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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:PLEKHA2-KCNU1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PLEKHA2-KCNU1
FusionPDB ID: 66162
FusionGDB2.0 ID: 66162
HgeneTgene
Gene symbol

PLEKHA2

KCNU1

Gene ID

59339

157855

Gene namepleckstrin homology domain containing A2potassium calcium-activated channel subfamily U member 1
SynonymsTAPP2KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3
Cytomap

8p11.22

8p11.23

Type of geneprotein-codingprotein-coding
Descriptionpleckstrin homology domain-containing family A member 2PH domain-containing family A member 2TAPP-2pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2tandem PH Domain containing protein-2tandem PH domain-contapotassium channel subfamily U member 1Calcium-activated potassium channel subunit alpha-3Calcium-activated potassium channel, subfamily M subunit alpha-3Slowpoke homolog 3potassium channel, subfamily U, member 1
Modification date2020031320200313
UniProtAcc.

A8MYU2

Main function of 5'-partner protein: FUNCTION: Testis-specific potassium channel activated by both intracellular pH and membrane voltage that mediates export of K(+). May represent the primary spermatozoan K(+) current. In contrast to KCNMA1/SLO1, it is not activated by Ca(2+) or Mg(2+). Critical for fertility. May play an important role in sperm osmoregulation required for the acquisition of normal morphology and motility when faced with osmotic challenges, such as those experienced after mixing with seminal fluid and entry into the vagina. {ECO:0000269|PubMed:23129643}.
Ensembl transtripts involved in fusion geneENST idsENST00000388745, ENST00000420274, 
ENST00000521746, 		ENST00000399881, 
ENST00000518904, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 5 X 7=3508 X 7 X 7=392
# samples 1211
** MAII scorelog2(12/350*10)=-1.54432051622381
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/392*10)=-1.83335013059055
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PLEKHA2 [Title/Abstract] AND KCNU1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PLEKHA2 [Title/Abstract] AND KCNU1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KCNU1(36642078)-PLEKHA2(38801354), # samples:1
PLEKHA2(38814904)-KCNU1(36663787), # samples:2
Anticipated loss of major functional domain due to fusion event.PLEKHA2-KCNU1 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.
PLEKHA2-KCNU1 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.
PLEKHA2-KCNU1 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.
PLEKHA2-KCNU1 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


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/chr8:36642078/chr8:38801354)
- 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 PLEKHA2 (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 KCNU1 (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)
ENST00000420274PLEKHA2chr838814904+ENST00000399881KCNU1chr836663786+4261107123440521272
ENST00000420274PLEKHA2chr838814904+ENST00000399881KCNU1chr836663787+4261107123440521272

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
ENST00000420274ENST00000399881PLEKHA2chr838814904+KCNU1chr836663786+0.0008221880.99917775
ENST00000420274ENST00000399881PLEKHA2chr838814904+KCNU1chr836663787+0.0008221880.99917775

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 PLEKHA2-KCNU1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PLEKHA2chr838814904KCNU1chr8366637861071279FEIITSSRTFYVQFMAADDKIKFWLE
PLEKHA2chr838814904KCNU1chr8366637871071279FEIITSSRTFYVQFMAADDKIKFWLE

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Potential FusionNeoAntigen Information of PLEKHA2-KCNU1 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.
PLEKHA2-KCNU1_38814904_36663786.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)
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:05SRTFYVQFM0.99970.7809615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:04SRTFYVQFM0.99960.5768615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:01SSRTFYVQF0.99830.9477514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B58:02SSRTFYVQF0.99560.8445514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B15:17SSRTFYVQF0.99480.7954514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B15:16SSRTFYVQF0.99220.5124514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:03SSRTFYVQF0.99040.9663514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B14:01SRTFYVQFM0.98840.58615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B14:02SRTFYVQFM0.98840.58615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-A30:08RTFYVQFMA0.95110.7324716
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-A32:13SSRTFYVQF0.83290.849514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-A30:08SSRTFYVQF0.75050.5266514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B08:09TFYVQFMAA0.39320.7017817
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:03TSSRTFYVQF0.99830.9849414
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-A30:08RTFYVQFMAA0.94010.7596717
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:03ITSSRTFYVQF0.99940.9573314
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:27SRTFYVQF0.99980.9557614
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:05SRTFYVQF0.99980.9699614
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:95SRTFYVQF0.99980.6994614
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:46SRTFYVQF0.99970.8637614
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:14SRTFYVQFM0.99970.7018615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:95SRTFYVQFM0.99880.6357615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:05SRTFYVQFM0.99750.961615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:27SRTFYVQFM0.99660.9424615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:29SRTFYVQFM0.99370.8365615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:46SRTFYVQFM0.99320.7968615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:03SRTFYVQFM0.9930.8131615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B39:12SRTFYVQFM0.99250.7802615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:19SRTFYVQFM0.99140.6618615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:13SRTFYVQFM0.98980.8419615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:67SRTFYVQFM0.98760.9217615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:80SRTFYVQFM0.98760.9217615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:10SRTFYVQFM0.9840.9314615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C15:04SSRTFYVQF0.97260.7936514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C12:12SSRTFYVQF0.93540.9059514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C03:14SSRTFYVQF0.76290.9606514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C12:04SSRTFYVQF0.71780.9872514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C06:03SSRTFYVQF0.71160.9867514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C12:16SRTFYVQFM0.15830.9548615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:14SRTFYVQFMA0.99920.6245616
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B73:01SRTFYVQFMA0.99250.6087616
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B73:01SRTFYVQFMAA0.99820.6723617
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:01SRTFYVQF0.99990.6655614
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:08SRTFYVQFM0.99970.6319615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:10SRTFYVQFM0.99960.7397615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:06SRTFYVQFM0.99960.605615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B27:09SRTFYVQFM0.99890.7525615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:01SRTFYVQFM0.99880.6001615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:10SSRTFYVQF0.99830.9477514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:17SRTFYVQFM0.9970.9514615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:04SSRTFYVQF0.99670.5526514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B58:06SSRTFYVQF0.99610.6342514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B39:31SRTFYVQFM0.99170.778615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C03:02SSRTFYVQF0.99140.9503514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:02SRTFYVQFM0.98760.9217615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B15:35SSRTFYVQF0.98130.7887514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:02SSRTFYVQF0.97720.7879514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-A32:01SSRTFYVQF0.97380.785514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C15:09SSRTFYVQF0.97260.7936514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C12:03SSRTFYVQF0.92580.9663514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C16:04SSRTFYVQF0.92350.9647514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C06:08SRTFYVQFM0.86110.9712615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C12:02SSRTFYVQF0.83790.9444514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C07:22SRTFYVQFM0.81120.6673615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-A30:01SSRTFYVQF0.77530.7625514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C16:01SSRTFYVQF0.73760.965514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C16:02SSRTFYVQF0.59940.9819514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C06:06SRTFYVQFM0.39320.9845615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C02:10SSRTFYVQF0.35660.9157514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C02:02SSRTFYVQF0.35660.9157514
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C06:17SRTFYVQFM0.18270.9922615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-C06:02SRTFYVQFM0.18270.9922615
PLEKHA2-KCNU1chr838814904chr8366637861071HLA-B57:02TSSRTFYVQF0.99730.8915414

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Potential FusionNeoAntigen Information of PLEKHA2-KCNU1 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.
PLEKHA2-KCNU1_38814904_36663786.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)
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0301VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0301YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0301FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0305VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0307VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0307YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0307FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0310VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0310YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0310FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0313VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0313YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0313FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0315VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0315YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0318VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0318YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0318FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0320VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0320YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0320FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0322VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0322YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0322FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0324VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0326VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0328VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0328YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0328FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0330VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0330YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0330FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0332VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0332YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0332FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0334VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0334YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0334FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0336VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0336YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0336FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0344VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0344YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0344FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0346VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0346YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0346FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0348VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0348YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0348FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0350VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0350YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0350FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0352VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0352YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0352FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0354VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0354YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0354FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0486RTFYVQFMAADDKIK722
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0486SRTFYVQFMAADDKI621
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0832RTFYVQFMAADDKIK722
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-0832SRTFYVQFMAADDKI621
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1107VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1107YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1107FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1476VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1476YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1476FYVQFMAADDKIKFW924
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1479VQFMAADDKIKFWLE1126
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1479YVQFMAADDKIKFWL1025
PLEKHA2-KCNU1chr838814904chr8366637861071DRB1-1479FYVQFMAADDKIKFW924

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Fusion breakpoint peptide structures of PLEKHA2-KCNU1

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
8990SRTFYVQFMAADDKPLEKHA2KCNU1chr838814904chr8366637861071

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PLEKHA2-KCNU1

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-B14:023BVN8990SRTFYVQFMAADDK-7.15543-7.26883
HLA-B14:023BVN8990SRTFYVQFMAADDK-4.77435-5.80965
HLA-B52:013W398990SRTFYVQFMAADDK-6.80875-6.92215
HLA-B52:013W398990SRTFYVQFMAADDK-4.20386-5.23916
HLA-A11:014UQ28990SRTFYVQFMAADDK-7.5194-8.5547
HLA-A11:014UQ28990SRTFYVQFMAADDK-6.9601-7.0735
HLA-A24:025HGA8990SRTFYVQFMAADDK-7.52403-7.63743
HLA-A24:025HGA8990SRTFYVQFMAADDK-5.82433-6.85963
HLA-B27:056PYJ8990SRTFYVQFMAADDK-3.28285-4.31815
HLA-B44:053DX88990SRTFYVQFMAADDK-5.91172-6.94702
HLA-B44:053DX88990SRTFYVQFMAADDK-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of PLEKHA2-KCNU1

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
PLEKHA2-KCNU1chr838814904chr836663786314ITSSRTFYVQFATAACAAGCTCCAGGACCTTCTACGTACAGTTT
PLEKHA2-KCNU1chr838814904chr836663786414TSSRTFYVQFACAAGCTCCAGGACCTTCTACGTACAGTTT
PLEKHA2-KCNU1chr838814904chr836663786514SSRTFYVQFAGCTCCAGGACCTTCTACGTACAGTTT
PLEKHA2-KCNU1chr838814904chr836663786614SRTFYVQFTCCAGGACCTTCTACGTACAGTTT
PLEKHA2-KCNU1chr838814904chr836663786615SRTFYVQFMTCCAGGACCTTCTACGTACAGTTTATG
PLEKHA2-KCNU1chr838814904chr836663786616SRTFYVQFMATCCAGGACCTTCTACGTACAGTTTATGGCA
PLEKHA2-KCNU1chr838814904chr836663786617SRTFYVQFMAATCCAGGACCTTCTACGTACAGTTTATGGCAGCT
PLEKHA2-KCNU1chr838814904chr836663786716RTFYVQFMAAGGACCTTCTACGTACAGTTTATGGCA
PLEKHA2-KCNU1chr838814904chr836663786717RTFYVQFMAAAGGACCTTCTACGTACAGTTTATGGCAGCT
PLEKHA2-KCNU1chr838814904chr836663786817TFYVQFMAAACCTTCTACGTACAGTTTATGGCAGCT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PLEKHA2-KCNU1chr838814904chr8366637861025YVQFMAADDKIKFWLTACGTACAGTTTATGGCAGCTGATGACAAGATCAAGTTCTGGCTG
PLEKHA2-KCNU1chr838814904chr8366637861126VQFMAADDKIKFWLEGTACAGTTTATGGCAGCTGATGACAAGATCAAGTTCTGGCTGGAG
PLEKHA2-KCNU1chr838814904chr836663786621SRTFYVQFMAADDKITCCAGGACCTTCTACGTACAGTTTATGGCAGCTGATGACAAGATC
PLEKHA2-KCNU1chr838814904chr836663786722RTFYVQFMAADDKIKAGGACCTTCTACGTACAGTTTATGGCAGCTGATGACAAGATCAAG
PLEKHA2-KCNU1chr838814904chr836663786924FYVQFMAADDKIKFWTTCTACGTACAGTTTATGGCAGCTGATGACAAGATCAAGTTCTGG

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Information of the samples that have these potential fusion neoantigens of PLEKHA2-KCNU1

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
UCECPLEKHA2-KCNU1chr838814904ENST00000420274chr836663786ENST00000399881TCGA-K6-A3WQ

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Potential target of CAR-T therapy development for PLEKHA2-KCNU1

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
TgeneKCNU1chr8:38814904chr8:36663786ENST00000399881327260_28201150.0IntramembranePore-forming%3B Name%3DP region
TgeneKCNU1chr8:38814904chr8:36663787ENST00000399881327260_28201150.0IntramembranePore-forming%3B Name%3DP region
TgeneKCNU1chr8:38814904chr8:36663786ENST00000399881327164_18401150.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNU1chr8:38814904chr8:36663786ENST00000399881327189_20901150.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNU1chr8:38814904chr8:36663786ENST00000399881327227_24701150.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNU1chr8:38814904chr8:36663786ENST00000399881327292_31201150.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNU1chr8:38814904chr8:36663787ENST00000399881327164_18401150.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNU1chr8:38814904chr8:36663787ENST00000399881327189_20901150.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNU1chr8:38814904chr8:36663787ENST00000399881327227_24701150.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNU1chr8:38814904chr8:36663787ENST00000399881327292_31201150.0TransmembraneHelical%3B Name%3DSegment S6

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 PLEKHA2-KCNU1

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 PLEKHA2-KCNU1

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