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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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

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

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

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

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:ARID2-ZNF641

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARID2-ZNF641
FusionPDB ID: 6447
FusionGDB2.0 ID: 6447
HgeneTgene
Gene symbol

ARID2

ZNF641

Gene ID

196528

121274

Gene nameAT-rich interaction domain 2zinc finger protein 641
SynonymsBAF200|CSS6|p200-
Cytomap

12q12

12q13.11

Type of geneprotein-codingprotein-coding
DescriptionAT-rich interactive domain-containing protein 2ARID domain-containing protein 2AT rich interactive domain 2 (ARID, RFX-like)BRG1-associated factor 200zinc finger protein with activation potentialzipzap/p200zinc finger protein 641
Modification date2020032020200313
UniProtAcc

Q68CP9

Main function of 5'-partner protein: FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Required for the stability of the SWI/SNF chromatin remodeling complex SWI/SNF-B (PBAF). May be involved in targeting the complex to different genes. May be involved in regulating transcriptional activation of cardiac genes. {ECO:0000269|PubMed:16782067, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000334344, ENST00000422737, 
ENST00000444670, ENST00000457135, 
ENST00000479608, 
ENST00000448928, 
ENST00000547026, ENST00000301042, 
ENST00000544117, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 9 X 12=18361 X 1 X 1=1
# samples 171
** MAII scorelog2(17/1836*10)=-3.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Fusion gene context

PubMed: ARID2 [Title/Abstract] AND ZNF641 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ARID2 [Title/Abstract] AND ZNF641 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARID2(46125097)-ZNF641(48741898), # samples:3
Anticipated loss of major functional domain due to fusion event.ARID2-ZNF641 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.
ARID2-ZNF641 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.
ARID2-ZNF641 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.
ARID2-ZNF641 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
HgeneARID2

GO:0006337

nucleosome disassembly

8895581

HgeneARID2

GO:0008285

negative regulation of cell proliferation

26169693

HgeneARID2

GO:0030336

negative regulation of cell migration

26169693



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/chr12:46125097/chr12:48741898)
- 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 ARID2 (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 ZNF641 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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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)
ENST00000334344ARID2chr1246125097+ENST00000301042ZNF641chr1248741898-47214561391755538
ENST00000334344ARID2chr1246125097+ENST00000544117ZNF641chr1248741898-46024561391755538

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
ENST00000334344ENST00000301042ARID2chr1246125097+ZNF641chr1248741898-0.0135381530.9864618
ENST00000334344ENST00000544117ARID2chr1246125097+ZNF641chr1248741898-0.0148794880.9851206

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

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Fusion Protein Breakpoint Sequences for ARID2-ZNF641

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ARID2chr1246125097ZNF641chr1248741898456105CSNAAFALKQYYLRSQFGSAAEMLSE

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Potential FusionNeoAntigen Information of ARID2-ZNF641 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.
ARID2-ZNF641_46125097_48741898.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)
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:01KQYYLRSQF0.99770.8547817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B08:09YLRSQFGSA0.99030.72351120
ARID2-ZNF641chr1246125097chr1248741898456HLA-B39:06LRSQFGSAA0.98660.8071221
ARID2-ZNF641chr1246125097chr1248741898456HLA-B27:04KQYYLRSQF0.98260.6542817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:25KQYYLRSQF0.93490.9079817
ARID2-ZNF641chr1246125097chr1248741898456HLA-A32:13KQYYLRSQF0.86860.9256817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:03KQYYLRSQF0.83680.6378817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B47:01KQYYLRSQF0.81710.6325817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B13:02KQYYLRSQF0.70380.5582817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B13:01KQYYLRSQF0.61770.9488817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B52:01KQYYLRSQF0.01330.7829817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B39:06YLRSQFGSAA0.58790.8591121
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:07KQYYLRSQF0.98930.6262817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B73:01LRSQFGSAA0.98820.88711221
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:04KQYYLRSQF0.98450.8876817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:05KQYYLRSQF0.60170.8134817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:07LKQYYLRSQF0.94090.6557717
ARID2-ZNF641chr1246125097chr1248741898456HLA-B73:01YLRSQFGSAA0.74220.90731121
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:07ALKQYYLRSQF0.99750.7486617
ARID2-ZNF641chr1246125097chr1248741898456HLA-B73:01YYLRSQFGSAA0.90390.89281021
ARID2-ZNF641chr1246125097chr1248741898456HLA-C14:02QYYLRSQF0.90930.9687917
ARID2-ZNF641chr1246125097chr1248741898456HLA-C14:03QYYLRSQF0.90930.9687917
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:34KQYYLRSQF0.99770.8547817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:33KQYYLRSQF0.99770.8547817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:125KQYYLRSQF0.99770.8547817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:27KQYYLRSQF0.99760.8992817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:135KQYYLRSQF0.99760.89817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:24KQYYLRSQF0.99520.9326817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:50KQYYLRSQF0.99410.8366817
ARID2-ZNF641chr1246125097chr1248741898456HLA-A02:03YLRSQFGSA0.99190.67521120
ARID2-ZNF641chr1246125097chr1248741898456HLA-B27:06KQYYLRSQF0.9880.6478817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:35KQYYLRSQF0.98630.7931817
ARID2-ZNF641chr1246125097chr1248741898456HLA-A32:01KQYYLRSQF0.98140.8908817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:12KQYYLRSQF0.97090.7962817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B27:09KQYYLRSQF0.96730.8918817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:53KQYYLRSQF0.9650.8153817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:39KQYYLRSQF0.94260.7759817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:68KQYYLRSQF0.92230.5508817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:54KQYYLRSQF0.8780.7829817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:73KQYYLRSQF0.83010.7614817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:30KQYYLRSQF0.60230.8615817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:20KQYYLRSQF0.60210.8873817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B35:28KQYYLRSQF0.57550.8925817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B48:02KQYYLRSQF0.46960.8736817
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:68LKQYYLRSQF0.97220.5796717
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:35LKQYYLRSQF0.93430.8347717
ARID2-ZNF641chr1246125097chr1248741898456HLA-B15:35ALKQYYLRSQF0.99630.8757617

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Potential FusionNeoAntigen Information of ARID2-ZNF641 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)

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Fusion breakpoint peptide structures of ARID2-ZNF641

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
380ALKQYYLRSQFGSAARID2ZNF641chr1246125097chr1248741898456

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARID2-ZNF641

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-B14:023BVN380ALKQYYLRSQFGSA-7.9962-8.1096
HLA-B14:023BVN380ALKQYYLRSQFGSA-5.70842-6.74372
HLA-B52:013W39380ALKQYYLRSQFGSA-6.83737-6.95077
HLA-B52:013W39380ALKQYYLRSQFGSA-4.4836-5.5189
HLA-A11:014UQ2380ALKQYYLRSQFGSA-10.0067-10.1201
HLA-A11:014UQ2380ALKQYYLRSQFGSA-9.03915-10.0745
HLA-A24:025HGA380ALKQYYLRSQFGSA-6.56204-6.67544
HLA-A24:025HGA380ALKQYYLRSQFGSA-5.42271-6.45801
HLA-B44:053DX8380ALKQYYLRSQFGSA-7.85648-8.89178
HLA-B44:053DX8380ALKQYYLRSQFGSA-5.3978-5.5112
HLA-A02:016TDR380ALKQYYLRSQFGSA-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ARID2-ZNF641

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
ARID2-ZNF641chr1246125097chr12487418981021YYLRSQFGSAATTACTTGCGGTCACAATTTGGGTCTGCAGCAGA
ARID2-ZNF641chr1246125097chr12487418981120YLRSQFGSACTTGCGGTCACAATTTGGGTCTGCAGC
ARID2-ZNF641chr1246125097chr12487418981121YLRSQFGSAACTTGCGGTCACAATTTGGGTCTGCAGCAGA
ARID2-ZNF641chr1246125097chr12487418981221LRSQFGSAAGCGGTCACAATTTGGGTCTGCAGCAGA
ARID2-ZNF641chr1246125097chr1248741898617ALKQYYLRSQFTTTAAAACAGTATTACTTGCGGTCACAATTTGG
ARID2-ZNF641chr1246125097chr1248741898717LKQYYLRSQFAAAACAGTATTACTTGCGGTCACAATTTGG
ARID2-ZNF641chr1246125097chr1248741898817KQYYLRSQFACAGTATTACTTGCGGTCACAATTTGG
ARID2-ZNF641chr1246125097chr1248741898917QYYLRSQFGTATTACTTGCGGTCACAATTTGG

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

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Information of the samples that have these potential fusion neoantigens of ARID2-ZNF641

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
BRCAARID2-ZNF641chr1246125097ENST00000334344chr1248741898ENST00000301042TCGA-AR-A1AV-01A

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Potential target of CAR-T therapy development for ARID2-ZNF641

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

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

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Related Drugs to ARID2-ZNF641

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

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Related Diseases to ARID2-ZNF641

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