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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:LDLRAD3-CD44

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LDLRAD3-CD44
FusionPDB ID: 44360
FusionGDB2.0 ID: 44360
HgeneTgene
Gene symbol

LDLRAD3

CD44

Gene ID

143458

960

Gene namelow density lipoprotein receptor class A domain containing 3CD44 molecule (Indian blood group)
SynonymsLRAD3CDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1
Cytomap

11p13

11p13

Type of geneprotein-codingprotein-coding
Descriptionlow-density lipoprotein receptor class A domain-containing protein 3LDLR class A domain-containing protein 3CD44 antigenGP90 lymphocyte homing/adhesion receptorHermes antigenIndian blood group antigencell surface glycoprotein CD44chondroitin sulfate proteoglycan 8epicanextracellular matrix receptor IIIhematopoietic cell E- and L-selectin ligandheparan
Modification date2020031320200329
UniProtAcc

Q86YD5

Main function of 5'-partner protein: FUNCTION: May influence APP processing, resulting in a decrease in sAPP-alpha production and increased amyloidogenic P3 peptide production. {ECO:0000250}.

P16070

Main function of 5'-partner protein: FUNCTION: Cell-surface receptor that plays a role in cell-cell interactions, cell adhesion and migration, helping them to sense and respond to changes in the tissue microenvironment (PubMed:16541107, PubMed:19703720, PubMed:22726066). Participates thereby in a wide variety of cellular functions including the activation, recirculation and homing of T-lymphocytes, hematopoiesis, inflammation and response to bacterial infection (PubMed:7528188). Engages, through its ectodomain, extracellular matrix components such as hyaluronan/HA, collagen, growth factors, cytokines or proteases and serves as a platform for signal transduction by assembling, via its cytoplasmic domain, protein complexes containing receptor kinases and membrane proteases (PubMed:18757307, PubMed:23589287). Such effectors include PKN2, the RhoGTPases RAC1 and RHOA, Rho-kinases and phospholipase C that coordinate signaling pathways promoting calcium mobilization and actin-mediated cytoskeleton reorganization essential for cell migration and adhesion (PubMed:15123640). {ECO:0000269|PubMed:15123640, ECO:0000269|PubMed:16541107, ECO:0000269|PubMed:18757307, ECO:0000269|PubMed:19703720, ECO:0000269|PubMed:22726066, ECO:0000269|PubMed:23589287, ECO:0000269|PubMed:7528188}.
Ensembl transtripts involved in fusion geneENST idsENST00000315571, ENST00000524419, 
ENST00000528989, ENST00000529759, 
ENST00000528922, ENST00000526025, 
ENST00000263398, ENST00000278386, 
ENST00000352818, ENST00000360158, 
ENST00000415148, ENST00000428726, 
ENST00000433354, ENST00000433892, 
ENST00000434472, ENST00000437706, 
ENST00000449691, ENST00000526669, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 6 X 10=96012 X 14 X 4=672
# samples 2016
** MAII scorelog2(20/960*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/672*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: LDLRAD3 [Title/Abstract] AND CD44 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: LDLRAD3 [Title/Abstract] AND CD44 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LDLRAD3(35965694)-CD44(35198122), # samples:2
Anticipated loss of major functional domain due to fusion event.LDLRAD3-CD44 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.
LDLRAD3-CD44 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.
LDLRAD3-CD44 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.
LDLRAD3-CD44 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.
LDLRAD3-CD44 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
LDLRAD3-CD44 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneCD44

GO:0007155

cell adhesion

19703720

TgeneCD44

GO:0016477

cell migration

22726066

TgeneCD44

GO:0030214

hyaluronan catabolic process

17170110

TgeneCD44

GO:0033138

positive regulation of peptidyl-serine phosphorylation

17045821

TgeneCD44

GO:0042110

T cell activation

7528188

TgeneCD44

GO:0043518

negative regulation of DNA damage response, signal transduction by p53 class mediator

17045821

TgeneCD44

GO:0044344

cellular response to fibroblast growth factor stimulus

19577615

TgeneCD44

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

17045821

TgeneCD44

GO:0070374

positive regulation of ERK1 and ERK2 cascade

17045821

TgeneCD44

GO:1902166

negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

17045821



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/chr11:35965694/chr11:35198122)
- 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 LDLRAD3 (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 CD44 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000524419LDLRAD3chr1135965694+ENST00000263398CD44chr1135198121+42521641181182354
ENST00000524419LDLRAD3chr1135965694+ENST00000449691CD44chr1135198121+23321641182196692
ENST00000524419LDLRAD3chr1135965694+ENST00000360158CD44chr1135198121+14231641181287389
ENST00000524419LDLRAD3chr1135965694+ENST00000415148CD44chr1135198121+23321641182196692
ENST00000524419LDLRAD3chr1135965694+ENST00000437706CD44chr1135198121+22571641182121667
ENST00000524419LDLRAD3chr1135965694+ENST00000433354CD44chr1135198121+23771641182241707
ENST00000524419LDLRAD3chr1135965694+ENST00000428726CD44chr1135198121+30201641182325735
ENST00000524419LDLRAD3chr1135965694+ENST00000526669CD44chr1135198121+845164118717199
ENST00000524419LDLRAD3chr1135965694+ENST00000433892CD44chr1135198121+22731641181578486
ENST00000524419LDLRAD3chr1135965694+ENST00000278386CD44chr1135198121+5631644471149
ENST00000524419LDLRAD3chr1135965694+ENST00000434472CD44chr1135198121+17201641181386422
ENST00000524419LDLRAD3chr1135965694+ENST00000352818CD44chr1135198121+11201641181119334
ENST00000528989LDLRAD3chr1135965694+ENST00000263398CD44chr1135198121+42521641181182354
ENST00000528989LDLRAD3chr1135965694+ENST00000449691CD44chr1135198121+23321641182196692
ENST00000528989LDLRAD3chr1135965694+ENST00000360158CD44chr1135198121+14231641181287389
ENST00000528989LDLRAD3chr1135965694+ENST00000415148CD44chr1135198121+23321641182196692
ENST00000528989LDLRAD3chr1135965694+ENST00000437706CD44chr1135198121+22571641182121667
ENST00000528989LDLRAD3chr1135965694+ENST00000433354CD44chr1135198121+23771641182241707
ENST00000528989LDLRAD3chr1135965694+ENST00000428726CD44chr1135198121+30201641182325735
ENST00000528989LDLRAD3chr1135965694+ENST00000526669CD44chr1135198121+845164118717199
ENST00000528989LDLRAD3chr1135965694+ENST00000433892CD44chr1135198121+22731641181578486
ENST00000528989LDLRAD3chr1135965694+ENST00000278386CD44chr1135198121+5631644471149
ENST00000528989LDLRAD3chr1135965694+ENST00000434472CD44chr1135198121+17201641181386422
ENST00000528989LDLRAD3chr1135965694+ENST00000352818CD44chr1135198121+11201641181119334
ENST00000315571LDLRAD3chr1135965694+ENST00000263398CD44chr1135198121+415567211085354
ENST00000315571LDLRAD3chr1135965694+ENST00000449691CD44chr1135198121+223567212099692
ENST00000315571LDLRAD3chr1135965694+ENST00000360158CD44chr1135198121+132667211190389
ENST00000315571LDLRAD3chr1135965694+ENST00000415148CD44chr1135198121+223567212099692
ENST00000315571LDLRAD3chr1135965694+ENST00000437706CD44chr1135198121+216067212024667
ENST00000315571LDLRAD3chr1135965694+ENST00000433354CD44chr1135198121+228067212144707
ENST00000315571LDLRAD3chr1135965694+ENST00000428726CD44chr1135198121+292367212228735
ENST00000315571LDLRAD3chr1135965694+ENST00000526669CD44chr1135198121+7486721620199
ENST00000315571LDLRAD3chr1135965694+ENST00000433892CD44chr1135198121+217667211481486
ENST00000315571LDLRAD3chr1135965694+ENST00000278386CD44chr1135198121+4666721419132
ENST00000315571LDLRAD3chr1135965694+ENST00000434472CD44chr1135198121+162367211289422
ENST00000315571LDLRAD3chr1135965694+ENST00000352818CD44chr1135198121+102367211022333
ENST00000524419LDLRAD3chr1135965694+ENST00000263398CD44chr1135198122+42521641181182354
ENST00000524419LDLRAD3chr1135965694+ENST00000449691CD44chr1135198122+23321641182196692
ENST00000524419LDLRAD3chr1135965694+ENST00000360158CD44chr1135198122+14231641181287389
ENST00000524419LDLRAD3chr1135965694+ENST00000415148CD44chr1135198122+23321641182196692
ENST00000524419LDLRAD3chr1135965694+ENST00000437706CD44chr1135198122+22571641182121667
ENST00000524419LDLRAD3chr1135965694+ENST00000433354CD44chr1135198122+23771641182241707
ENST00000524419LDLRAD3chr1135965694+ENST00000428726CD44chr1135198122+30201641182325735
ENST00000524419LDLRAD3chr1135965694+ENST00000526669CD44chr1135198122+845164118717199
ENST00000524419LDLRAD3chr1135965694+ENST00000433892CD44chr1135198122+22731641181578486
ENST00000524419LDLRAD3chr1135965694+ENST00000278386CD44chr1135198122+5631644471149
ENST00000524419LDLRAD3chr1135965694+ENST00000434472CD44chr1135198122+17201641181386422
ENST00000524419LDLRAD3chr1135965694+ENST00000352818CD44chr1135198122+11201641181119334
ENST00000528989LDLRAD3chr1135965694+ENST00000263398CD44chr1135198122+42521641181182354
ENST00000528989LDLRAD3chr1135965694+ENST00000449691CD44chr1135198122+23321641182196692
ENST00000528989LDLRAD3chr1135965694+ENST00000360158CD44chr1135198122+14231641181287389
ENST00000528989LDLRAD3chr1135965694+ENST00000415148CD44chr1135198122+23321641182196692
ENST00000528989LDLRAD3chr1135965694+ENST00000437706CD44chr1135198122+22571641182121667
ENST00000528989LDLRAD3chr1135965694+ENST00000433354CD44chr1135198122+23771641182241707
ENST00000528989LDLRAD3chr1135965694+ENST00000428726CD44chr1135198122+30201641182325735
ENST00000528989LDLRAD3chr1135965694+ENST00000526669CD44chr1135198122+845164118717199
ENST00000528989LDLRAD3chr1135965694+ENST00000433892CD44chr1135198122+22731641181578486
ENST00000528989LDLRAD3chr1135965694+ENST00000278386CD44chr1135198122+5631644471149
ENST00000528989LDLRAD3chr1135965694+ENST00000434472CD44chr1135198122+17201641181386422
ENST00000528989LDLRAD3chr1135965694+ENST00000352818CD44chr1135198122+11201641181119334
ENST00000315571LDLRAD3chr1135965694+ENST00000263398CD44chr1135198122+415567211085354
ENST00000315571LDLRAD3chr1135965694+ENST00000449691CD44chr1135198122+223567212099692
ENST00000315571LDLRAD3chr1135965694+ENST00000360158CD44chr1135198122+132667211190389
ENST00000315571LDLRAD3chr1135965694+ENST00000415148CD44chr1135198122+223567212099692
ENST00000315571LDLRAD3chr1135965694+ENST00000437706CD44chr1135198122+216067212024667
ENST00000315571LDLRAD3chr1135965694+ENST00000433354CD44chr1135198122+228067212144707
ENST00000315571LDLRAD3chr1135965694+ENST00000428726CD44chr1135198122+292367212228735
ENST00000315571LDLRAD3chr1135965694+ENST00000526669CD44chr1135198122+7486721620199
ENST00000315571LDLRAD3chr1135965694+ENST00000433892CD44chr1135198122+217667211481486
ENST00000315571LDLRAD3chr1135965694+ENST00000278386CD44chr1135198122+4666721419132
ENST00000315571LDLRAD3chr1135965694+ENST00000434472CD44chr1135198122+162367211289422
ENST00000315571LDLRAD3chr1135965694+ENST00000352818CD44chr1135198122+102367211022333

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
ENST00000524419ENST00000263398LDLRAD3chr1135965694+CD44chr1135198121+9.01E-050.9999099
ENST00000524419ENST00000449691LDLRAD3chr1135965694+CD44chr1135198121+0.0116993980.9883007
ENST00000524419ENST00000360158LDLRAD3chr1135965694+CD44chr1135198121+0.0005842690.99941576
ENST00000524419ENST00000415148LDLRAD3chr1135965694+CD44chr1135198121+0.0106838240.9893162
ENST00000524419ENST00000437706LDLRAD3chr1135965694+CD44chr1135198121+0.0241966730.97580326
ENST00000524419ENST00000433354LDLRAD3chr1135965694+CD44chr1135198121+0.0125310530.98746896
ENST00000524419ENST00000428726LDLRAD3chr1135965694+CD44chr1135198121+0.0053266790.9946733
ENST00000524419ENST00000526669LDLRAD3chr1135965694+CD44chr1135198121+0.0031438240.9968562
ENST00000524419ENST00000433892LDLRAD3chr1135965694+CD44chr1135198121+0.0003232840.9996767
ENST00000524419ENST00000278386LDLRAD3chr1135965694+CD44chr1135198121+0.025823280.97417665
ENST00000524419ENST00000434472LDLRAD3chr1135965694+CD44chr1135198121+0.0004465750.9995534
ENST00000524419ENST00000352818LDLRAD3chr1135965694+CD44chr1135198121+0.0007754950.99922454
ENST00000528989ENST00000263398LDLRAD3chr1135965694+CD44chr1135198121+9.01E-050.9999099
ENST00000528989ENST00000449691LDLRAD3chr1135965694+CD44chr1135198121+0.0116993980.9883007
ENST00000528989ENST00000360158LDLRAD3chr1135965694+CD44chr1135198121+0.0005842690.99941576
ENST00000528989ENST00000415148LDLRAD3chr1135965694+CD44chr1135198121+0.0106838240.9893162
ENST00000528989ENST00000437706LDLRAD3chr1135965694+CD44chr1135198121+0.0241966730.97580326
ENST00000528989ENST00000433354LDLRAD3chr1135965694+CD44chr1135198121+0.0125310530.98746896
ENST00000528989ENST00000428726LDLRAD3chr1135965694+CD44chr1135198121+0.0053266790.9946733
ENST00000528989ENST00000526669LDLRAD3chr1135965694+CD44chr1135198121+0.0031438240.9968562
ENST00000528989ENST00000433892LDLRAD3chr1135965694+CD44chr1135198121+0.0003232840.9996767
ENST00000528989ENST00000278386LDLRAD3chr1135965694+CD44chr1135198121+0.025823280.97417665
ENST00000528989ENST00000434472LDLRAD3chr1135965694+CD44chr1135198121+0.0004465750.9995534
ENST00000528989ENST00000352818LDLRAD3chr1135965694+CD44chr1135198121+0.0007754950.99922454
ENST00000315571ENST00000263398LDLRAD3chr1135965694+CD44chr1135198121+7.92E-050.9999207
ENST00000315571ENST00000449691LDLRAD3chr1135965694+CD44chr1135198121+0.0118330490.988167
ENST00000315571ENST00000360158LDLRAD3chr1135965694+CD44chr1135198121+0.0007031140.9992969
ENST00000315571ENST00000415148LDLRAD3chr1135965694+CD44chr1135198121+0.010759750.9892402
ENST00000315571ENST00000437706LDLRAD3chr1135965694+CD44chr1135198121+0.0259778130.97402215
ENST00000315571ENST00000433354LDLRAD3chr1135965694+CD44chr1135198121+0.0128980040.987102
ENST00000315571ENST00000428726LDLRAD3chr1135965694+CD44chr1135198121+0.0050536530.9949464
ENST00000315571ENST00000526669LDLRAD3chr1135965694+CD44chr1135198121+0.0029411450.99705887
ENST00000315571ENST00000433892LDLRAD3chr1135965694+CD44chr1135198121+0.0003021460.9996979
ENST00000315571ENST00000278386LDLRAD3chr1135965694+CD44chr1135198121+0.0418077740.9581922
ENST00000315571ENST00000434472LDLRAD3chr1135965694+CD44chr1135198121+0.0004993390.99950063
ENST00000315571ENST00000352818LDLRAD3chr1135965694+CD44chr1135198121+0.0007244340.9992756
ENST00000524419ENST00000263398LDLRAD3chr1135965694+CD44chr1135198122+9.01E-050.9999099
ENST00000524419ENST00000449691LDLRAD3chr1135965694+CD44chr1135198122+0.0116993980.9883007
ENST00000524419ENST00000360158LDLRAD3chr1135965694+CD44chr1135198122+0.0005842690.99941576
ENST00000524419ENST00000415148LDLRAD3chr1135965694+CD44chr1135198122+0.0106838240.9893162
ENST00000524419ENST00000437706LDLRAD3chr1135965694+CD44chr1135198122+0.0241966730.97580326
ENST00000524419ENST00000433354LDLRAD3chr1135965694+CD44chr1135198122+0.0125310530.98746896
ENST00000524419ENST00000428726LDLRAD3chr1135965694+CD44chr1135198122+0.0053266790.9946733
ENST00000524419ENST00000526669LDLRAD3chr1135965694+CD44chr1135198122+0.0031438240.9968562
ENST00000524419ENST00000433892LDLRAD3chr1135965694+CD44chr1135198122+0.0003232840.9996767
ENST00000524419ENST00000278386LDLRAD3chr1135965694+CD44chr1135198122+0.025823280.97417665
ENST00000524419ENST00000434472LDLRAD3chr1135965694+CD44chr1135198122+0.0004465750.9995534
ENST00000524419ENST00000352818LDLRAD3chr1135965694+CD44chr1135198122+0.0007754950.99922454
ENST00000528989ENST00000263398LDLRAD3chr1135965694+CD44chr1135198122+9.01E-050.9999099
ENST00000528989ENST00000449691LDLRAD3chr1135965694+CD44chr1135198122+0.0116993980.9883007
ENST00000528989ENST00000360158LDLRAD3chr1135965694+CD44chr1135198122+0.0005842690.99941576
ENST00000528989ENST00000415148LDLRAD3chr1135965694+CD44chr1135198122+0.0106838240.9893162
ENST00000528989ENST00000437706LDLRAD3chr1135965694+CD44chr1135198122+0.0241966730.97580326
ENST00000528989ENST00000433354LDLRAD3chr1135965694+CD44chr1135198122+0.0125310530.98746896
ENST00000528989ENST00000428726LDLRAD3chr1135965694+CD44chr1135198122+0.0053266790.9946733
ENST00000528989ENST00000526669LDLRAD3chr1135965694+CD44chr1135198122+0.0031438240.9968562
ENST00000528989ENST00000433892LDLRAD3chr1135965694+CD44chr1135198122+0.0003232840.9996767
ENST00000528989ENST00000278386LDLRAD3chr1135965694+CD44chr1135198122+0.025823280.97417665
ENST00000528989ENST00000434472LDLRAD3chr1135965694+CD44chr1135198122+0.0004465750.9995534
ENST00000528989ENST00000352818LDLRAD3chr1135965694+CD44chr1135198122+0.0007754950.99922454
ENST00000315571ENST00000263398LDLRAD3chr1135965694+CD44chr1135198122+7.92E-050.9999207
ENST00000315571ENST00000449691LDLRAD3chr1135965694+CD44chr1135198122+0.0118330490.988167
ENST00000315571ENST00000360158LDLRAD3chr1135965694+CD44chr1135198122+0.0007031140.9992969
ENST00000315571ENST00000415148LDLRAD3chr1135965694+CD44chr1135198122+0.010759750.9892402
ENST00000315571ENST00000437706LDLRAD3chr1135965694+CD44chr1135198122+0.0259778130.97402215
ENST00000315571ENST00000433354LDLRAD3chr1135965694+CD44chr1135198122+0.0128980040.987102
ENST00000315571ENST00000428726LDLRAD3chr1135965694+CD44chr1135198122+0.0050536530.9949464
ENST00000315571ENST00000526669LDLRAD3chr1135965694+CD44chr1135198122+0.0029411450.99705887
ENST00000315571ENST00000433892LDLRAD3chr1135965694+CD44chr1135198122+0.0003021460.9996979
ENST00000315571ENST00000278386LDLRAD3chr1135965694+CD44chr1135198122+0.0418077740.9581922
ENST00000315571ENST00000434472LDLRAD3chr1135965694+CD44chr1135198122+0.0004993390.99950063
ENST00000315571ENST00000352818LDLRAD3chr1135965694+CD44chr1135198122+0.0007244340.9992756

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 LDLRAD3-CD44

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

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Potential FusionNeoAntigen Information of LDLRAD3-CD44 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.

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)

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Potential FusionNeoAntigen Information of LDLRAD3-CD44 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 LDLRAD3-CD44

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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of LDLRAD3-CD44

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

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Vaccine Design for the FusionNeoAntigens of LDLRAD3-CD44

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

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 LDLRAD3-CD44

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

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Potential target of CAR-T therapy development for LDLRAD3-CD44

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
TgeneCD44chr11:35965694chr11:35198121ENST0000026339809650_6700362.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST0000027838604650_6700140.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST0000035281808650_6700341.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST00000360158010650_6700397.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST00000415148017650_6700700.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST00000428726018650_6700743.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST00000433892012650_6700494.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST00000434472010650_6700430.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST00000437706017650_6700675.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198121ENST00000449691017650_6700700.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST0000026339809650_6700362.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST0000027838604650_6700140.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST0000035281808650_6700341.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST00000360158010650_6700397.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST00000415148017650_6700700.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST00000428726018650_6700743.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST00000433892012650_6700494.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST00000434472010650_6700430.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST00000437706017650_6700675.0TransmembraneHelical
TgeneCD44chr11:35965694chr11:35198122ENST00000449691017650_6700700.0TransmembraneHelical

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to LDLRAD3-CD44

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 LDLRAD3-CD44

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