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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:ABCC3-CCNI

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ABCC3-CCNI
FusionPDB ID: 253
FusionGDB2.0 ID: 253
HgeneTgene
Gene symbol

ABCC3

CCNI

Gene ID

8714

10983

Gene nameATP binding cassette subfamily C member 3cyclin I
SynonymsABC31|EST90757|MLP2|MOAT-D|MRP3|cMOAT2CCNI1|CYC1|CYI
Cytomap

17q21.33

4q21.1

Type of geneprotein-codingprotein-coding
Descriptioncanalicular multispecific organic anion transporter 2ATP-binding cassette sub-family C member 3ATP-binding cassette, sub-family C (CFTR/MRP), member 3canicular multispecific organic anion transportermulti-specific organic anion transporter Dmultidrugcyclin-Icyclin ITI
Modification date2020031320200327
UniProtAcc

O15438

Main function of 5'-partner protein: FUNCTION: ATP-dependent transporter of the ATP-binding cassette (ABC) family that bind and hydrolyze ATP to enable active transport of various substrates including many drugs, toxicants and endogenous compound across cell membranes (PubMed:11581266, PubMed:15083066, PubMed:10359813). Transports glucuronide conjugates such as bilirubin diglucuronide, estradiol-17-beta-o-glucuronide and GSH conjugates such as leukotriene C4 (LTC4) (PubMed:15083066, PubMed:11581266). Transports also various bile salts (taurocholate, glycocholate, taurochenodeoxycholate-3-sulfate, taurolithocholate- 3-sulfate) (By similarity). Does not contribute substantially to bile salt physiology but provides an alternative route for the export of bile acids and glucuronides from cholestatic hepatocytes (By similarity). Can confers resistance to various anticancer drugs, methotrexate, tenoposide and etoposide, by decreasing accumulation of these drugs in cells (PubMed:11581266, PubMed:10359813). {ECO:0000250|UniProtKB:O88563, ECO:0000269|PubMed:10359813, ECO:0000269|PubMed:11581266, ECO:0000269|PubMed:15083066}.

Q6ZMN8

Main function of 5'-partner protein:
Ensembl transtripts involved in fusion geneENST idsENST00000285238, ENST00000427699, 
ENST00000510891, ENST00000515707, 
ENST00000504697, ENST00000237654, 
ENST00000537948, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 12 X 7=134417 X 12 X 5=1020
# samples 1819
** MAII scorelog2(18/1344*10)=-2.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1020*10)=-2.42449782852791
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ABCC3 [Title/Abstract] AND CCNI [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ABCC3 [Title/Abstract] AND CCNI [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ABCC3(48733369)-CCNI(77976533), # samples:1
Anticipated loss of major functional domain due to fusion event.ABCC3-CCNI 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.
ABCC3-CCNI 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
HgeneABCC3

GO:0042908

xenobiotic transport

18698235|19334674



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/chr17:48733369/chr4:77976533)
- 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 ABCC3 (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 CCNI (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)
ENST00000285238ABCC3chr1748733369+ENST00000237654CCNIchr477976533-203830259976305
ENST00000285238ABCC3chr1748733369+ENST00000537948CCNIchr477976533-106130259976305
ENST00000427699ABCC3chr1748733369+ENST00000237654CCNIchr477976533-203830259976305
ENST00000427699ABCC3chr1748733369+ENST00000537948CCNIchr477976533-106130259976305

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
ENST00000285238ENST00000237654ABCC3chr1748733369+CCNIchr477976533-0.0245789920.975421
ENST00000285238ENST00000537948ABCC3chr1748733369+CCNIchr477976533-0.115250240.88474977
ENST00000427699ENST00000237654ABCC3chr1748733369+CCNIchr477976533-0.0245789920.975421
ENST00000427699ENST00000537948ABCC3chr1748733369+CCNIchr477976533-0.115250240.88474977

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 ABCC3-CCNI

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ABCC3chr1748733369CCNIchr47797653330281GYIILSHLSKLKMFHAIAVSTRPQLL

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Potential FusionNeoAntigen Information of ABCC3-CCNI 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.
ABCC3-CCNI_48733369_77976533.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)
ABCC3-CCNIchr1748733369chr477976533302HLA-B39:06LKMFHAIAV0.99570.82671019
ABCC3-CCNIchr1748733369chr477976533302HLA-B14:01SKLKMFHAI0.98590.5536817
ABCC3-CCNIchr1748733369chr477976533302HLA-B14:02SKLKMFHAI0.98590.5536817
ABCC3-CCNIchr1748733369chr477976533302HLA-B38:01SHLSKLKMF0.90280.9685514
ABCC3-CCNIchr1748733369chr477976533302HLA-B38:02SHLSKLKMF0.88170.9755514
ABCC3-CCNIchr1748733369chr477976533302HLA-B14:02SHLSKLKMF0.74030.6249514
ABCC3-CCNIchr1748733369chr477976533302HLA-B14:01SHLSKLKMF0.74030.6249514
ABCC3-CCNIchr1748733369chr477976533302HLA-B15:18SHLSKLKMF0.58860.5193514
ABCC3-CCNIchr1748733369chr477976533302HLA-B52:01SKLKMFHAI0.00720.7167817
ABCC3-CCNIchr1748733369chr477976533302HLA-A31:02MFHAIAVSTR0.98040.54351222
ABCC3-CCNIchr1748733369chr477976533302HLA-A74:11KMFHAIAVSTR0.99740.68191122
ABCC3-CCNIchr1748733369chr477976533302HLA-A74:09KMFHAIAVSTR0.99740.68191122
ABCC3-CCNIchr1748733369chr477976533302HLA-A74:03KMFHAIAVSTR0.99740.68191122
ABCC3-CCNIchr1748733369chr477976533302HLA-A31:02KMFHAIAVSTR0.99240.67871122
ABCC3-CCNIchr1748733369chr477976533302HLA-B39:12SHLSKLKMF0.94890.9414514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:27SHLSKLKMF0.78860.9156514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:46SHLSKLKMF0.77020.7009514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:13SHLSKLKMF0.76270.8115514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:19SHLSKLKMF0.74880.5124514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:67SHLSKLKMF0.71850.8402514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:80SHLSKLKMF0.71850.8402514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:10SHLSKLKMF0.71040.906514
ABCC3-CCNIchr1748733369chr477976533302HLA-B14:03SHLSKLKMF0.06270.7587514
ABCC3-CCNIchr1748733369chr477976533302HLA-C12:16SHLSKLKMF0.01750.9481514
ABCC3-CCNIchr1748733369chr477976533302HLA-A31:01KMFHAIAVSTR0.99720.6571122
ABCC3-CCNIchr1748733369chr477976533302HLA-B39:31SHLSKLKMF0.920.9363514
ABCC3-CCNIchr1748733369chr477976533302HLA-B38:05SHLSKLKMF0.90280.9685514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:17SHLSKLKMF0.79950.9508514
ABCC3-CCNIchr1748733369chr477976533302HLA-C07:02SHLSKLKMF0.71850.8402514
ABCC3-CCNIchr1748733369chr477976533302HLA-C06:06SHLSKLKMF0.03690.9849514
ABCC3-CCNIchr1748733369chr477976533302HLA-A74:01KMFHAIAVSTR0.99740.68191122

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Potential FusionNeoAntigen Information of ABCC3-CCNI 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.
ABCC3-CCNI_48733369_77976533.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)
ABCC3-CCNIchr1748733369chr477976533302DRB1-0115LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-0819LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-0834LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1117KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1152KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1401KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1404KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1405KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1407KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1408KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1418KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1423KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1426KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1428KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1432KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1435KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1438KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1443KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1445KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1450KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1454KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1455KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1456KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1458KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1459KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1460KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1461KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1462KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1464KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1470KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1471KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1472KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1475KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1482KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1486KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1487KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1488KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1490KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1491KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1495KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1496KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1497KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1499KMFHAIAVSTRPQLL1126
ABCC3-CCNIchr1748733369chr477976533302DRB1-1499LKMFHAIAVSTRPQL1025
ABCC3-CCNIchr1748733369chr477976533302DRB1-1501LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1501SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1501HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1502LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1504LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1504SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1504HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1505LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1505SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1505HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1506LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1506SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1506HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1507LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1507HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1507SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1508LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1509LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1509SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1509HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1510LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1510SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1510HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1511LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1512LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1512HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1512SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1513LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1513SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1513HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1514LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1515LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1516LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1516SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1516HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1518LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1518SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1518HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1519LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1520LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1520SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1520HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1521LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1521SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1521HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1521SHLSKLKMFHAIAVS520
ABCC3-CCNIchr1748733369chr477976533302DRB1-1522LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1522SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1522HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1524LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1524SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1524HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1526LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1527LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1528LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1528SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1528HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1529LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1529HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1530LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1531LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1532LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1532SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1532HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1533LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1533SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1533HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1535LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1535SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1535HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1536LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1536SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1536HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1537LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1537SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1537HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1538LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1539LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1540LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1540SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1540HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1541LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1541SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1541HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1542LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1542SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1542HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1543LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1543SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1543HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1544LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1545LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1545SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1545HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1546LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1546SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1546HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1547LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1548LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1548HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1548SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1549LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1549SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB1-1549HLSKLKMFHAIAVST621
ABCC3-CCNIchr1748733369chr477976533302DRB1-1610LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1615LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB1-1615SKLKMFHAIAVSTRP823
ABCC3-CCNIchr1748733369chr477976533302DRB5-0101KLKMFHAIAVSTRPQ924
ABCC3-CCNIchr1748733369chr477976533302DRB5-0101LKMFHAIAVSTRPQL1025
ABCC3-CCNIchr1748733369chr477976533302DRB5-0104KLKMFHAIAVSTRPQ924
ABCC3-CCNIchr1748733369chr477976533302DRB5-0104LKMFHAIAVSTRPQL1025
ABCC3-CCNIchr1748733369chr477976533302DRB5-0105KLKMFHAIAVSTRPQ924
ABCC3-CCNIchr1748733369chr477976533302DRB5-0105LKMFHAIAVSTRPQL1025
ABCC3-CCNIchr1748733369chr477976533302DRB5-0111KLKMFHAIAVSTRPQ924
ABCC3-CCNIchr1748733369chr477976533302DRB5-0112KLKMFHAIAVSTRPQ924
ABCC3-CCNIchr1748733369chr477976533302DRB5-0113KLKMFHAIAVSTRPQ924
ABCC3-CCNIchr1748733369chr477976533302DRB5-0113LKMFHAIAVSTRPQL1025
ABCC3-CCNIchr1748733369chr477976533302DRB5-0114KLKMFHAIAVSTRPQ924
ABCC3-CCNIchr1748733369chr477976533302DRB5-0114LKMFHAIAVSTRPQL1025
ABCC3-CCNIchr1748733369chr477976533302DRB5-0202LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB5-0204LSKLKMFHAIAVSTR722
ABCC3-CCNIchr1748733369chr477976533302DRB5-0205LSKLKMFHAIAVSTR722

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Fusion breakpoint peptide structures of ABCC3-CCNI

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
3415HLSKLKMFHAIAVSABCC3CCNIchr1748733369chr477976533302

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ABCC3-CCNI

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-B14:023BVN3415HLSKLKMFHAIAVS-7.9962-8.1096
HLA-B14:023BVN3415HLSKLKMFHAIAVS-5.70842-6.74372
HLA-B52:013W393415HLSKLKMFHAIAVS-6.83737-6.95077
HLA-B52:013W393415HLSKLKMFHAIAVS-4.4836-5.5189
HLA-A11:014UQ23415HLSKLKMFHAIAVS-10.0067-10.1201
HLA-A11:014UQ23415HLSKLKMFHAIAVS-9.03915-10.0745
HLA-A24:025HGA3415HLSKLKMFHAIAVS-6.56204-6.67544
HLA-A24:025HGA3415HLSKLKMFHAIAVS-5.42271-6.45801
HLA-B44:053DX83415HLSKLKMFHAIAVS-7.85648-8.89178
HLA-B44:053DX83415HLSKLKMFHAIAVS-5.3978-5.5112
HLA-A02:016TDR3415HLSKLKMFHAIAVS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ABCC3-CCNI

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
ABCC3-CCNIchr1748733369chr4779765331019LKMFHAIAVCTCAAGATGTTCCATGCCATTGCAGTG
ABCC3-CCNIchr1748733369chr4779765331122KMFHAIAVSTRAAGATGTTCCATGCCATTGCAGTGTCAACTAGG
ABCC3-CCNIchr1748733369chr4779765331222MFHAIAVSTRATGTTCCATGCCATTGCAGTGTCAACTAGG
ABCC3-CCNIchr1748733369chr477976533514SHLSKLKMFTCCCACCTGTCCAAGCTCAAGATGTTC
ABCC3-CCNIchr1748733369chr477976533817SKLKMFHAITCCAAGCTCAAGATGTTCCATGCCATT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ABCC3-CCNIchr1748733369chr4779765331025LKMFHAIAVSTRPQLCTCAAGATGTTCCATGCCATTGCAGTGTCAACTAGGCCTCAGTTA
ABCC3-CCNIchr1748733369chr4779765331126KMFHAIAVSTRPQLLAAGATGTTCCATGCCATTGCAGTGTCAACTAGGCCTCAGTTACTT
ABCC3-CCNIchr1748733369chr477976533520SHLSKLKMFHAIAVSTCCCACCTGTCCAAGCTCAAGATGTTCCATGCCATTGCAGTGTCA
ABCC3-CCNIchr1748733369chr477976533621HLSKLKMFHAIAVSTCACCTGTCCAAGCTCAAGATGTTCCATGCCATTGCAGTGTCAACT
ABCC3-CCNIchr1748733369chr477976533722LSKLKMFHAIAVSTRCTGTCCAAGCTCAAGATGTTCCATGCCATTGCAGTGTCAACTAGG
ABCC3-CCNIchr1748733369chr477976533823SKLKMFHAIAVSTRPTCCAAGCTCAAGATGTTCCATGCCATTGCAGTGTCAACTAGGCCT
ABCC3-CCNIchr1748733369chr477976533924KLKMFHAIAVSTRPQAAGCTCAAGATGTTCCATGCCATTGCAGTGTCAACTAGGCCTCAG

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Information of the samples that have these potential fusion neoantigens of ABCC3-CCNI

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
STADABCC3-CCNIchr1748733369ENST00000285238chr477976533ENST00000237654TCGA-CG-5724-01A

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Potential target of CAR-T therapy development for ABCC3-CCNI

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
HgeneABCC3chr17:48733369chr4:77976533ENST00000285238+23133_53741528.0TransmembraneHelical%3B Name%3D1
HgeneABCC3chr17:48733369chr4:77976533ENST00000427699+21233_5374573.0TransmembraneHelical%3B Name%3D1

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 ABCC3-CCNI

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 ABCC3-CCNI

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