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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:ACPP-RNF13

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ACPP-RNF13
FusionPDB ID: 1461
FusionGDB2.0 ID: 1461
HgeneTgene
Gene symbol

ACPP

RNF13

Gene ID

55

11342

Gene nameacid phosphatase 3ring finger protein 13
Synonyms5'-NT|ACP-3|ACPP|TM-PAPEIEE73|RZF
Cytomap

3q22.1

3q25.1

Type of geneprotein-codingprotein-coding
Descriptionprostatic acid phosphataseTMPaseacid phosphatase, prostateecto-5'-nucleotidaseprostatic acid phosphotasethiamine monophosphataseE3 ubiquitin-protein ligase RNF13RING zinc finger proteinRING-type E3 ubiquitin transferase RNF13
Modification date2020031320200313
UniProtAcc.

Q8WVD3

Main function of 5'-partner protein: FUNCTION: E3 ubiquitin-protein ligase involved in DNA damage response by promoting DNA resection and homologous recombination (PubMed:26502055, PubMed:26502057). Recruited to sites of double-strand breaks following DNA damage and specifically promotes double-strand break repair via homologous recombination (PubMed:26502055, PubMed:26502057). Two different, non-exclusive, mechanisms have been proposed. According to a report, regulates the choice of double-strand break repair by favoring homologous recombination over non-homologous end joining (NHEJ): acts by mediating ubiquitination of XRCC5/Ku80, leading to remove the Ku complex from DNA breaks, thereby promoting homologous recombination (PubMed:26502055). According to another report, cooperates with UBE2Ds E2 ubiquitin ligases (UBE2D1, UBE2D2, UBE2D3 or UBE2D4) to promote homologous recombination by mediating ubiquitination of RBBP8/CtIP (PubMed:26502057). Together with NLK, involved in the ubiquitination and degradation of TCF/LEF (PubMed:16714285). Also exhibits auto-ubiquitination activity in combination with UBE2K (PubMed:16714285). May act as a negative regulator in the Wnt/beta-catenin-mediated signaling pathway (PubMed:16714285). {ECO:0000269|PubMed:16714285, ECO:0000269|PubMed:26502055, ECO:0000269|PubMed:26502057}.
Ensembl transtripts involved in fusion geneENST idsENST00000489084, ENST00000336375, 
ENST00000351273, ENST00000475741, 
ENST00000344229, ENST00000392894, 
ENST00000361785, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score28 X 17 X 4=190417 X 12 X 8=1632
# samples 3117
** MAII scorelog2(31/1904*10)=-2.61869335803371
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(17/1632*10)=-3.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ACPP [Title/Abstract] AND RNF13 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ACPP [Title/Abstract] AND RNF13 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ACPP(132036420)-RNF13(149613260), # samples:1
Anticipated loss of major functional domain due to fusion event.ACPP-RNF13 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.
ACPP-RNF13 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.
ACPP-RNF13 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.
ACPP-RNF13 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
HgeneACPP

GO:0046085

adenosine metabolic process

18940592



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/chr3:132036420/chr3:149613260)
- 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 ACPP (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 RNF13 (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)
ENST00000336375ACPPchr3132036420+ENST00000392894RNF13chr3149613260+2070210661034322
ENST00000336375ACPPchr3132036420+ENST00000344229RNF13chr3149613260+2053210661034322
ENST00000475741ACPPchr3132036420+ENST00000392894RNF13chr3149613260+203117127995322
ENST00000475741ACPPchr3132036420+ENST00000344229RNF13chr3149613260+201417127995322
ENST00000351273ACPPchr3132036420+ENST00000392894RNF13chr3149613260+203017026994322
ENST00000351273ACPPchr3132036420+ENST00000344229RNF13chr3149613260+201317026994322

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
ENST00000336375ENST00000392894ACPPchr3132036420+RNF13chr3149613260+0.0001314540.9998685
ENST00000336375ENST00000344229ACPPchr3132036420+RNF13chr3149613260+0.0001293120.99987066
ENST00000475741ENST00000392894ACPPchr3132036420+RNF13chr3149613260+0.0001272410.9998727
ENST00000475741ENST00000344229ACPPchr3132036420+RNF13chr3149613260+0.0001230330.999877
ENST00000351273ENST00000392894ACPPchr3132036420+RNF13chr3149613260+0.0001268190.99987316
ENST00000351273ENST00000344229ACPPchr3132036420+RNF13chr3149613260+0.0001225120.99987745

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 ACPP-RNF13

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ACPPchr3132036420RNF13chr314961326017048RSVLAKELKFVTLVLNAQRAGYKAAI
ACPPchr3132036420RNF13chr314961326017148RSVLAKELKFVTLVLNAQRAGYKAAI
ACPPchr3132036420RNF13chr314961326021048RSVLAKELKFVTLVLNAQRAGYKAAI

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Potential FusionNeoAntigen Information of ACPP-RNF13 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.
ACPP-RNF13_132036420_149613260.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)
ACPP-RNF13chr3132036420chr3149613260210HLA-B45:01KELKFVTLV0.99850.949514
ACPP-RNF13chr3132036420chr3149613260210HLA-B50:02KELKFVTLV0.99820.795514
ACPP-RNF13chr3132036420chr3149613260210HLA-B13:02KELKFVTLV0.9960.6444514
ACPP-RNF13chr3132036420chr3149613260210HLA-B13:01KELKFVTLV0.97650.9831514
ACPP-RNF13chr3132036420chr3149613260210HLA-B08:01ELKFVTLVL0.97270.8024615
ACPP-RNF13chr3132036420chr3149613260210HLA-B08:09ELKFVTLVL0.96310.818615
ACPP-RNF13chr3132036420chr3149613260210HLA-B47:01KELKFVTLV0.91060.7216514
ACPP-RNF13chr3132036420chr3149613260210HLA-A74:03VTLVLNAQR0.90220.72851019
ACPP-RNF13chr3132036420chr3149613260210HLA-A74:11VTLVLNAQR0.90220.72851019
ACPP-RNF13chr3132036420chr3149613260210HLA-A74:09VTLVLNAQR0.90220.72851019
ACPP-RNF13chr3132036420chr3149613260210HLA-A31:02VTLVLNAQR0.83950.66541019
ACPP-RNF13chr3132036420chr3149613260210HLA-B41:01KELKFVTLV0.72380.9687514
ACPP-RNF13chr3132036420chr3149613260210HLA-B50:01KELKFVTLV0.43530.8327514
ACPP-RNF13chr3132036420chr3149613260210HLA-B39:13KELKFVTLV0.35730.9695514
ACPP-RNF13chr3132036420chr3149613260210HLA-B52:01KELKFVTLV0.04410.9811514
ACPP-RNF13chr3132036420chr3149613260210HLA-B47:01KELKFVTLVL0.96020.7155515
ACPP-RNF13chr3132036420chr3149613260210HLA-A31:02KFVTLVLNAQR0.97080.6903819
ACPP-RNF13chr3132036420chr3149613260210HLA-B40:06KELKFVTLV0.99960.7119514
ACPP-RNF13chr3132036420chr3149613260210HLA-B40:03KELKFVTLV0.9730.5916514
ACPP-RNF13chr3132036420chr3149613260210HLA-B44:10KELKFVTLV0.95740.6689514
ACPP-RNF13chr3132036420chr3149613260210HLA-A31:01VTLVLNAQR0.92450.64081019
ACPP-RNF13chr3132036420chr3149613260210HLA-B39:08KELKFVTLV0.44560.9346514
ACPP-RNF13chr3132036420chr3149613260210HLA-B40:03KELKFVTLVL0.98630.5167515
ACPP-RNF13chr3132036420chr3149613260210HLA-A31:01KFVTLVLNAQR0.97260.6697819
ACPP-RNF13chr3132036420chr3149613260210HLA-B40:04KELKFVTLV0.99580.7924514
ACPP-RNF13chr3132036420chr3149613260210HLA-B08:18ELKFVTLVL0.97270.8024615
ACPP-RNF13chr3132036420chr3149613260210HLA-A74:01VTLVLNAQR0.90220.72851019
ACPP-RNF13chr3132036420chr3149613260210HLA-B41:03KELKFVTLV0.79010.7048514
ACPP-RNF13chr3132036420chr3149613260210HLA-B08:12ELKFVTLVL0.72410.886615
ACPP-RNF13chr3132036420chr3149613260210HLA-B50:04KELKFVTLV0.43530.8327514
ACPP-RNF13chr3132036420chr3149613260210HLA-B50:05KELKFVTLV0.43530.8327514
ACPP-RNF13chr3132036420chr3149613260210HLA-B39:02KELKFVTLV0.22180.9701514
ACPP-RNF13chr3132036420chr3149613260210HLA-B40:04KELKFVTLVL0.98450.7799515

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Potential FusionNeoAntigen Information of ACPP-RNF13 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.
ACPP-RNF13_132036420_149613260.msa

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)
ACPP-RNF13chr3132036420chr3149613260210DRB1-1418VTLVLNAQRAGYKAA1025

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Fusion breakpoint peptide structures of ACPP-RNF13

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
1906ELKFVTLVLNAQRAACPPRNF13chr3132036420chr3149613260210

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ACPP-RNF13

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-B14:023BVN1906ELKFVTLVLNAQRA-7.15543-7.26883
HLA-B14:023BVN1906ELKFVTLVLNAQRA-4.77435-5.80965
HLA-B52:013W391906ELKFVTLVLNAQRA-6.80875-6.92215
HLA-B52:013W391906ELKFVTLVLNAQRA-4.20386-5.23916
HLA-A11:014UQ21906ELKFVTLVLNAQRA-7.5194-8.5547
HLA-A11:014UQ21906ELKFVTLVLNAQRA-6.9601-7.0735
HLA-A24:025HGA1906ELKFVTLVLNAQRA-7.52403-7.63743
HLA-A24:025HGA1906ELKFVTLVLNAQRA-5.82433-6.85963
HLA-B27:056PYJ1906ELKFVTLVLNAQRA-3.28285-4.31815
HLA-B44:053DX81906ELKFVTLVLNAQRA-5.91172-6.94702
HLA-B44:053DX81906ELKFVTLVLNAQRA-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of ACPP-RNF13

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
ACPP-RNF13chr3132036420chr31496132601019VTLVLNAQRGTGACTTTGGTTTTAAATGCACAGAGA
ACPP-RNF13chr3132036420chr3149613260514KELKFVTLVAAGGAGTTGAAGTTTGTGACTTTGGTT
ACPP-RNF13chr3132036420chr3149613260515KELKFVTLVLAAGGAGTTGAAGTTTGTGACTTTGGTTTTA
ACPP-RNF13chr3132036420chr3149613260615ELKFVTLVLGAGTTGAAGTTTGTGACTTTGGTTTTA
ACPP-RNF13chr3132036420chr3149613260819KFVTLVLNAQRAAGTTTGTGACTTTGGTTTTAAATGCACAGAGA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ACPP-RNF13chr3132036420chr31496132601025VTLVLNAQRAGYKAAGTGACTTTGGTTTTAAATGCACAGAGAGCAGGATACAAGGCAGCC

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Information of the samples that have these potential fusion neoantigens of ACPP-RNF13

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
Non-CancerACPP-RNF13chr3132036420ENST00000336375chr3149613260ENST00000344229ERR315376

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Potential target of CAR-T therapy development for ACPP-RNF13

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
TgeneRNF13chr3:132036420chr3:149613260ENST00000344229411183_2030382.0TransmembraneHelical
TgeneRNF13chr3:132036420chr3:149613260ENST00000392894310183_2030382.0TransmembraneHelical

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 ACPP-RNF13

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 ACPP-RNF13

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