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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:BPTF-PITPNC1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BPTF-PITPNC1
FusionPDB ID: 10097
FusionGDB2.0 ID: 10097
HgeneTgene
Gene symbol

BPTF

PITPNC1

Gene ID

2186

26207

Gene namebromodomain PHD finger transcription factorphosphatidylinositol transfer protein cytoplasmic 1
SynonymsFAC1|FALZ|NEDDFL|NURF301M-RDGB-beta|MRDGBbeta|RDGB-BETA|RDGBB|RDGBB1
Cytomap

17q24.2

17q24.2

Type of geneprotein-codingprotein-coding
Descriptionnucleosome-remodeling factor subunit BPTFbromodomain and PHD domain transcription factorbromodomain and PHD finger-containing transcription factorfetal Alz-50 clone 1 proteinfetal Alz-50 reactive clone 1fetal Alzheimer antigennucleosome remodeling fcytoplasmic phosphatidylinositol transfer protein 1M-rdgB betamammalian rdgB homolog betaretinal degeneration B beta 1retinal degeneration B homolog beta
Modification date2020031320200313
UniProtAcc

Q12830

Main function of 5'-partner protein: FUNCTION: Histone-binding component of NURF (nucleosome-remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. May also regulate transcription through direct binding to DNA or transcription factors.		.
Ensembl transtripts involved in fusion geneENST idsENST00000577770, ENST00000306378, 
ENST00000321892, ENST00000335221, 
ENST00000424123, 		ENST00000299954, 
ENST00000335257, ENST00000580974, 
ENST00000581322, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score27 X 21 X 13=737131 X 22 X 12=8184
# samples 4252
** MAII scorelog2(42/7371*10)=-4.1333991254172
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(52/8184*10)=-3.97622261671687
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: BPTF [Title/Abstract] AND PITPNC1 [Title/Abstract] AND fusion [Title/Abstract]

The landscape and therapeutic relevance of cancer-associated transcript fusions (pmid: 25500544)
Fusion neoantigen context

PubMed: BPTF [Title/Abstract] AND PITPNC1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BPTF(65936772)-PITPNC1(65665624), # samples:2
BPTF(65850878)-PITPNC1(65665624), # samples:2
BPTF(65944422)-PITPNC1(65665624), # samples:2
PITPNC1(65574373)-BPTF(65914830), # samples:2
Anticipated loss of major functional domain due to fusion event.BPTF-PITPNC1 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.
BPTF-PITPNC1 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.
BPTF-PITPNC1 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.
BPTF-PITPNC1 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.
BPTF-PITPNC1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
BPTF-PITPNC1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
BPTF-PITPNC1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
BPTF-PITPNC1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
BPTF-PITPNC1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PITPNC1-BPTF seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PITPNC1-BPTF seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
PITPNC1-BPTF seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PITPNC1-BPTF seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PITPNC1-BPTF seems lost the major protein functional domain in Tgene 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
HgeneBPTF

GO:0000122

negative regulation of transcription by RNA polymerase II

10727212

HgeneBPTF

GO:0006338

chromatin remodeling

14609955

TgenePITPNC1

GO:0015914

phospholipid transport

22822086



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/chr17:65936772/chr17:65665624)
- 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 BPTF (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 PITPNC1 (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)
ENST00000335221BPTFchr1765936772+ENST00000580974PITPNC1chr1765665623+1194069166172602399
ENST00000335221BPTFchr1765936772+ENST00000299954PITPNC1chr1765665623+821369166172602399
ENST00000335221BPTFchr1765936772+ENST00000335257PITPNC1chr1765665623+809469166174522463
ENST00000335221BPTFchr1765936772+ENST00000581322PITPNC1chr1765665623+757869166174522463
ENST00000321892BPTFchr1765936772+ENST00000580974PITPNC1chr1765665623+1194069166172602399
ENST00000321892BPTFchr1765936772+ENST00000299954PITPNC1chr1765665623+821369166172602399
ENST00000321892BPTFchr1765936772+ENST00000335257PITPNC1chr1765665623+809469166174522463
ENST00000321892BPTFchr1765936772+ENST00000581322PITPNC1chr1765665623+757869166174522463
ENST00000306378BPTFchr1765936772+ENST00000580974PITPNC1chr1765665623+1156165376068812273
ENST00000306378BPTFchr1765936772+ENST00000299954PITPNC1chr1765665623+783465376068812273
ENST00000306378BPTFchr1765936772+ENST00000335257PITPNC1chr1765665623+771565376070732337
ENST00000306378BPTFchr1765936772+ENST00000581322PITPNC1chr1765665623+719965376070732337
ENST00000424123BPTFchr1765936772+ENST00000580974PITPNC1chr1765665623+114626438067822260
ENST00000424123BPTFchr1765936772+ENST00000299954PITPNC1chr1765665623+77356438067822260
ENST00000424123BPTFchr1765936772+ENST00000335257PITPNC1chr1765665623+76166438069742324
ENST00000424123BPTFchr1765936772+ENST00000581322PITPNC1chr1765665623+71006438069742324
ENST00000335221BPTFchr1765936772+ENST00000580974PITPNC1chr1765665624+1194069166172602399
ENST00000335221BPTFchr1765936772+ENST00000299954PITPNC1chr1765665624+821369166172602399
ENST00000335221BPTFchr1765936772+ENST00000335257PITPNC1chr1765665624+809469166174522463
ENST00000335221BPTFchr1765936772+ENST00000581322PITPNC1chr1765665624+757869166174522463
ENST00000321892BPTFchr1765936772+ENST00000580974PITPNC1chr1765665624+1194069166172602399
ENST00000321892BPTFchr1765936772+ENST00000299954PITPNC1chr1765665624+821369166172602399
ENST00000321892BPTFchr1765936772+ENST00000335257PITPNC1chr1765665624+809469166174522463
ENST00000321892BPTFchr1765936772+ENST00000581322PITPNC1chr1765665624+757869166174522463
ENST00000306378BPTFchr1765936772+ENST00000580974PITPNC1chr1765665624+1156165376068812273
ENST00000306378BPTFchr1765936772+ENST00000299954PITPNC1chr1765665624+783465376068812273
ENST00000306378BPTFchr1765936772+ENST00000335257PITPNC1chr1765665624+771565376070732337
ENST00000306378BPTFchr1765936772+ENST00000581322PITPNC1chr1765665624+719965376070732337
ENST00000424123BPTFchr1765936772+ENST00000580974PITPNC1chr1765665624+114626438067822260
ENST00000424123BPTFchr1765936772+ENST00000299954PITPNC1chr1765665624+77356438067822260
ENST00000424123BPTFchr1765936772+ENST00000335257PITPNC1chr1765665624+76166438069742324
ENST00000424123BPTFchr1765936772+ENST00000581322PITPNC1chr1765665624+71006438069742324
ENST00000335221BPTFchr1765944422+ENST00000580974PITPNC1chr1765665624+1296079366182802739
ENST00000335221BPTFchr1765944422+ENST00000299954PITPNC1chr1765665624+923379366182802739
ENST00000335221BPTFchr1765944422+ENST00000335257PITPNC1chr1765665624+911479366184722803
ENST00000335221BPTFchr1765944422+ENST00000581322PITPNC1chr1765665624+859879366184722803
ENST00000321892BPTFchr1765944422+ENST00000580974PITPNC1chr1765665624+1338983656187092882
ENST00000321892BPTFchr1765944422+ENST00000299954PITPNC1chr1765665624+966283656187092882
ENST00000321892BPTFchr1765944422+ENST00000335257PITPNC1chr1765665624+954383656189012946
ENST00000321892BPTFchr1765944422+ENST00000581322PITPNC1chr1765665624+902783656189012946
ENST00000306378BPTFchr1765944422+ENST00000580974PITPNC1chr1765665624+1301079866083302756
ENST00000306378BPTFchr1765944422+ENST00000299954PITPNC1chr1765665624+928379866083302756
ENST00000306378BPTFchr1765944422+ENST00000335257PITPNC1chr1765665624+916479866085222820
ENST00000306378BPTFchr1765944422+ENST00000581322PITPNC1chr1765665624+864879866085222820
ENST00000424123BPTFchr1765944422+ENST00000580974PITPNC1chr1765665624+124827458078022600
ENST00000424123BPTFchr1765944422+ENST00000299954PITPNC1chr1765665624+87557458078022600
ENST00000424123BPTFchr1765944422+ENST00000335257PITPNC1chr1765665624+86367458079942664
ENST00000424123BPTFchr1765944422+ENST00000581322PITPNC1chr1765665624+81207458079942664
ENST00000335221BPTFchr1765871136+ENST00000299954PITPNC1chr1765574302+33921925612439792
ENST00000335221BPTFchr1765871136+ENST00000335257PITPNC1chr1765574302+32731925612631856
ENST00000321892BPTFchr1765871136+ENST00000299954PITPNC1chr1765574302+33921925612439792
ENST00000321892BPTFchr1765871136+ENST00000335257PITPNC1chr1765574302+32731925612631856
ENST00000306378BPTFchr1765871136+ENST00000299954PITPNC1chr1765574302+33911924602438792
ENST00000306378BPTFchr1765871136+ENST00000335257PITPNC1chr1765574302+32721924602630856
ENST00000424123BPTFchr1765871136+ENST00000299954PITPNC1chr1765574302+2914144701961653
ENST00000424123BPTFchr1765871136+ENST00000335257PITPNC1chr1765574302+2795144702153717
ENST00000335221BPTFchr1765936771+ENST00000580974PITPNC1chr1765665623+1194069166172602399
ENST00000335221BPTFchr1765936771+ENST00000299954PITPNC1chr1765665623+821369166172602399
ENST00000335221BPTFchr1765936771+ENST00000335257PITPNC1chr1765665623+809469166174522463
ENST00000335221BPTFchr1765936771+ENST00000581322PITPNC1chr1765665623+757869166174522463
ENST00000321892BPTFchr1765936771+ENST00000580974PITPNC1chr1765665623+1194069166172602399
ENST00000321892BPTFchr1765936771+ENST00000299954PITPNC1chr1765665623+821369166172602399
ENST00000321892BPTFchr1765936771+ENST00000335257PITPNC1chr1765665623+809469166174522463
ENST00000321892BPTFchr1765936771+ENST00000581322PITPNC1chr1765665623+757869166174522463
ENST00000306378BPTFchr1765936771+ENST00000580974PITPNC1chr1765665623+1156165376068812273
ENST00000306378BPTFchr1765936771+ENST00000299954PITPNC1chr1765665623+783465376068812273
ENST00000306378BPTFchr1765936771+ENST00000335257PITPNC1chr1765665623+771565376070732337
ENST00000306378BPTFchr1765936771+ENST00000581322PITPNC1chr1765665623+719965376070732337
ENST00000424123BPTFchr1765936771+ENST00000580974PITPNC1chr1765665623+114626438067822260
ENST00000424123BPTFchr1765936771+ENST00000299954PITPNC1chr1765665623+77356438067822260
ENST00000424123BPTFchr1765936771+ENST00000335257PITPNC1chr1765665623+76166438069742324
ENST00000424123BPTFchr1765936771+ENST00000581322PITPNC1chr1765665623+71006438069742324

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
ENST00000335221ENST00000580974BPTFchr1765936772+PITPNC1chr1765665623+0.0001224350.9998776
ENST00000335221ENST00000299954BPTFchr1765936772+PITPNC1chr1765665623+0.0002842980.9997156
ENST00000335221ENST00000335257BPTFchr1765936772+PITPNC1chr1765665623+0.0002039160.9997961
ENST00000335221ENST00000581322BPTFchr1765936772+PITPNC1chr1765665623+0.0002470710.99975294
ENST00000321892ENST00000580974BPTFchr1765936772+PITPNC1chr1765665623+0.0001224350.9998776
ENST00000321892ENST00000299954BPTFchr1765936772+PITPNC1chr1765665623+0.0002842980.9997156
ENST00000321892ENST00000335257BPTFchr1765936772+PITPNC1chr1765665623+0.0002039160.9997961
ENST00000321892ENST00000581322BPTFchr1765936772+PITPNC1chr1765665623+0.0002470710.99975294
ENST00000306378ENST00000580974BPTFchr1765936772+PITPNC1chr1765665623+0.0001115940.9998884
ENST00000306378ENST00000299954BPTFchr1765936772+PITPNC1chr1765665623+0.0002624680.99973756
ENST00000306378ENST00000335257BPTFchr1765936772+PITPNC1chr1765665623+0.0001878880.9998122
ENST00000306378ENST00000581322BPTFchr1765936772+PITPNC1chr1765665623+0.0002288650.9997712
ENST00000424123ENST00000580974BPTFchr1765936772+PITPNC1chr1765665623+0.0001081110.9998919
ENST00000424123ENST00000299954BPTFchr1765936772+PITPNC1chr1765665623+0.000245340.9997546
ENST00000424123ENST00000335257BPTFchr1765936772+PITPNC1chr1765665623+0.000173330.9998267
ENST00000424123ENST00000581322BPTFchr1765936772+PITPNC1chr1765665623+0.0002179640.999782
ENST00000335221ENST00000580974BPTFchr1765936772+PITPNC1chr1765665624+0.0001224350.9998776
ENST00000335221ENST00000299954BPTFchr1765936772+PITPNC1chr1765665624+0.0002842980.9997156
ENST00000335221ENST00000335257BPTFchr1765936772+PITPNC1chr1765665624+0.0002039160.9997961
ENST00000335221ENST00000581322BPTFchr1765936772+PITPNC1chr1765665624+0.0002470710.99975294
ENST00000321892ENST00000580974BPTFchr1765936772+PITPNC1chr1765665624+0.0001224350.9998776
ENST00000321892ENST00000299954BPTFchr1765936772+PITPNC1chr1765665624+0.0002842980.9997156
ENST00000321892ENST00000335257BPTFchr1765936772+PITPNC1chr1765665624+0.0002039160.9997961
ENST00000321892ENST00000581322BPTFchr1765936772+PITPNC1chr1765665624+0.0002470710.99975294
ENST00000306378ENST00000580974BPTFchr1765936772+PITPNC1chr1765665624+0.0001115940.9998884
ENST00000306378ENST00000299954BPTFchr1765936772+PITPNC1chr1765665624+0.0002624680.99973756
ENST00000306378ENST00000335257BPTFchr1765936772+PITPNC1chr1765665624+0.0001878880.9998122
ENST00000306378ENST00000581322BPTFchr1765936772+PITPNC1chr1765665624+0.0002288650.9997712
ENST00000424123ENST00000580974BPTFchr1765936772+PITPNC1chr1765665624+0.0001081110.9998919
ENST00000424123ENST00000299954BPTFchr1765936772+PITPNC1chr1765665624+0.000245340.9997546
ENST00000424123ENST00000335257BPTFchr1765936772+PITPNC1chr1765665624+0.000173330.9998267
ENST00000424123ENST00000581322BPTFchr1765936772+PITPNC1chr1765665624+0.0002179640.999782
ENST00000335221ENST00000580974BPTFchr1765944422+PITPNC1chr1765665624+0.0001685820.99983144
ENST00000335221ENST00000299954BPTFchr1765944422+PITPNC1chr1765665624+0.0003833080.9996166
ENST00000335221ENST00000335257BPTFchr1765944422+PITPNC1chr1765665624+0.0004154080.9995846
ENST00000335221ENST00000581322BPTFchr1765944422+PITPNC1chr1765665624+0.0005192950.9994808
ENST00000321892ENST00000580974BPTFchr1765944422+PITPNC1chr1765665624+0.0001505550.99984944
ENST00000321892ENST00000299954BPTFchr1765944422+PITPNC1chr1765665624+0.0003439380.9996561
ENST00000321892ENST00000335257BPTFchr1765944422+PITPNC1chr1765665624+0.0005566380.99944335
ENST00000321892ENST00000581322BPTFchr1765944422+PITPNC1chr1765665624+0.0006965150.99930346
ENST00000306378ENST00000580974BPTFchr1765944422+PITPNC1chr1765665624+0.0001388660.9998611
ENST00000306378ENST00000299954BPTFchr1765944422+PITPNC1chr1765665624+0.0003142490.99968576
ENST00000306378ENST00000335257BPTFchr1765944422+PITPNC1chr1765665624+0.00050990.99949
ENST00000306378ENST00000581322BPTFchr1765944422+PITPNC1chr1765665624+0.0006357610.9993642
ENST00000424123ENST00000580974BPTFchr1765944422+PITPNC1chr1765665624+0.0001468360.99985313
ENST00000424123ENST00000299954BPTFchr1765944422+PITPNC1chr1765665624+0.000359640.99964035
ENST00000424123ENST00000335257BPTFchr1765944422+PITPNC1chr1765665624+0.0003862690.9996137
ENST00000424123ENST00000581322BPTFchr1765944422+PITPNC1chr1765665624+0.0004977250.9995023
ENST00000335221ENST00000299954BPTFchr1765871136+PITPNC1chr1765574302+0.0014551340.99854493
ENST00000335221ENST00000335257BPTFchr1765871136+PITPNC1chr1765574302+0.0011718580.9988281
ENST00000321892ENST00000299954BPTFchr1765871136+PITPNC1chr1765574302+0.0014551340.99854493
ENST00000321892ENST00000335257BPTFchr1765871136+PITPNC1chr1765574302+0.0011718580.9988281
ENST00000306378ENST00000299954BPTFchr1765871136+PITPNC1chr1765574302+0.0014586770.99854136
ENST00000306378ENST00000335257BPTFchr1765871136+PITPNC1chr1765574302+0.0011738820.9988261
ENST00000424123ENST00000299954BPTFchr1765871136+PITPNC1chr1765574302+0.0004830040.99951696
ENST00000424123ENST00000335257BPTFchr1765871136+PITPNC1chr1765574302+0.0004945140.9995055
ENST00000335221ENST00000580974BPTFchr1765936771+PITPNC1chr1765665623+0.0001224350.9998776
ENST00000335221ENST00000299954BPTFchr1765936771+PITPNC1chr1765665623+0.0002842980.9997156
ENST00000335221ENST00000335257BPTFchr1765936771+PITPNC1chr1765665623+0.0002039160.9997961
ENST00000335221ENST00000581322BPTFchr1765936771+PITPNC1chr1765665623+0.0002470710.99975294
ENST00000321892ENST00000580974BPTFchr1765936771+PITPNC1chr1765665623+0.0001224350.9998776
ENST00000321892ENST00000299954BPTFchr1765936771+PITPNC1chr1765665623+0.0002842980.9997156
ENST00000321892ENST00000335257BPTFchr1765936771+PITPNC1chr1765665623+0.0002039160.9997961
ENST00000321892ENST00000581322BPTFchr1765936771+PITPNC1chr1765665623+0.0002470710.99975294
ENST00000306378ENST00000580974BPTFchr1765936771+PITPNC1chr1765665623+0.0001115940.9998884
ENST00000306378ENST00000299954BPTFchr1765936771+PITPNC1chr1765665623+0.0002624680.99973756
ENST00000306378ENST00000335257BPTFchr1765936771+PITPNC1chr1765665623+0.0001878880.9998122
ENST00000306378ENST00000581322BPTFchr1765936771+PITPNC1chr1765665623+0.0002288650.9997712
ENST00000424123ENST00000580974BPTFchr1765936771+PITPNC1chr1765665623+0.0001081110.9998919
ENST00000424123ENST00000299954BPTFchr1765936771+PITPNC1chr1765665623+0.000245340.9997546
ENST00000424123ENST00000335257BPTFchr1765936771+PITPNC1chr1765665623+0.000173330.9998267
ENST00000424123ENST00000581322BPTFchr1765936771+PITPNC1chr1765665623+0.0002179640.999782

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 BPTF-PITPNC1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
BPTFchr1765871136PITPNC1chr17655743021447483TPDDDPEQGKSEECSFLPKFSIHIET
BPTFchr1765871136PITPNC1chr17655743021924622TPDDDPEQGKSEECSFLPKFSIHIET
BPTFchr1765871136PITPNC1chr17655743021925622TPDDDPEQGKSEECSFLPKFSIHIET
BPTFchr1765936771PITPNC1chr176566562364382146LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936771PITPNC1chr176566562365372159LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936771PITPNC1chr176566562369162285LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936772PITPNC1chr176566562364382146LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936772PITPNC1chr176566562365372159LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936772PITPNC1chr176566562369162285LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936772PITPNC1chr176566562464382146LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936772PITPNC1chr176566562465372159LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765936772PITPNC1chr176566562469162285LTMAQLTQLTQGHDPKHFKSEKTGRG
BPTFchr1765944422PITPNC1chr176566562474582486RALLDKDLQIEVQDPKHFKSEKTGRG
BPTFchr1765944422PITPNC1chr176566562479362625RALLDKDLQIEVQDPKHFKSEKTGRG
BPTFchr1765944422PITPNC1chr176566562479862642RALLDKDLQIEVQDPKHFKSEKTGRG
BPTFchr1765944422PITPNC1chr176566562483652768RALLDKDLQIEVQDPKHFKSEKTGRG

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Potential FusionNeoAntigen Information of BPTF-PITPNC1 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.
BPTF-PITPNC1_65871136_65574302.msa
BPTF-PITPNC1_65936771_65665623.msa
BPTF-PITPNC1_65944422_65665624.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)
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:03EECSFLPKF0.99830.91931120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:01EECSFLPKF0.99430.92181120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:03SEECSFLPKF0.99790.93341020
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B57:03KSEECSFLPKF0.9980.9329920
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:13EECSFLPKF0.99830.91931120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:07EECSFLPKF0.99830.91931120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:26EECSFLPKF0.99830.91931120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:07EECSFLPKF0.9960.90081120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:04EECSFLPKF0.99590.92811120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:08EECSFLPKF0.99470.86011120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:05EECSFLPKF0.99430.92181120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:06EECSFLPKF0.99360.92591120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:03EECSFLPKF0.9870.91721120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B18:11EECSFLPKF0.96490.88611120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B35:20EECSFLPKF0.63180.84811120
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:26SEECSFLPKF0.99790.93341020
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:13SEECSFLPKF0.99790.93341020
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B44:07SEECSFLPKF0.99790.93341020
BPTF-PITPNC1chr1765871136chr17655743021924HLA-B57:02KSEECSFLPKF0.98550.8162920
BPTF-PITPNC1chr1765936771chr17656656236537HLA-B15:24TQGHDPKHF0.910.9278918
BPTF-PITPNC1chr1765936771chr17656656236537HLA-A30:01QGHDPKHFK0.87990.75911019
BPTF-PITPNC1chr1765936771chr17656656236537HLA-B15:12TQGHDPKHF0.71460.8561918
BPTF-PITPNC1chr1765936771chr17656656236537HLA-B15:53TQGHDPKHF0.69680.8621918
BPTF-PITPNC1chr1765936771chr17656656236537HLA-B15:54TQGHDPKHF0.65740.8283918
BPTF-PITPNC1chr1765936771chr17656656236537HLA-B57:02LTQGHDPKHF0.98680.9336818
BPTF-PITPNC1chr1765936771chr17656656236537HLA-A30:01TQGHDPKHFK0.88570.7348919
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B18:01IEVQDPKHF0.99630.84918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:03IEVQDPKHF0.99410.8256918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:03QIEVQDPKHF0.82580.9122818
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B13:01LQIEVQDPKHF0.99330.9712718
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B18:05IEVQDPKHF0.99630.84918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B18:08IEVQDPKHF0.9960.8064918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B18:04IEVQDPKHF0.9950.8522918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B18:06IEVQDPKHF0.99480.8458918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:07IEVQDPKHF0.99410.8256918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:13IEVQDPKHF0.99410.8256918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:26IEVQDPKHF0.99410.8256918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B18:03IEVQDPKHF0.98260.8281918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B40:04IEVQDPKHF0.97910.631918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B18:11IEVQDPKHF0.96690.8353918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B15:53IEVQDPKHF0.4350.9099918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B48:02IEVQDPKHF0.33490.9183918
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:13QIEVQDPKHF0.82580.9122818
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:26QIEVQDPKHF0.82580.9122818
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B44:07QIEVQDPKHF0.82580.9122818
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B15:24LQIEVQDPKHF10.9005718
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B15:53LQIEVQDPKHF0.99990.8307718
BPTF-PITPNC1chr1765944422chr17656656247986HLA-B15:12LQIEVQDPKHF0.99980.9027718

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Potential FusionNeoAntigen Information of BPTF-PITPNC1 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.
BPTF-PITPNC1_65944422_65665624.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)
BPTF-PITPNC1chr1765944422chr17656656247986DRB1-1212DLQIEVQDPKHFKSE621
BPTF-PITPNC1chr1765944422chr17656656247986DRB1-1220DLQIEVQDPKHFKSE621
BPTF-PITPNC1chr1765944422chr17656656247986DRB1-1220KDLQIEVQDPKHFKS520
BPTF-PITPNC1chr1765944422chr17656656247986DRB1-1221DLQIEVQDPKHFKSE621

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Fusion breakpoint peptide structures of BPTF-PITPNC1

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
1242DLQIEVQDPKHFKSBPTFPITPNC1chr1765944422chr17656656247986
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
2047EQGKSEECSFLPKFBPTFPITPNC1chr1765871136chr17655743021924
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
9572TQLTQGHDPKHFKSBPTFPITPNC1chr1765936771chr17656656236537

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BPTF-PITPNC1

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-B14:023BVN1242DLQIEVQDPKHFKS-5.67398-5.78738
HLA-B14:023BVN1242DLQIEVQDPKHFKS-4.72816-5.76346
HLA-B52:013W391242DLQIEVQDPKHFKS-4.43637-5.47167
HLA-B52:013W391242DLQIEVQDPKHFKS-2.42523-2.53863
HLA-A11:014UQ21242DLQIEVQDPKHFKS-8.76571-8.87911
HLA-A24:025HGA1242DLQIEVQDPKHFKS-5.86552-5.97892
HLA-A24:025HGA1242DLQIEVQDPKHFKS-4.3528-5.3881
HLA-B44:053DX81242DLQIEVQDPKHFKS-4.55859-4.67199
HLA-B44:053DX81242DLQIEVQDPKHFKS-3.98607-5.02137
HLA-A02:016TDR1242DLQIEVQDPKHFKS-1.27724-2.31254
HLA-B14:023BVN2047EQGKSEECSFLPKF-6.18902-6.30242
HLA-B14:023BVN2047EQGKSEECSFLPKF-5.51674-6.55204
HLA-B52:013W392047EQGKSEECSFLPKF-6.26372-6.37712
HLA-B52:013W392047EQGKSEECSFLPKF-2.88933-3.92463
HLA-A11:014UQ22047EQGKSEECSFLPKF-8.95966-9.99496
HLA-A24:025HGA2047EQGKSEECSFLPKF-7.97421-8.08761
HLA-A24:025HGA2047EQGKSEECSFLPKF-4.46014-5.49544
HLA-B44:053DX82047EQGKSEECSFLPKF-4.21738-4.33078
HLA-B44:053DX82047EQGKSEECSFLPKF-3.79801-4.83331
HLA-A02:016TDR2047EQGKSEECSFLPKF-6.07498-7.11028
HLA-B14:023BVN9572TQLTQGHDPKHFKS-7.9962-8.1096
HLA-B14:023BVN9572TQLTQGHDPKHFKS-5.70842-6.74372
HLA-B52:013W399572TQLTQGHDPKHFKS-6.83737-6.95077
HLA-B52:013W399572TQLTQGHDPKHFKS-4.4836-5.5189
HLA-A11:014UQ29572TQLTQGHDPKHFKS-10.0067-10.1201
HLA-A11:014UQ29572TQLTQGHDPKHFKS-9.03915-10.0745
HLA-A24:025HGA9572TQLTQGHDPKHFKS-6.56204-6.67544
HLA-A24:025HGA9572TQLTQGHDPKHFKS-5.42271-6.45801
HLA-B44:053DX89572TQLTQGHDPKHFKS-7.85648-8.89178
HLA-B44:053DX89572TQLTQGHDPKHFKS-5.3978-5.5112
HLA-A02:016TDR9572TQLTQGHDPKHFKS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of BPTF-PITPNC1

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
BPTF-PITPNC1chr1765871136chr17655743021020SEECSFLPKFAATCTGAGGAGTGTTCCTTTCTGCCGAAAT
BPTF-PITPNC1chr1765871136chr17655743021120EECSFLPKFCTGAGGAGTGTTCCTTTCTGCCGAAAT
BPTF-PITPNC1chr1765871136chr1765574302920KSEECSFLPKFGAAAATCTGAGGAGTGTTCCTTTCTGCCGAAAT
BPTF-PITPNC1chr1765936771chr17656656231019QGHDPKHFKCAGGGCCACGATCCTAAGCACTTCAAG
BPTF-PITPNC1chr1765936771chr1765665623818LTQGHDPKHFTTAACACAGGGCCACGATCCTAAGCACTTC
BPTF-PITPNC1chr1765936771chr1765665623918TQGHDPKHFACACAGGGCCACGATCCTAAGCACTTC
BPTF-PITPNC1chr1765936771chr1765665623919TQGHDPKHFKACACAGGGCCACGATCCTAAGCACTTCAAG
BPTF-PITPNC1chr1765944422chr1765665624718LQIEVQDPKHFCTGCAAATTGAAGTGCAGGATCCTAAGCACTTC
BPTF-PITPNC1chr1765944422chr1765665624818QIEVQDPKHFCAAATTGAAGTGCAGGATCCTAAGCACTTC
BPTF-PITPNC1chr1765944422chr1765665624918IEVQDPKHFATTGAAGTGCAGGATCCTAAGCACTTC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
BPTF-PITPNC1chr1765944422chr1765665624520KDLQIEVQDPKHFKSAAGGATCTGCAAATTGAAGTGCAGGATCCTAAGCACTTCAAGTCA
BPTF-PITPNC1chr1765944422chr1765665624621DLQIEVQDPKHFKSEGATCTGCAAATTGAAGTGCAGGATCCTAAGCACTTCAAGTCAGAG

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Information of the samples that have these potential fusion neoantigens of BPTF-PITPNC1

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
BRCABPTF-PITPNC1chr1765936771ENST00000306378chr1765665623ENST00000299954TCGA-BH-A1F6-01A
BRCABPTF-PITPNC1chr1765944422ENST00000306378chr1765665624ENST00000299954TCGA-GI-A2C9-01A
LUADBPTF-PITPNC1chr1765871136ENST00000306378chr1765574302ENST00000299954TCGA-55-8506-01A

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Potential target of CAR-T therapy development for BPTF-PITPNC1

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 BPTF-PITPNC1

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 BPTF-PITPNC1

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