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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:NFIC-CRB3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NFIC-CRB3
FusionPDB ID: 58905
FusionGDB2.0 ID: 58905
HgeneTgene
Gene symbol

NFIC

CRB3

Gene ID

4782

92359

Gene namenuclear factor I Ccrumbs cell polarity complex component 3
SynonymsCTF|CTF5|NF-I|NFI-
Cytomap

19p13.3

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionnuclear factor 1 C-typeCCAAT-box-binding transcription factorNF-I/CNF1-CTGGCA-binding proteinnuclear factor I/C (CCAAT-binding transcription factor)protein crumbs homolog 3crumbs 3, cell polarity complex componentcrumbs family member 3
Modification date2020031320200313
UniProtAcc

P08651

Main function of 5'-partner protein: FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.

Q9BUF7

Main function of 5'-partner protein: FUNCTION: Involved in the establishment of cell polarity in mammalian epithelial cells (PubMed:12771187, PubMed:14718572). Regulates the morphogenesis of tight junctions (PubMed:12771187, PubMed:14718572). Involved in promoting phosphorylation and cytoplasmic retention of transcriptional coactivators YAP1 and WWTR1/TAZ which leads to suppression of TGFB1-dependent transcription of target genes such as CCN2/CTGF, SERPINE1/PAI1, SNAI1/SNAIL1 and SMAD7 (By similarity). {ECO:0000250|UniProtKB:Q8QZT4, ECO:0000269|PubMed:12771187, ECO:0000269|PubMed:14718572}.
Ensembl transtripts involved in fusion geneENST idsENST00000341919, ENST00000346156, 
ENST00000395111, ENST00000443272, 
ENST00000586919, ENST00000589123, 
ENST00000590282, ENST00000588839, 
ENST00000308243, ENST00000356762, 
ENST00000598494, ENST00000600229, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score30 X 20 X 13=78004 X 5 X 2=40
# samples 365
** MAII scorelog2(36/7800*10)=-4.4374053123073
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/40*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: NFIC [Title/Abstract] AND CRB3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NFIC [Title/Abstract] AND CRB3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NFIC(3452664)-CRB3(6466477), # samples:1
Anticipated loss of major functional domain due to fusion event.NFIC-CRB3 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.
NFIC-CRB3 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.
NFIC-CRB3 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.
NFIC-CRB3 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.
NFIC-CRB3 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted 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
HgeneNFIC

GO:0000122

negative regulation of transcription by RNA polymerase II

19706729

HgeneNFIC

GO:0045944

positive regulation of transcription by RNA polymerase II

1524678|19706729

TgeneCRB3

GO:0072659

protein localization to plasma membrane

17332497



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/chr19:3452664/chr19:6466477)
- 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 NFIC (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 CRB3 (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)
ENST00000589123NFICchr193452664+ENST00000598494CRB3chr196466477+21181362481568506
ENST00000589123NFICchr193452664+ENST00000600229CRB3chr196466477+21181362481568506
ENST00000589123NFICchr193452664+ENST00000356762CRB3chr196466477+17771362481577509
ENST00000346156NFICchr193452664+ENST00000598494CRB3chr196466477+19911235651441458
ENST00000346156NFICchr193452664+ENST00000600229CRB3chr196466477+19911235651441458
ENST00000346156NFICchr193452664+ENST00000356762CRB3chr196466477+16501235651450461
ENST00000395111NFICchr193452664+ENST00000598494CRB3chr196466477+20341278361484482
ENST00000395111NFICchr193452664+ENST00000600229CRB3chr196466477+20341278361484482
ENST00000395111NFICchr193452664+ENST00000356762CRB3chr196466477+16931278361493485
ENST00000586919NFICchr193452664+ENST00000598494CRB3chr196466477+1926117001376458
ENST00000586919NFICchr193452664+ENST00000600229CRB3chr196466477+1926117001376458
ENST00000586919NFICchr193452664+ENST00000356762CRB3chr196466477+1585117001385461
ENST00000341919NFICchr193452664+ENST00000598494CRB3chr196466477+21131357881563491
ENST00000341919NFICchr193452664+ENST00000600229CRB3chr196466477+21131357881563491
ENST00000341919NFICchr193452664+ENST00000356762CRB3chr196466477+17721357881572494
ENST00000590282NFICchr193452664+ENST00000598494CRB3chr196466477+20791323541529491
ENST00000590282NFICchr193452664+ENST00000600229CRB3chr196466477+20791323541529491
ENST00000590282NFICchr193452664+ENST00000356762CRB3chr196466477+17381323541538494
ENST00000443272NFICchr193452664+ENST00000598494CRB3chr196466477+20761320511526491
ENST00000443272NFICchr193452664+ENST00000600229CRB3chr196466477+20761320511526491
ENST00000443272NFICchr193452664+ENST00000356762CRB3chr196466477+17351320511535494

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
ENST00000589123ENST00000598494NFICchr193452664+CRB3chr196466477+0.034284710.96571535
ENST00000589123ENST00000600229NFICchr193452664+CRB3chr196466477+0.034284710.96571535
ENST00000589123ENST00000356762NFICchr193452664+CRB3chr196466477+0.0353821740.96461785
ENST00000346156ENST00000598494NFICchr193452664+CRB3chr196466477+0.037437290.96256274
ENST00000346156ENST00000600229NFICchr193452664+CRB3chr196466477+0.037437290.96256274
ENST00000346156ENST00000356762NFICchr193452664+CRB3chr196466477+0.0385657470.96143425
ENST00000395111ENST00000598494NFICchr193452664+CRB3chr196466477+0.03359610.9664039
ENST00000395111ENST00000600229NFICchr193452664+CRB3chr196466477+0.03359610.9664039
ENST00000395111ENST00000356762NFICchr193452664+CRB3chr196466477+0.034278790.96572125
ENST00000586919ENST00000598494NFICchr193452664+CRB3chr196466477+0.035263320.96473664
ENST00000586919ENST00000600229NFICchr193452664+CRB3chr196466477+0.035263320.96473664
ENST00000586919ENST00000356762NFICchr193452664+CRB3chr196466477+0.034732540.9652675
ENST00000341919ENST00000598494NFICchr193452664+CRB3chr196466477+0.0332893730.96671057
ENST00000341919ENST00000600229NFICchr193452664+CRB3chr196466477+0.0332893730.96671057
ENST00000341919ENST00000356762NFICchr193452664+CRB3chr196466477+0.0307968460.9692031
ENST00000590282ENST00000598494NFICchr193452664+CRB3chr196466477+0.0364408570.96355915
ENST00000590282ENST00000600229NFICchr193452664+CRB3chr196466477+0.0364408570.96355915
ENST00000590282ENST00000356762NFICchr193452664+CRB3chr196466477+0.0351063350.96489364
ENST00000443272ENST00000598494NFICchr193452664+CRB3chr196466477+0.0370519980.962948
ENST00000443272ENST00000600229NFICchr193452664+CRB3chr196466477+0.0370519980.962948
ENST00000443272ENST00000356762NFICchr193452664+CRB3chr196466477+0.0360332130.96396685

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 NFIC-CRB3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NFICchr193452664CRB3chr1964664771170390SLACDPASQQPGPRPEAITAIIVVFS
NFICchr193452664CRB3chr1964664771235390SLACDPASQQPGPRPEAITAIIVVFS
NFICchr193452664CRB3chr1964664771278414SLACDPASQQPGPRPEAITAIIVVFS
NFICchr193452664CRB3chr1964664771320423SLACDPASQQPGPRPEAITAIIVVFS
NFICchr193452664CRB3chr1964664771323423SLACDPASQQPGPRPEAITAIIVVFS
NFICchr193452664CRB3chr1964664771357423SLACDPASQQPGPRPEAITAIIVVFS
NFICchr193452664CRB3chr1964664771362438SLACDPASQQPGPRPEAITAIIVVFS

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Potential FusionNeoAntigen Information of NFIC-CRB3 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.
NFIC-CRB3_3452664_6466477.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)
NFIC-CRB3chr193452664chr1964664771357HLA-B08:09QPGPRPEA0.99270.8401917
NFIC-CRB3chr193452664chr1964664771357HLA-B55:01QPGPRPEA0.96810.662917
NFIC-CRB3chr193452664chr1964664771357HLA-B56:01QPGPRPEA0.9580.7683917
NFIC-CRB3chr193452664chr1964664771357HLA-B07:02GPRPEAITA0.99940.68511120
NFIC-CRB3chr193452664chr1964664771357HLA-B07:05GPRPEAITA0.99940.67091120
NFIC-CRB3chr193452664chr1964664771357HLA-B07:02QPGPRPEAI0.99860.6937918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:05QPGPRPEAI0.99850.7536918
NFIC-CRB3chr193452664chr1964664771357HLA-B08:01QPGPRPEAI0.96190.6904918
NFIC-CRB3chr193452664chr1964664771357HLA-B08:09QPGPRPEAI0.95310.8808918
NFIC-CRB3chr193452664chr1964664771357HLA-B51:01QPGPRPEAI0.79740.9173918
NFIC-CRB3chr193452664chr1964664771357HLA-B51:02QPGPRPEAI0.75430.9217918
NFIC-CRB3chr193452664chr1964664771357HLA-B08:09GPRPEAITA0.66650.78081120
NFIC-CRB3chr193452664chr1964664771357HLA-B35:03QPGPRPEAI0.57060.9746918
NFIC-CRB3chr193452664chr1964664771357HLA-B35:02QPGPRPEAI0.52960.993918
NFIC-CRB3chr193452664chr1964664771357HLA-B35:04QPGPRPEAI0.52960.993918
NFIC-CRB3chr193452664chr1964664771357HLA-B82:01QPGPRPEAI0.41340.7317918
NFIC-CRB3chr193452664chr1964664771357HLA-B81:01GPRPEAITA0.31740.66981120
NFIC-CRB3chr193452664chr1964664771357HLA-B82:01GPRPEAITA0.2980.58791120
NFIC-CRB3chr193452664chr1964664771357HLA-B81:01QPGPRPEAI0.24610.8114918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:02GPRPEAITAI0.99830.62441121
NFIC-CRB3chr193452664chr1964664771357HLA-B07:05GPRPEAITAI0.99830.58221121
NFIC-CRB3chr193452664chr1964664771357HLA-B81:01GPRPEAITAI0.62710.6751121
NFIC-CRB3chr193452664chr1964664771357HLA-B07:05GPRPEAITAII0.99980.50271122
NFIC-CRB3chr193452664chr1964664771357HLA-B07:02GPRPEAITAII0.99980.55971122
NFIC-CRB3chr193452664chr1964664771357HLA-B55:01QPGPRPEAITA0.99710.7148920
NFIC-CRB3chr193452664chr1964664771357HLA-B13:02SQQPGPRPEAI0.97950.9492718
NFIC-CRB3chr193452664chr1964664771357HLA-B56:01QPGPRPEAITA0.97880.8826920
NFIC-CRB3chr193452664chr1964664771357HLA-B13:01SQQPGPRPEAI0.92390.9689718
NFIC-CRB3chr193452664chr1964664771357HLA-B42:02QPGPRPEAI0.9790.6937918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:12GPRPEAITA0.97370.78971120
NFIC-CRB3chr193452664chr1964664771357HLA-B42:01QPGPRPEAI0.97020.686918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:12QPGPRPEAI0.95860.8261918
NFIC-CRB3chr193452664chr1964664771357HLA-B14:03QPGPRPEAI0.95190.9493918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:04GPRPEAITA0.86730.64821120
NFIC-CRB3chr193452664chr1964664771357HLA-B07:04QPGPRPEAI0.85260.6853918
NFIC-CRB3chr193452664chr1964664771357HLA-B42:02GPRPEAITA0.83560.59571120
NFIC-CRB3chr193452664chr1964664771357HLA-B51:08QPGPRPEAI0.83440.7398918
NFIC-CRB3chr193452664chr1964664771357HLA-B78:01QPGPRPEAI0.82930.9523918
NFIC-CRB3chr193452664chr1964664771357HLA-B54:01GPRPEAITA0.79480.64681120
NFIC-CRB3chr193452664chr1964664771357HLA-B42:01GPRPEAITA0.74340.58971120
NFIC-CRB3chr193452664chr1964664771357HLA-B56:04QPGPRPEAI0.66010.8922918
NFIC-CRB3chr193452664chr1964664771357HLA-B56:04GPRPEAITA0.58740.62421120
NFIC-CRB3chr193452664chr1964664771357HLA-B35:12QPGPRPEAI0.52960.993918
NFIC-CRB3chr193452664chr1964664771357HLA-B78:01GPRPEAITA0.41970.73871120
NFIC-CRB3chr193452664chr1964664771357HLA-B39:10QPGPRPEAI0.29580.9851918
NFIC-CRB3chr193452664chr1964664771357HLA-B39:10GPRPEAITA0.13420.91961120
NFIC-CRB3chr193452664chr1964664771357HLA-B07:12GPRPEAITAI0.99440.78391121
NFIC-CRB3chr193452664chr1964664771357HLA-B07:04GPRPEAITAI0.93150.59141121
NFIC-CRB3chr193452664chr1964664771357HLA-B42:02GPRPEAITAI0.8120.59181121
NFIC-CRB3chr193452664chr1964664771357HLA-B42:01GPRPEAITAI0.78630.58441121
NFIC-CRB3chr193452664chr1964664771357HLA-B07:04GPRPEAITAII0.99380.54421122
NFIC-CRB3chr193452664chr1964664771357HLA-B54:01QPGPRPEAITA0.99140.908920
NFIC-CRB3chr193452664chr1964664771357HLA-B56:05QPGPRPEA0.98540.8391917
NFIC-CRB3chr193452664chr1964664771357HLA-B55:02QPGPRPEA0.92940.7103917
NFIC-CRB3chr193452664chr1964664771357HLA-B07:22GPRPEAITA0.99940.68511120
NFIC-CRB3chr193452664chr1964664771357HLA-B07:09GPRPEAITA0.99920.66211120
NFIC-CRB3chr193452664chr1964664771357HLA-B07:22QPGPRPEAI0.99860.6937918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:09QPGPRPEAI0.99790.6907918
NFIC-CRB3chr193452664chr1964664771357HLA-B08:18QPGPRPEAI0.96190.6904918
NFIC-CRB3chr193452664chr1964664771357HLA-B56:05QPGPRPEAI0.90040.8181918
NFIC-CRB3chr193452664chr1964664771357HLA-B78:02QPGPRPEAI0.8190.9537918
NFIC-CRB3chr193452664chr1964664771357HLA-B51:09QPGPRPEAI0.7910.9221918
NFIC-CRB3chr193452664chr1964664771357HLA-B51:13QPGPRPEAI0.78830.9057918
NFIC-CRB3chr193452664chr1964664771357HLA-B51:29QPGPRPEAI0.77330.8332918
NFIC-CRB3chr193452664chr1964664771357HLA-B35:22QPGPRPEAI0.75870.8962918
NFIC-CRB3chr193452664chr1964664771357HLA-B56:05GPRPEAITA0.75140.52921120
NFIC-CRB3chr193452664chr1964664771357HLA-B55:02GPRPEAITA0.74520.50941120
NFIC-CRB3chr193452664chr1964664771357HLA-B51:14QPGPRPEAI0.74460.895918
NFIC-CRB3chr193452664chr1964664771357HLA-B55:04GPRPEAITA0.72480.57281120
NFIC-CRB3chr193452664chr1964664771357HLA-B55:04QPGPRPEAI0.70310.7224918
NFIC-CRB3chr193452664chr1964664771357HLA-B59:01GPRPEAITA0.70110.5731120
NFIC-CRB3chr193452664chr1964664771357HLA-B56:02QPGPRPEAI0.66010.8922918
NFIC-CRB3chr193452664chr1964664771357HLA-B51:21QPGPRPEAI0.64090.8763918
NFIC-CRB3chr193452664chr1964664771357HLA-B51:06QPGPRPEAI0.62760.9284918
NFIC-CRB3chr193452664chr1964664771357HLA-B59:01QPGPRPEAI0.60820.7577918
NFIC-CRB3chr193452664chr1964664771357HLA-B08:12QPGPRPEAI0.59750.841918
NFIC-CRB3chr193452664chr1964664771357HLA-B56:02GPRPEAITA0.58740.62421120
NFIC-CRB3chr193452664chr1964664771357HLA-B51:05QPGPRPEAI0.5490.6928918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:26GPRPEAITA0.54590.58531120
NFIC-CRB3chr193452664chr1964664771357HLA-B35:09QPGPRPEAI0.52960.993918
NFIC-CRB3chr193452664chr1964664771357HLA-B07:26QPGPRPEAI0.45560.7439918
NFIC-CRB3chr193452664chr1964664771357HLA-B82:02QPGPRPEAI0.41340.7317918
NFIC-CRB3chr193452664chr1964664771357HLA-B67:01QPGPRPEAI0.40710.9849918
NFIC-CRB3chr193452664chr1964664771357HLA-B82:02GPRPEAITA0.2980.58791120
NFIC-CRB3chr193452664chr1964664771357HLA-B78:02GPRPEAITA0.29120.79821120
NFIC-CRB3chr193452664chr1964664771357HLA-B67:01GPRPEAITA0.21310.90061120
NFIC-CRB3chr193452664chr1964664771357HLA-B07:22GPRPEAITAI0.99830.62441121
NFIC-CRB3chr193452664chr1964664771357HLA-B07:09GPRPEAITAI0.99760.60781121
NFIC-CRB3chr193452664chr1964664771357HLA-B07:26GPRPEAITAI0.80880.561121
NFIC-CRB3chr193452664chr1964664771357HLA-B55:04GPRPEAITAI0.62620.57451121
NFIC-CRB3chr193452664chr1964664771357HLA-B07:22GPRPEAITAII0.99980.55971122
NFIC-CRB3chr193452664chr1964664771357HLA-B56:05QPGPRPEAITA0.98990.8701920
NFIC-CRB3chr193452664chr1964664771357HLA-B55:02QPGPRPEAITA0.97670.79920
NFIC-CRB3chr193452664chr1964664771357HLA-B07:26GPRPEAITAII0.96750.52841122

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Potential FusionNeoAntigen Information of NFIC-CRB3 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 NFIC-CRB3

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
612ASQQPGPRPEAITANFICCRB3chr193452664chr1964664771357

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NFIC-CRB3

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-B14:023BVN612ASQQPGPRPEAITA-8.79968-8.91308
HLA-B14:023BVN612ASQQPGPRPEAITA-2.93446-3.96976
HLA-B52:013W39612ASQQPGPRPEAITA-5.96997-6.08337
HLA-B52:013W39612ASQQPGPRPEAITA-4.23042-5.26572
HLA-A11:014UQ2612ASQQPGPRPEAITA-8.20522-8.31862
HLA-A11:014UQ2612ASQQPGPRPEAITA-4.67476-5.71006
HLA-A24:025HGA612ASQQPGPRPEAITA-9.05525-9.16865
HLA-A24:025HGA612ASQQPGPRPEAITA-6.47443-7.50973
HLA-B44:053DX8612ASQQPGPRPEAITA-6.9286-7.042
HLA-B44:053DX8612ASQQPGPRPEAITA-2.31135-3.34665
HLA-A02:016TDR612ASQQPGPRPEAITA-4.18158-5.21688

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Vaccine Design for the FusionNeoAntigens of NFIC-CRB3

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
NFIC-CRB3chr193452664chr1964664771120GPRPEAITAGGACCGCGTCCAGAAGCCATCACTGCT
NFIC-CRB3chr193452664chr1964664771121GPRPEAITAIGGACCGCGTCCAGAAGCCATCACTGCTATC
NFIC-CRB3chr193452664chr1964664771122GPRPEAITAIIGGACCGCGTCCAGAAGCCATCACTGCTATCATC
NFIC-CRB3chr193452664chr196466477718SQQPGPRPEAIAGCCAGCAACCTGGACCGCGTCCAGAAGCCATC
NFIC-CRB3chr193452664chr196466477917QPGPRPEACAACCTGGACCGCGTCCAGAAGCC
NFIC-CRB3chr193452664chr196466477918QPGPRPEAICAACCTGGACCGCGTCCAGAAGCCATC
NFIC-CRB3chr193452664chr196466477920QPGPRPEAITACAACCTGGACCGCGTCCAGAAGCCATCACTGCT

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 NFIC-CRB3

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
LUADNFIC-CRB3chr193452664ENST00000341919chr196466477ENST00000356762TCGA-05-4427-01A

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Potential target of CAR-T therapy development for NFIC-CRB3

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
TgeneCRB3chr19:3452664chr19:6466477ENST000003082431360_800121.0TransmembraneHelical
TgeneCRB3chr19:3452664chr19:6466477ENST000003567622560_800124.0TransmembraneHelical
TgeneCRB3chr19:3452664chr19:6466477ENST000005984942460_800121.0TransmembraneHelical
TgeneCRB3chr19:3452664chr19:6466477ENST000006002292460_800121.0TransmembraneHelical

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 NFIC-CRB3

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 NFIC-CRB3

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