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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:PELP1-CAMTA2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PELP1-CAMTA2
FusionPDB ID: 64263
FusionGDB2.0 ID: 64263
HgeneTgene
Gene symbol

PELP1

CAMTA2

Gene ID

27043

23125

Gene nameproline, glutamate and leucine rich protein 1calmodulin binding transcription activator 2
SynonymsMNAR|P160-
Cytomap

17p13.2

17p13.2

Type of geneprotein-codingprotein-coding
Descriptionproline-, glutamic acid- and leucine-rich protein 1modulator of non-genomic activity of estrogen receptorproline and glutamic acid rich nuclear proteintranscription factor HMX3calmodulin-binding transcription activator 2
Modification date2020032920200313
UniProtAcc.

O94983

Main function of 5'-partner protein: FUNCTION: Transcription activator. May act as tumor suppressor. {ECO:0000269|PubMed:11925432}.
Ensembl transtripts involved in fusion geneENST idsENST00000301396, ENST00000436683, 
ENST00000572293, ENST00000574876, 
ENST00000269230, ENST00000570823, 
ENST00000571831, ENST00000348066, 
ENST00000358183, ENST00000361571, 
ENST00000381311, ENST00000414043, 
ENST00000572543, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 5 X 4=805 X 4 X 4=80
# samples 66
** MAII scorelog2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PELP1 [Title/Abstract] AND CAMTA2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PELP1 [Title/Abstract] AND CAMTA2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PELP1(4577805)-CAMTA2(4877795), # samples:2
Anticipated loss of major functional domain due to fusion event.PELP1-CAMTA2 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.
PELP1-CAMTA2 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.
PELP1-CAMTA2 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.
PELP1-CAMTA2 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.
PELP1-CAMTA2 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
PELP1-CAMTA2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PELP1-CAMTA2 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
HgenePELP1

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

HgenePELP1

GO:0071391

cellular response to estrogen stimulus

17505058

TgeneCAMTA2

GO:0006357

regulation of transcription by RNA polymerase II

16678093

TgeneCAMTA2

GO:0014898

cardiac muscle hypertrophy in response to stress

16678093



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/chr17:4577805/chr17:4877795)
- 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 PELP1 (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 CAMTA2 (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)
ENST00000574876PELP1chr174577805-ENST00000358183CAMTA2chr174877795-405216001832871089
ENST00000574876PELP1chr174577805-ENST00000414043CAMTA2chr174877795-406616001833561112
ENST00000574876PELP1chr174577805-ENST00000361571CAMTA2chr174877795-406816001833081096
ENST00000574876PELP1chr174577805-ENST00000572543CAMTA2chr174877795-406816001833081096
ENST00000574876PELP1chr174577805-ENST00000381311CAMTA2chr174877795-404716001832871089
ENST00000574876PELP1chr174577805-ENST00000348066CAMTA2chr174877795-406716001833081096
ENST00000572293PELP1chr174577805-ENST00000358183CAMTA2chr174877795-424817964934831144
ENST00000572293PELP1chr174577805-ENST00000414043CAMTA2chr174877795-426217964935521167
ENST00000572293PELP1chr174577805-ENST00000361571CAMTA2chr174877795-426417964935041151
ENST00000572293PELP1chr174577805-ENST00000572543CAMTA2chr174877795-426417964935041151
ENST00000572293PELP1chr174577805-ENST00000381311CAMTA2chr174877795-424317964934831144
ENST00000572293PELP1chr174577805-ENST00000348066CAMTA2chr174877795-426317964935041151
ENST00000301396PELP1chr174577805-ENST00000358183CAMTA2chr174877795-469222406139271288
ENST00000301396PELP1chr174577805-ENST00000414043CAMTA2chr174877795-470622406139961311
ENST00000301396PELP1chr174577805-ENST00000361571CAMTA2chr174877795-470822406139481295
ENST00000301396PELP1chr174577805-ENST00000572543CAMTA2chr174877795-470822406139481295
ENST00000301396PELP1chr174577805-ENST00000381311CAMTA2chr174877795-468722406139271288
ENST00000301396PELP1chr174577805-ENST00000348066CAMTA2chr174877795-470722406139481295
ENST00000574876PELP1chr174577804-ENST00000358183CAMTA2chr174877795-405216001832871089
ENST00000574876PELP1chr174577804-ENST00000414043CAMTA2chr174877795-406616001833561112
ENST00000574876PELP1chr174577804-ENST00000361571CAMTA2chr174877795-406816001833081096
ENST00000574876PELP1chr174577804-ENST00000572543CAMTA2chr174877795-406816001833081096
ENST00000574876PELP1chr174577804-ENST00000381311CAMTA2chr174877795-404716001832871089
ENST00000574876PELP1chr174577804-ENST00000348066CAMTA2chr174877795-406716001833081096
ENST00000572293PELP1chr174577804-ENST00000358183CAMTA2chr174877795-424817964934831144
ENST00000572293PELP1chr174577804-ENST00000414043CAMTA2chr174877795-426217964935521167
ENST00000572293PELP1chr174577804-ENST00000361571CAMTA2chr174877795-426417964935041151
ENST00000572293PELP1chr174577804-ENST00000572543CAMTA2chr174877795-426417964935041151
ENST00000572293PELP1chr174577804-ENST00000381311CAMTA2chr174877795-424317964934831144
ENST00000572293PELP1chr174577804-ENST00000348066CAMTA2chr174877795-426317964935041151
ENST00000301396PELP1chr174577804-ENST00000358183CAMTA2chr174877795-469222406139271288
ENST00000301396PELP1chr174577804-ENST00000414043CAMTA2chr174877795-470622406139961311
ENST00000301396PELP1chr174577804-ENST00000361571CAMTA2chr174877795-470822406139481295
ENST00000301396PELP1chr174577804-ENST00000572543CAMTA2chr174877795-470822406139481295
ENST00000301396PELP1chr174577804-ENST00000381311CAMTA2chr174877795-468722406139271288
ENST00000301396PELP1chr174577804-ENST00000348066CAMTA2chr174877795-470722406139481295

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
ENST00000574876ENST00000358183PELP1chr174577805-CAMTA2chr174877795-0.0095996750.9904004
ENST00000574876ENST00000414043PELP1chr174577805-CAMTA2chr174877795-0.0096386130.99036145
ENST00000574876ENST00000361571PELP1chr174577805-CAMTA2chr174877795-0.0096294130.9903706
ENST00000574876ENST00000572543PELP1chr174577805-CAMTA2chr174877795-0.0096294130.9903706
ENST00000574876ENST00000381311PELP1chr174577805-CAMTA2chr174877795-0.0096094070.99039054
ENST00000574876ENST00000348066PELP1chr174577805-CAMTA2chr174877795-0.0096595550.9903404
ENST00000572293ENST00000358183PELP1chr174577805-CAMTA2chr174877795-0.0110941790.9889058
ENST00000572293ENST00000414043PELP1chr174577805-CAMTA2chr174877795-0.0112432350.9887567
ENST00000572293ENST00000361571PELP1chr174577805-CAMTA2chr174877795-0.011630280.9883697
ENST00000572293ENST00000572543PELP1chr174577805-CAMTA2chr174877795-0.011630280.9883697
ENST00000572293ENST00000381311PELP1chr174577805-CAMTA2chr174877795-0.0110979570.9889021
ENST00000572293ENST00000348066PELP1chr174577805-CAMTA2chr174877795-0.0116525660.9883475
ENST00000301396ENST00000358183PELP1chr174577805-CAMTA2chr174877795-0.0055189330.9944811
ENST00000301396ENST00000414043PELP1chr174577805-CAMTA2chr174877795-0.0064157290.9935842
ENST00000301396ENST00000361571PELP1chr174577805-CAMTA2chr174877795-0.0073641250.9926359
ENST00000301396ENST00000572543PELP1chr174577805-CAMTA2chr174877795-0.0073641250.9926359
ENST00000301396ENST00000381311PELP1chr174577805-CAMTA2chr174877795-0.0055077590.9944923
ENST00000301396ENST00000348066PELP1chr174577805-CAMTA2chr174877795-0.0073639430.99263614
ENST00000574876ENST00000358183PELP1chr174577804-CAMTA2chr174877795-0.0095996750.9904004
ENST00000574876ENST00000414043PELP1chr174577804-CAMTA2chr174877795-0.0096386130.99036145
ENST00000574876ENST00000361571PELP1chr174577804-CAMTA2chr174877795-0.0096294130.9903706
ENST00000574876ENST00000572543PELP1chr174577804-CAMTA2chr174877795-0.0096294130.9903706
ENST00000574876ENST00000381311PELP1chr174577804-CAMTA2chr174877795-0.0096094070.99039054
ENST00000574876ENST00000348066PELP1chr174577804-CAMTA2chr174877795-0.0096595550.9903404
ENST00000572293ENST00000358183PELP1chr174577804-CAMTA2chr174877795-0.0110941790.9889058
ENST00000572293ENST00000414043PELP1chr174577804-CAMTA2chr174877795-0.0112432350.9887567
ENST00000572293ENST00000361571PELP1chr174577804-CAMTA2chr174877795-0.011630280.9883697
ENST00000572293ENST00000572543PELP1chr174577804-CAMTA2chr174877795-0.011630280.9883697
ENST00000572293ENST00000381311PELP1chr174577804-CAMTA2chr174877795-0.0110979570.9889021
ENST00000572293ENST00000348066PELP1chr174577804-CAMTA2chr174877795-0.0116525660.9883475
ENST00000301396ENST00000358183PELP1chr174577804-CAMTA2chr174877795-0.0055189330.9944811
ENST00000301396ENST00000414043PELP1chr174577804-CAMTA2chr174877795-0.0064157290.9935842
ENST00000301396ENST00000361571PELP1chr174577804-CAMTA2chr174877795-0.0073641250.9926359
ENST00000301396ENST00000572543PELP1chr174577804-CAMTA2chr174877795-0.0073641250.9926359
ENST00000301396ENST00000381311PELP1chr174577804-CAMTA2chr174877795-0.0055077590.9944923
ENST00000301396ENST00000348066PELP1chr174577804-CAMTA2chr174877795-0.0073639430.99263614

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 PELP1-CAMTA2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PELP1chr174577804CAMTA2chr1748777951600527SNANSDVCAAALRDNQFRMSILERLE
PELP1chr174577804CAMTA2chr1748777951796582SNANSDVCAAALRDNQFRMSILERLE
PELP1chr174577804CAMTA2chr1748777952240726SNANSDVCAAALRDNQFRMSILERLE
PELP1chr174577805CAMTA2chr1748777951600527SNANSDVCAAALRDNQFRMSILERLE
PELP1chr174577805CAMTA2chr1748777951796582SNANSDVCAAALRDNQFRMSILERLE
PELP1chr174577805CAMTA2chr1748777952240726SNANSDVCAAALRDNQFRMSILERLE

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Potential FusionNeoAntigen Information of PELP1-CAMTA2 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.
PELP1-CAMTA2_4577804_4877795.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)
PELP1-CAMTA2chr174577804chr1748777952240HLA-B15:04ALRDNQFRM0.89990.84321019
PELP1-CAMTA2chr174577804chr1748777952240HLA-C03:14AAALRDNQF0.49790.9776817
PELP1-CAMTA2chr174577804chr1748777952240HLA-C12:12AAALRDNQF0.47480.9536817
PELP1-CAMTA2chr174577804chr1748777952240HLA-C03:02AAALRDNQF0.99330.9778817
PELP1-CAMTA2chr174577804chr1748777952240HLA-B15:73ALRDNQFRM0.83360.80781019
PELP1-CAMTA2chr174577804chr1748777952240HLA-B15:30ALRDNQFRM0.73270.86261019
PELP1-CAMTA2chr174577804chr1748777952240HLA-C16:04AAALRDNQF0.69210.9884817
PELP1-CAMTA2chr174577804chr1748777952240HLA-C12:02AAALRDNQF0.62010.9793817
PELP1-CAMTA2chr174577804chr1748777952240HLA-C16:01AAALRDNQF0.58920.99817
PELP1-CAMTA2chr174577804chr1748777952240HLA-C02:02AAALRDNQF0.47880.9747817
PELP1-CAMTA2chr174577804chr1748777952240HLA-C02:10AAALRDNQF0.47880.9747817
PELP1-CAMTA2chr174577804chr1748777952240HLA-C16:02AAALRDNQF0.28490.9949817

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Potential FusionNeoAntigen Information of PELP1-CAMTA2 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 PELP1-CAMTA2

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
9811VCAAALRDNQFRMSPELP1CAMTA2chr174577804chr1748777952240

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PELP1-CAMTA2

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-B14:023BVN9811VCAAALRDNQFRMS-7.9962-8.1096
HLA-B14:023BVN9811VCAAALRDNQFRMS-5.70842-6.74372
HLA-B52:013W399811VCAAALRDNQFRMS-6.83737-6.95077
HLA-B52:013W399811VCAAALRDNQFRMS-4.4836-5.5189
HLA-A11:014UQ29811VCAAALRDNQFRMS-10.0067-10.1201
HLA-A11:014UQ29811VCAAALRDNQFRMS-9.03915-10.0745
HLA-A24:025HGA9811VCAAALRDNQFRMS-6.56204-6.67544
HLA-A24:025HGA9811VCAAALRDNQFRMS-5.42271-6.45801
HLA-B44:053DX89811VCAAALRDNQFRMS-7.85648-8.89178
HLA-B44:053DX89811VCAAALRDNQFRMS-5.3978-5.5112
HLA-A02:016TDR9811VCAAALRDNQFRMS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PELP1-CAMTA2

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
PELP1-CAMTA2chr174577804chr1748777951019ALRDNQFRMCACTCAGAGACAACCAGTTCCGGATGT
PELP1-CAMTA2chr174577804chr174877795817AAALRDNQFCGGCTGCACTCAGAGACAACCAGTTCC

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 PELP1-CAMTA2

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
OVPELP1-CAMTA2chr174577804ENST00000301396chr174877795ENST00000348066TCGA-61-1733

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Potential target of CAR-T therapy development for PELP1-CAMTA2

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 PELP1-CAMTA2

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 PELP1-CAMTA2

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