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:MIDN-ARID3A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MIDN-ARID3A
FusionPDB ID: 53601
FusionGDB2.0 ID: 53601
HgeneTgene
Gene symbol

MIDN

ARID3A

Gene ID

90007

1820

Gene namemidnolinAT-rich interaction domain 3A
Synonyms-BRIGHT|DRIL1|DRIL3|E2FBP1
Cytomap

19p13.3

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionmidnolinmidbrain nucleolar proteinAT-rich interactive domain-containing protein 3AARID domain-containing 3AARID domain-containing protein 3AAT rich interactive domain 3A (BRIGHT- like) proteinAT rich interactive domain 3A (BRIGHT-like)B-cell regulator of IgH transcriptionE2F-binding
Modification date2020031320200313
UniProtAcc

Q504T8

Main function of 5'-partner protein: FUNCTION: Facilitates ubiquitin-independent proteasomal degradation of polycomb protein CBX4. Plays a role in inhibiting the activity of glucokinase GCK and both glucose-induced and basal insulin secretion. {ECO:0000250|UniProtKB:D4AE48, ECO:0000250|UniProtKB:Q3TPJ7}.

Q99856

Main function of 5'-partner protein: FUNCTION: Transcription factor which may be involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation. {ECO:0000269|PubMed:11812999, ECO:0000269|PubMed:12692263}.
Ensembl transtripts involved in fusion geneENST idsENST00000300952, ENST00000591446, 
ENST00000592216, ENST00000263620, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 7 X 6=3788 X 9 X 5=360
# samples 1310
** MAII scorelog2(13/378*10)=-1.53987461119262
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: MIDN [Title/Abstract] AND ARID3A [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MIDN [Title/Abstract] AND ARID3A [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MIDN(1250528)-ARID3A(971878), # samples:1
Anticipated loss of major functional domain due to fusion event.MIDN-ARID3A 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.
MIDN-ARID3A 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.
MIDN-ARID3A 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.
MIDN-ARID3A 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


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/chr19:1250528/chr19:971878)
- 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 MIDN (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 ARID3A (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)
ENST00000300952MIDNchr191250528+ENST00000263620ARID3Achr19971878+48107483941143249
ENST00000591446MIDNchr191250528+ENST00000263620ARID3Achr19971878+47046422881037249

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
ENST00000300952ENST00000263620MIDNchr191250528+ARID3Achr19971878+0.813460950.18653902
ENST00000591446ENST00000263620MIDNchr191250528+ARID3Achr19971878+0.80490010.19509992

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 MIDN-ARID3A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
MIDNchr191250528ARID3Achr1997187864229LAPVPEARRGLAAPAAPSPPARAGDG
MIDNchr191250528ARID3Achr1997187874829LAPVPEARRGLAAPAAPSPPARAGDG

Top

Potential FusionNeoAntigen Information of MIDN-ARID3A 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.
MIDN-ARID3A_1250528_971878.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)
MIDN-ARID3Achr191250528chr19971878748HLA-B56:01AAPAAPSPPA0.98590.57981121
MIDN-ARID3Achr191250528chr19971878748HLA-B55:01AAPAAPSPPA0.97570.51281121
MIDN-ARID3Achr191250528chr19971878748HLA-B56:01LAAPAAPSPPA0.99890.67711021
MIDN-ARID3Achr191250528chr19971878748HLA-B55:01APAAPSPPARA0.99680.69681223
MIDN-ARID3Achr191250528chr19971878748HLA-B56:01APAAPSPPARA0.99430.82351223
MIDN-ARID3Achr191250528chr19971878748HLA-B73:01RRGLAAPAA0.96490.9478716
MIDN-ARID3Achr191250528chr19971878748HLA-B73:01ARRGLAAPA0.95640.9468615
MIDN-ARID3Achr191250528chr19971878748HLA-B54:01AAPAAPSPPA0.9940.78451121
MIDN-ARID3Achr191250528chr19971878748HLA-B54:01LAAPAAPSPPA0.99950.90721021
MIDN-ARID3Achr191250528chr19971878748HLA-B55:02AAPAAPSPPA0.97770.60371121
MIDN-ARID3Achr191250528chr19971878748HLA-B55:02APAAPSPPARA0.99780.87241223
MIDN-ARID3Achr191250528chr19971878748HLA-B55:02LAAPAAPSPPA0.99760.76851021

Top

Potential FusionNeoAntigen Information of MIDN-ARID3A 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 MIDN-ARID3A

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
561ARRGLAAPAAPSPPMIDNARID3Achr191250528chr19971878748

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MIDN-ARID3A

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-B14:023BVN561ARRGLAAPAAPSPP-7.26591-7.45601
HLA-B14:023BVN561ARRGLAAPAAPSPP-2.93533-3.70133
HLA-B52:013W39561ARRGLAAPAAPSPP-4.36175-5.12775
HLA-A24:025HGA561ARRGLAAPAAPSPP-6.25806-6.44816
HLA-A24:025HGA561ARRGLAAPAAPSPP-6.06554-6.83154
HLA-B27:056PYJ561ARRGLAAPAAPSPP-6.9502-7.1403
HLA-B44:053DX8561ARRGLAAPAAPSPP-2.85917-3.62517

Top

Vaccine Design for the FusionNeoAntigens of MIDN-ARID3A

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
MIDN-ARID3Achr191250528chr199718781021LAAPAAPSPPACAAAGACACGAGTTCTGTTTGCTCAGCCGCCGG
MIDN-ARID3Achr191250528chr199718781121AAPAAPSPPAAGACACGAGTTCTGTTTGCTCAGCCGCCGG
MIDN-ARID3Achr191250528chr199718781223APAAPSPPARACACGAGTTCTGTTTGCTCAGCCGCCGGCCCCCA
MIDN-ARID3Achr191250528chr19971878615ARRGLAAPAGGCTCTTCTCCACAAAGACACGAGTTC
MIDN-ARID3Achr191250528chr19971878716RRGLAAPAATCTTCTCCACAAAGACACGAGTTCTGT

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 MIDN-ARID3A

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
LUADMIDN-ARID3Achr191250528ENST00000300952chr19971878ENST00000263620TCGA-44-2668-01A

Top

Potential target of CAR-T therapy development for MIDN-ARID3A

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

Top

Related Drugs to MIDN-ARID3A

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

Top

Related Diseases to MIDN-ARID3A

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