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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:FARP1-NME1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FARP1-NME1
FusionPDB ID: 29378
FusionGDB2.0 ID: 29378
HgeneTgene
Gene symbol

FARP1

NME1

Gene ID

10160

6023

Gene nameFERM, ARH/RhoGEF and pleckstrin domain protein 1RNA component of mitochondrial RNA processing endoribonuclease
SynonymsCDEP|FARP1-IT1|PLEKHC2|PPP1R75CHH|NME1|RMRPR|RRP2
Cytomap

13q32.2

9p13.3

Type of geneprotein-codingncRNA
DescriptionFERM, ARHGEF and pleckstrin domain-containing protein 1FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)FERM, RhoGEF and pleckstrin domain-containing protein 1PH domain-containing family C member 2chondrocyte-derived ezrin-li-
Modification date2020031320200313
UniProtAcc

Q9Y4F1

Main function of 5'-partner protein: FUNCTION: Functions as guanine nucleotide exchange factor for RAC1. May play a role in semaphorin signaling. Plays a role in the assembly and disassembly of dendritic filopodia, the formation of dendritic spines, regulation of dendrite length and ultimately the formation of synapses (By similarity). {ECO:0000250}.

P15531

Main function of 5'-partner protein: FUNCTION: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination. During GZMA-mediated cell death, works in concert with TREX1. NME1 nicks one strand of DNA and TREX1 removes bases from the free 3' end to enhance DNA damage and prevent DNA end reannealing and rapid repair. {ECO:0000269|PubMed:12628186, ECO:0000269|PubMed:16818237, ECO:0000269|PubMed:8810265}.
Ensembl transtripts involved in fusion geneENST idsENST00000319562, ENST00000376581, 
ENST00000376586, ENST00000595437, 
ENST00000593990, 		ENST00000013034, 
ENST00000336097, ENST00000393196, 
ENST00000480143, ENST00000511355, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score19 X 13 X 10=24703 X 4 X 3=36
# samples 224
** MAII scorelog2(22/2470*10)=-3.48893561294738
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: FARP1 [Title/Abstract] AND NME1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: FARP1 [Title/Abstract] AND NME1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FARP1(98865667)-NME1(49237341), # samples:1
FARP1(98865667)-NME1(49233011), # samples:1
FARP1(98865667)-NME1(49237340), # samples:1
Anticipated loss of major functional domain due to fusion event.FARP1-NME1 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.
FARP1-NME1 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
HgeneFARP1

GO:0010923

negative regulation of phosphatase activity

19389623

TgeneNME1

GO:0001172

transcription, RNA-templated

19701182

TgeneNME1

GO:0030422

production of siRNA involved in RNA interference

19701182



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/chr13:98865667/chr17:49237341)
- 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 FARP1 (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 NME1 (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)
ENST00000595437FARP1chr1398865667+ENST00000393196NME1chr1749237341+1093410239742167
ENST00000595437FARP1chr1398865667+ENST00000336097NME1chr1749237341+959410239742167
ENST00000595437FARP1chr1398865667+ENST00000480143NME1chr1749237341+939410239628129
ENST00000595437FARP1chr1398865667+ENST00000511355NME1chr1749237341+1843410785426119
ENST00000595437FARP1chr1398865667+ENST00000013034NME1chr1749237341+796410239742167
ENST00000376586FARP1chr1398865667+ENST00000393196NME1chr1749237341+1190507336839167
ENST00000376586FARP1chr1398865667+ENST00000336097NME1chr1749237341+1056507336839167
ENST00000376586FARP1chr1398865667+ENST00000480143NME1chr1749237341+1036507336725129
ENST00000376586FARP1chr1398865667+ENST00000511355NME1chr1749237341+1940507882523119
ENST00000376586FARP1chr1398865667+ENST00000013034NME1chr1749237341+893507336839167
ENST00000319562FARP1chr1398865667+ENST00000393196NME1chr1749237341+1119436265768167
ENST00000319562FARP1chr1398865667+ENST00000336097NME1chr1749237341+985436265768167
ENST00000319562FARP1chr1398865667+ENST00000480143NME1chr1749237341+965436265654129
ENST00000319562FARP1chr1398865667+ENST00000511355NME1chr1749237341+1869436811452119
ENST00000319562FARP1chr1398865667+ENST00000013034NME1chr1749237341+822436265768167
ENST00000376581FARP1chr1398865667+ENST00000393196NME1chr1749237341+89020736539167
ENST00000376581FARP1chr1398865667+ENST00000336097NME1chr1749237341+75620736539167
ENST00000376581FARP1chr1398865667+ENST00000480143NME1chr1749237341+73620736425129
ENST00000376581FARP1chr1398865667+ENST00000511355NME1chr1749237341+1640207582223119
ENST00000376581FARP1chr1398865667+ENST00000013034NME1chr1749237341+59320736539167
ENST00000595437FARP1chr1398865667+ENST00000393196NME1chr1749237340+1093410239742167
ENST00000595437FARP1chr1398865667+ENST00000336097NME1chr1749237340+959410239742167
ENST00000595437FARP1chr1398865667+ENST00000480143NME1chr1749237340+939410239628129
ENST00000595437FARP1chr1398865667+ENST00000511355NME1chr1749237340+1843410785426119
ENST00000595437FARP1chr1398865667+ENST00000013034NME1chr1749237340+796410239742167
ENST00000376586FARP1chr1398865667+ENST00000393196NME1chr1749237340+1190507336839167
ENST00000376586FARP1chr1398865667+ENST00000336097NME1chr1749237340+1056507336839167
ENST00000376586FARP1chr1398865667+ENST00000480143NME1chr1749237340+1036507336725129
ENST00000376586FARP1chr1398865667+ENST00000511355NME1chr1749237340+1940507882523119
ENST00000376586FARP1chr1398865667+ENST00000013034NME1chr1749237340+893507336839167
ENST00000319562FARP1chr1398865667+ENST00000393196NME1chr1749237340+1119436265768167
ENST00000319562FARP1chr1398865667+ENST00000336097NME1chr1749237340+985436265768167
ENST00000319562FARP1chr1398865667+ENST00000480143NME1chr1749237340+965436265654129
ENST00000319562FARP1chr1398865667+ENST00000511355NME1chr1749237340+1869436811452119
ENST00000319562FARP1chr1398865667+ENST00000013034NME1chr1749237340+822436265768167
ENST00000376581FARP1chr1398865667+ENST00000393196NME1chr1749237340+89020736539167
ENST00000376581FARP1chr1398865667+ENST00000336097NME1chr1749237340+75620736539167
ENST00000376581FARP1chr1398865667+ENST00000480143NME1chr1749237340+73620736425129
ENST00000376581FARP1chr1398865667+ENST00000511355NME1chr1749237340+1640207582223119
ENST00000376581FARP1chr1398865667+ENST00000013034NME1chr1749237340+59320736539167

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
ENST00000595437ENST00000393196FARP1chr1398865667+NME1chr1749237341+0.0043591380.9956409
ENST00000595437ENST00000336097FARP1chr1398865667+NME1chr1749237341+0.0038875130.9961125
ENST00000595437ENST00000480143FARP1chr1398865667+NME1chr1749237341+0.0090278180.99097216
ENST00000595437ENST00000511355FARP1chr1398865667+NME1chr1749237341+0.0283091050.97169095
ENST00000595437ENST00000013034FARP1chr1398865667+NME1chr1749237341+0.0024795580.9975204
ENST00000376586ENST00000393196FARP1chr1398865667+NME1chr1749237341+0.0034452610.99655473
ENST00000376586ENST00000336097FARP1chr1398865667+NME1chr1749237341+0.0027951320.99720484
ENST00000376586ENST00000480143FARP1chr1398865667+NME1chr1749237341+0.0071589310.9928411
ENST00000376586ENST00000511355FARP1chr1398865667+NME1chr1749237341+0.0336672330.96633273
ENST00000376586ENST00000013034FARP1chr1398865667+NME1chr1749237341+0.0017968980.99820304
ENST00000319562ENST00000393196FARP1chr1398865667+NME1chr1749237341+0.0040682440.9959318
ENST00000319562ENST00000336097FARP1chr1398865667+NME1chr1749237341+0.0037859040.9962141
ENST00000319562ENST00000480143FARP1chr1398865667+NME1chr1749237341+0.0081812490.9918188
ENST00000319562ENST00000511355FARP1chr1398865667+NME1chr1749237341+0.0162965770.98370343
ENST00000319562ENST00000013034FARP1chr1398865667+NME1chr1749237341+0.0025715770.99742836
ENST00000376581ENST00000393196FARP1chr1398865667+NME1chr1749237341+0.0026719130.99732804
ENST00000376581ENST00000336097FARP1chr1398865667+NME1chr1749237341+0.0024755790.99752444
ENST00000376581ENST00000480143FARP1chr1398865667+NME1chr1749237341+0.0074285870.9925714
ENST00000376581ENST00000511355FARP1chr1398865667+NME1chr1749237341+0.0478901970.95210975
ENST00000376581ENST00000013034FARP1chr1398865667+NME1chr1749237341+0.0013738520.9986261
ENST00000595437ENST00000393196FARP1chr1398865667+NME1chr1749237340+0.0043591380.9956409
ENST00000595437ENST00000336097FARP1chr1398865667+NME1chr1749237340+0.0038875130.9961125
ENST00000595437ENST00000480143FARP1chr1398865667+NME1chr1749237340+0.0090278180.99097216
ENST00000595437ENST00000511355FARP1chr1398865667+NME1chr1749237340+0.0283091050.97169095
ENST00000595437ENST00000013034FARP1chr1398865667+NME1chr1749237340+0.0024795580.9975204
ENST00000376586ENST00000393196FARP1chr1398865667+NME1chr1749237340+0.0034452610.99655473
ENST00000376586ENST00000336097FARP1chr1398865667+NME1chr1749237340+0.0027951320.99720484
ENST00000376586ENST00000480143FARP1chr1398865667+NME1chr1749237340+0.0071589310.9928411
ENST00000376586ENST00000511355FARP1chr1398865667+NME1chr1749237340+0.0336672330.96633273
ENST00000376586ENST00000013034FARP1chr1398865667+NME1chr1749237340+0.0017968980.99820304
ENST00000319562ENST00000393196FARP1chr1398865667+NME1chr1749237340+0.0040682440.9959318
ENST00000319562ENST00000336097FARP1chr1398865667+NME1chr1749237340+0.0037859040.9962141
ENST00000319562ENST00000480143FARP1chr1398865667+NME1chr1749237340+0.0081812490.9918188
ENST00000319562ENST00000511355FARP1chr1398865667+NME1chr1749237340+0.0162965770.98370343
ENST00000319562ENST00000013034FARP1chr1398865667+NME1chr1749237340+0.0025715770.99742836
ENST00000376581ENST00000393196FARP1chr1398865667+NME1chr1749237340+0.0026719130.99732804
ENST00000376581ENST00000336097FARP1chr1398865667+NME1chr1749237340+0.0024755790.99752444
ENST00000376581ENST00000480143FARP1chr1398865667+NME1chr1749237340+0.0074285870.9925714
ENST00000376581ENST00000511355FARP1chr1398865667+NME1chr1749237340+0.0478901970.95210975
ENST00000376581ENST00000013034FARP1chr1398865667+NME1chr1749237340+0.0013738520.9986261

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 FARP1-NME1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
FARP1chr1398865667NME1chr174923734020757QMLDDTQEAFEVPASEDLLKEHYVDL
FARP1chr1398865667NME1chr174923734041057QMLDDTQEAFEVPASEDLLKEHYVDL
FARP1chr1398865667NME1chr174923734043657QMLDDTQEAFEVPASEDLLKEHYVDL
FARP1chr1398865667NME1chr174923734050757QMLDDTQEAFEVPASEDLLKEHYVDL
FARP1chr1398865667NME1chr174923734120757QMLDDTQEAFEVPASEDLLKEHYVDL
FARP1chr1398865667NME1chr174923734141057QMLDDTQEAFEVPASEDLLKEHYVDL
FARP1chr1398865667NME1chr174923734143657QMLDDTQEAFEVPASEDLLKEHYVDL
FARP1chr1398865667NME1chr174923734150757QMLDDTQEAFEVPASEDLLKEHYVDL

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Potential FusionNeoAntigen Information of FARP1-NME1 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.
FARP1-NME1-NME2_98865667_49237341.msa
FARP1-NME1_98865667_49237340.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)
FARP1-NME1chr1398865667chr1749237340436HLA-B45:01QEAFEVPAS0.98590.9854615
FARP1-NME1chr1398865667chr1749237340436HLA-B50:02QEAFEVPAS0.96680.7995615
FARP1-NME1chr1398865667chr1749237340436HLA-B18:01FEVPASEDL0.72540.952918
FARP1-NME1chr1398865667chr1749237340436HLA-B39:13FEVPASEDL0.39760.8801918
FARP1-NME1chr1398865667chr1749237340436HLA-B39:08FEVPASEDL0.36830.6733918
FARP1-NME1chr1398865667chr1749237340436HLA-B40:04FEVPASEDL0.9880.6989918
FARP1-NME1chr1398865667chr1749237340436HLA-B18:05FEVPASEDL0.72540.952918
FARP1-NME1chr1398865667chr1749237340436HLA-B18:03FEVPASEDL0.65670.948918
FARP1-NME1chr1398865667chr1749237340436HLA-B18:11FEVPASEDL0.58670.8543918
FARP1-NME1chr1398865667chr1749237340436HLA-B39:31FEVPASEDL0.45460.883918
FARP1-NME1chr1398865667chr1749237340436HLA-B39:02FEVPASEDL0.42450.8844918
FARP1-NME1chr1398865667chr1749237340436HLA-B39:11FEVPASEDL0.39890.6713918
FARP1-NME1chr1398865667chr1749237340436HLA-B41:03FEVPASEDL0.37980.5267918
FARP1-NME1chr1398865667chr1749237340436HLA-B40:04FEVPASEDLL0.94420.6508919
FARP1-NME1chr1398865667chr1749237340436HLA-B40:04AFEVPASEDL0.35950.7528818
FARP1-NME1chr1398865667chr1749237340436HLA-A68:02EAFEVPASEDL0.99650.6673718

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Potential FusionNeoAntigen Information of FARP1-NME1 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 FARP1-NME1

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
1084DFCIQVGRTMANLEFARP1NME1NME2chr1398865667chr1749237341
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
7205QEAFEVPASEDLLKFARP1NME1chr1398865667chr1749237340436

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FARP1-NME1

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-B14:023BVN1084DFCIQVGRTMANLE-7.9962-8.1096
HLA-B14:023BVN1084DFCIQVGRTMANLE-5.70842-6.74372
HLA-B52:013W391084DFCIQVGRTMANLE-6.83737-6.95077
HLA-B52:013W391084DFCIQVGRTMANLE-4.4836-5.5189
HLA-A11:014UQ21084DFCIQVGRTMANLE-10.0067-10.1201
HLA-A11:014UQ21084DFCIQVGRTMANLE-9.03915-10.0745
HLA-A24:025HGA1084DFCIQVGRTMANLE-6.56204-6.67544
HLA-A24:025HGA1084DFCIQVGRTMANLE-5.42271-6.45801
HLA-B44:053DX81084DFCIQVGRTMANLE-7.85648-8.89178
HLA-B44:053DX81084DFCIQVGRTMANLE-5.3978-5.5112
HLA-A02:016TDR1084DFCIQVGRTMANLE-3.37154-4.40684
HLA-B14:023BVN7205QEAFEVPASEDLLK-7.15543-7.26883
HLA-B14:023BVN7205QEAFEVPASEDLLK-4.77435-5.80965
HLA-B52:013W397205QEAFEVPASEDLLK-6.80875-6.92215
HLA-B52:013W397205QEAFEVPASEDLLK-4.20386-5.23916
HLA-A11:014UQ27205QEAFEVPASEDLLK-7.5194-8.5547
HLA-A11:014UQ27205QEAFEVPASEDLLK-6.9601-7.0735
HLA-A24:025HGA7205QEAFEVPASEDLLK-7.52403-7.63743
HLA-A24:025HGA7205QEAFEVPASEDLLK-5.82433-6.85963
HLA-B27:056PYJ7205QEAFEVPASEDLLK-3.28285-4.31815
HLA-B44:053DX87205QEAFEVPASEDLLK-5.91172-6.94702
HLA-B44:053DX87205QEAFEVPASEDLLK-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of FARP1-NME1

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
FARP1-NME1chr1398865667chr1749237340615QEAFEVPASCAGGAGGCATTTGAAGTTCCAGCTTCC
FARP1-NME1chr1398865667chr1749237340718EAFEVPASEDLGAGGCATTTGAAGTTCCAGCTTCCGAAGATCTT
FARP1-NME1chr1398865667chr1749237340818AFEVPASEDLGCATTTGAAGTTCCAGCTTCCGAAGATCTT
FARP1-NME1chr1398865667chr1749237340918FEVPASEDLTTTGAAGTTCCAGCTTCCGAAGATCTT
FARP1-NME1chr1398865667chr1749237340919FEVPASEDLLTTTGAAGTTCCAGCTTCCGAAGATCTTCTC
FARP1-NME1chr1398865667chr17492373411223GRTMANLERTFCCAGCTTCCGAAGATCTTCTCAAGGAACACTAC
FARP1-NME1chr1398865667chr1749237341716FCIQVGRTMGAGGCATTTGAAGTTCCAGCTTCCGAA

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 FARP1-NME1

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
LGGFARP1-NME1chr1398865667ENST00000319562chr1749237340ENST00000013034TCGA-DB-5275

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Potential target of CAR-T therapy development for FARP1-NME1

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 FARP1-NME1

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 FARP1-NME1

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