMT1chr1910266529EMR1chr196890492167259GFLSSNGQNHFKDPGVRCKDINECLT
DNMT1chr1910266529EMR1chr196890492168059GFLSSNGQNHFKDPGVRCKDINECLT

Top

Potential FusionNeoAntigen Information of DNMT1-EMR1 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
DNMT1-EMR1_10266529_6890492.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
DNMT1-EMR1chr1910266529chr1968904921680HLA-B39:06NHFKDPGV0.9990.8254816
DNMT1-EMR1chr1910266529chr1968904921680HLA-B39:06NHFKDPGVRC0.97240.8926818
DNMT1-EMR1chr1910266529chr1968904921680HLA-B39:05NHFKDPGV0.99740.8876816
DNMT1-EMR1chr1910266529chr1968904921680HLA-A30:01HFKDPGVRCK0.98460.9456919

Top

Potential FusionNeoAntigen Information of DNMT1-EMR1 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)

Top

Fusion breakpoint peptide structures of DNMT1-EMR1

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
3058GQNHFKDPGVRCKDDNMT1EMR1chr1910266529chr1968904921680

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of DNMT1-EMR1

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN3058GQNHFKDPGVRCKD-7.9962-8.1096
HLA-B14:023BVN3058GQNHFKDPGVRCKD-5.70842-6.74372
HLA-B52:013W393058GQNHFKDPGVRCKD-6.83737-6.95077
HLA-B52:013W393058GQNHFKDPGVRCKD-4.4836-5.5189
HLA-A11:014UQ23058GQNHFKDPGVRCKD-10.0067-10.1201
HLA-A11:014UQ23058GQNHFKDPGVRCKD-9.03915-10.0745
HLA-A24:025HGA3058GQNHFKDPGVRCKD-6.56204-6.67544
HLA-A24:025HGA3058GQNHFKDPGVRCKD-5.42271-6.45801
HLA-B44:053DX83058GQNHFKDPGVRCKD-7.85648-8.89178
HLA-B44:053DX83058GQNHFKDPGVRCKD-5.3978-5.5112
HLA-A02:016TDR3058GQNHFKDPGVRCKD-3.37154-4.40684

Top

Vaccine Design for the FusionNeoAntigens of DNMT1-EMR1

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
DNMT1-EMR1chr1910266529chr196890492816NHFKDPGVTCGGCTTCAGCACCTGATGTTGTG
DNMT1-EMR1chr1910266529chr196890492818NHFKDPGVRCTCGGCTTCAGCACCTGATGTTGTGTTATGC
DNMT1-EMR1chr1910266529chr196890492919HFKDPGVRCKGCTTCAGCACCTGATGTTGTGTTATGCACA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence

Top

Information of the samples that have these potential fusion neoantigens of DNMT1-EMR1

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
BLCADNMT1-EMR1chr1910266529ENST00000340748chr196890492ENST00000381404TCGA-FJ-A3ZE-01A

Top

Potential target of CAR-T therapy development for DNMT1-EMR1

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneEMR1chr19:10266529chr19:6890492ENST00000250572020600_6270822.0TransmembraneHelical%3B Name%3D1
TgeneEMR1chr19:10266529chr19:6890492ENST00000250572020635_6560822.0TransmembraneHelical%3B Name%3D2
TgeneEMR1chr19:10266529chr19:6890492ENST00000250572020667_6900822.0TransmembraneHelical%3B Name%3D3
TgeneEMR1chr19:10266529chr19:6890492ENST00000250572020710_7310822.0TransmembraneHelical%3B Name%3D4
TgeneEMR1chr19:10266529chr19:6890492ENST00000250572020748_7760822.0TransmembraneHelical%3B Name%3D5
TgeneEMR1chr19:10266529chr19:6890492ENST00000250572020795_8140822.0TransmembraneHelical%3B Name%3D6
TgeneEMR1chr19:10266529chr19:6890492ENST00000250572020830_8520822.0TransmembraneHelical%3B Name%3D7
TgeneEMR1chr19:10266529chr19:6890492ENST00000312053021600_6270887.0TransmembraneHelical%3B Name%3D1
TgeneEMR1chr19:10266529chr19:6890492ENST00000312053021635_6560887.0TransmembraneHelical%3B Name%3D2
TgeneEMR1chr19:10266529chr19:6890492ENST00000312053021667_6900887.0TransmembraneHelical%3B Name%3D3
TgeneEMR1chr19:10266529chr19:6890492ENST00000312053021710_7310887.0TransmembraneHelical%3B Name%3D4
TgeneEMR1chr19:10266529chr19:6890492ENST00000312053021748_7760887.0TransmembraneHelical%3B Name%3D5
TgeneEMR1chr19:10266529chr19:6890492ENST00000312053021795_8140887.0TransmembraneHelical%3B Name%3D6
TgeneEMR1chr19:10266529chr19:6890492ENST00000312053021830_8520887.0TransmembraneHelical%3B Name%3D7
TgeneEMR1chr19:10266529chr19:6890492ENST00000381404020600_6270868.0TransmembraneHelical%3B Name%3D1
TgeneEMR1chr19:10266529chr19:6890492ENST00000381404020635_6560868.0TransmembraneHelical%3B Name%3D2
TgeneEMR1chr19:10266529chr19:6890492ENST00000381404020667_6900868.0TransmembraneHelical%3B Name%3D3
TgeneEMR1chr19:10266529chr19:6890492ENST00000381404020710_7310868.0TransmembraneHelical%3B Name%3D4
TgeneEMR1chr19:10266529chr19:6890492ENST00000381404020748_7760868.0TransmembraneHelical%3B Name%3D5
TgeneEMR1chr19:10266529chr19:6890492ENST00000381404020795_8140868.0TransmembraneHelical%3B Name%3D6
TgeneEMR1chr19:10266529chr19:6890492ENST00000381404020830_8520868.0TransmembraneHelical%3B Name%3D7
TgeneEMR1chr19:10266529chr19:6890492ENST00000381407018600_6270746.0TransmembraneHelical%3B Name%3D1
TgeneEMR1chr19:10266529chr19:6890492ENST00000381407018635_6560746.0TransmembraneHelical%3B Name%3D2
TgeneEMR1chr19:10266529chr19:6890492ENST00000381407018667_6900746.0TransmembraneHelical%3B Name%3D3
TgeneEMR1chr19:10266529chr19:6890492ENST00000381407018710_7310746.0TransmembraneHelical%3B Name%3D4
TgeneEMR1chr19:10266529chr19:6890492ENST00000381407018748_7760746.0TransmembraneHelical%3B Name%3D5
TgeneEMR1chr19:10266529chr19:6890492ENST00000381407018795_8140746.0TransmembraneHelical%3B Name%3D6
TgeneEMR1chr19:10266529chr19:6890492ENST00000381407018830_8520746.0TransmembraneHelical%3B Name%3D7
TgeneEMR1chr19:10266529chr19:6890492ENST00000450315018600_6270710.0TransmembraneHelical%3B Name%3D1
TgeneEMR1chr19:10266529chr19:6890492ENST00000450315018635_6560710.0TransmembraneHelical%3B Name%3D2
TgeneEMR1chr19:10266529chr19:6890492ENST00000450315018667_6900710.0TransmembraneHelical%3B Name%3D3
TgeneEMR1chr19:10266529chr19:6890492ENST00000450315018710_7310710.0TransmembraneHelical%3B Name%3D4
TgeneEMR1chr19:10266529chr19:6890492ENST00000450315018748_7760710.0TransmembraneHelical%3B Name%3D5
TgeneEMR1chr19:10266529chr19:6890492ENST00000450315018795_8140710.0TransmembraneHelical%3B Name%3D6
TgeneEMR1chr19:10266529chr19:6890492ENST00000450315018830_8520710.0TransmembraneHelical%3B Name%3D7

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

Top

Related Drugs to DNMT1-EMR1

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to DNMT1-EMR1

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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