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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:LDLR-MRPL4

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LDLR-MRPL4
FusionPDB ID: 44415
FusionGDB2.0 ID: 44415
HgeneTgene
Gene symbol

LDLR

MRPL4

Gene ID

3949

51073

Gene namelow density lipoprotein receptormitochondrial ribosomal protein L4
SynonymsFH|FHC|FHCL1|LDLCQ2CGI-28|L4mt
Cytomap

19p13.2

19p13.2

Type of geneprotein-codingprotein-coding
Descriptionlow-density lipoprotein receptorLDL receptorlow-density lipoprotein receptor class A domain-containing protein 339S ribosomal protein L4, mitochondrialMRP-L4mitochondrial large ribosomal subunit protein uL4m
Modification date2020032220200313
UniProtAcc

Q5SW96

Main function of 5'-partner protein: FUNCTION: Adapter protein (clathrin-associated sorting protein (CLASP)) required for efficient endocytosis of the LDL receptor (LDLR) in polarized cells such as hepatocytes and lymphocytes, but not in non-polarized cells (fibroblasts). May be required for LDL binding and internalization but not for receptor clustering in coated pits. May facilitate the endocytocis of LDLR and LDLR-LDL complexes from coated pits by stabilizing the interaction between the receptor and the structural components of the pits. May also be involved in the internalization of other LDLR family members. Binds to phosphoinositides, which regulate clathrin bud assembly at the cell surface. Required for trafficking of LRP2 to the endocytic recycling compartment which is necessary for LRP2 proteolysis, releasing a tail fragment which translocates to the nucleus and mediates transcriptional repression (By similarity). {ECO:0000250|UniProtKB:D3ZAR1, ECO:0000269|PubMed:15728179}.

Q13405

Main function of 5'-partner protein:
Ensembl transtripts involved in fusion geneENST idsENST00000455727, ENST00000535915, 
ENST00000545707, ENST00000557933, 
ENST00000558013, ENST00000558518, 
ENST00000560628, 		ENST00000253099, 
ENST00000307422, ENST00000393733, 
ENST00000588502, ENST00000590669, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score23 X 17 X 15=58657 X 7 X 6=294
# samples 338
** MAII scorelog2(33/5865*10)=-4.15159317867005
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/294*10)=-1.877744249949
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: LDLR [Title/Abstract] AND MRPL4 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: LDLR [Title/Abstract] AND MRPL4 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LDLR(11218190)-MRPL4(10368898), # samples:2
Anticipated loss of major functional domain due to fusion event.LDLR-MRPL4 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.
LDLR-MRPL4 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.
LDLR-MRPL4 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.
LDLR-MRPL4 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/chr19:11218190/chr19:10368898)
- 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 LDLR (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 MRPL4 (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)
ENST00000558518LDLRchr1911218190+ENST00000307422MRPL4chr1910368898+184811271691617482
ENST00000558518LDLRchr1911218190+ENST00000253099MRPL4chr1910368898+185011271691617482
ENST00000558518LDLRchr1911218190+ENST00000590669MRPL4chr1910368898+186111271691473434
ENST00000558518LDLRchr1911218190+ENST00000393733MRPL4chr1910368898+227511271691755528
ENST00000558518LDLRchr1911218190+ENST00000588502MRPL4chr1910368898+144511271691347392
ENST00000557933LDLRchr1911218190+ENST00000307422MRPL4chr1910368898+17481027691517482
ENST00000557933LDLRchr1911218190+ENST00000253099MRPL4chr1910368898+17501027691517482
ENST00000557933LDLRchr1911218190+ENST00000590669MRPL4chr1910368898+17611027691373434
ENST00000557933LDLRchr1911218190+ENST00000393733MRPL4chr1910368898+21751027691655528
ENST00000557933LDLRchr1911218190+ENST00000588502MRPL4chr1910368898+13451027691247392
ENST00000455727LDLRchr1911218190+ENST00000307422MRPL4chr1910368898+1243522681012314
ENST00000455727LDLRchr1911218190+ENST00000253099MRPL4chr1910368898+1245522681012314
ENST00000455727LDLRchr1911218190+ENST00000590669MRPL4chr1910368898+125652268868266
ENST00000455727LDLRchr1911218190+ENST00000393733MRPL4chr1910368898+1670522681150360
ENST00000455727LDLRchr1911218190+ENST00000588502MRPL4chr1910368898+84052268742224
ENST00000535915LDLRchr1911218190+ENST00000307422MRPL4chr1910368898+1624903681393441
ENST00000535915LDLRchr1911218190+ENST00000253099MRPL4chr1910368898+1626903681393441
ENST00000535915LDLRchr1911218190+ENST00000590669MRPL4chr1910368898+1637903681249393
ENST00000535915LDLRchr1911218190+ENST00000393733MRPL4chr1910368898+2051903681531487
ENST00000535915LDLRchr1911218190+ENST00000588502MRPL4chr1910368898+1221903681123351
ENST00000545707LDLRchr1911218190+ENST00000307422MRPL4chr1910368898+1366645681135355
ENST00000545707LDLRchr1911218190+ENST00000253099MRPL4chr1910368898+1368645681135355
ENST00000545707LDLRchr1911218190+ENST00000590669MRPL4chr1910368898+137964568991307
ENST00000545707LDLRchr1911218190+ENST00000393733MRPL4chr1910368898+1793645681273401
ENST00000545707LDLRchr1911218190+ENST00000588502MRPL4chr1910368898+96364568865265
ENST00000558013LDLRchr1911218190+ENST00000307422MRPL4chr1910368898+17321011531501482
ENST00000558013LDLRchr1911218190+ENST00000253099MRPL4chr1910368898+17341011531501482
ENST00000558013LDLRchr1911218190+ENST00000590669MRPL4chr1910368898+17451011531357434
ENST00000558013LDLRchr1911218190+ENST00000393733MRPL4chr1910368898+21591011531639528
ENST00000558013LDLRchr1911218190+ENST00000588502MRPL4chr1910368898+13291011531231392
ENST00000558518LDLRchr1911218190+ENST00000307422MRPL4chr1910368897+184811271691617482
ENST00000558518LDLRchr1911218190+ENST00000253099MRPL4chr1910368897+185011271691617482
ENST00000558518LDLRchr1911218190+ENST00000590669MRPL4chr1910368897+186111271691473434
ENST00000558518LDLRchr1911218190+ENST00000393733MRPL4chr1910368897+227511271691755528
ENST00000558518LDLRchr1911218190+ENST00000588502MRPL4chr1910368897+144511271691347392
ENST00000557933LDLRchr1911218190+ENST00000307422MRPL4chr1910368897+17481027691517482
ENST00000557933LDLRchr1911218190+ENST00000253099MRPL4chr1910368897+17501027691517482
ENST00000557933LDLRchr1911218190+ENST00000590669MRPL4chr1910368897+17611027691373434
ENST00000557933LDLRchr1911218190+ENST00000393733MRPL4chr1910368897+21751027691655528
ENST00000557933LDLRchr1911218190+ENST00000588502MRPL4chr1910368897+13451027691247392
ENST00000455727LDLRchr1911218190+ENST00000307422MRPL4chr1910368897+1243522681012314
ENST00000455727LDLRchr1911218190+ENST00000253099MRPL4chr1910368897+1245522681012314
ENST00000455727LDLRchr1911218190+ENST00000590669MRPL4chr1910368897+125652268868266
ENST00000455727LDLRchr1911218190+ENST00000393733MRPL4chr1910368897+1670522681150360
ENST00000455727LDLRchr1911218190+ENST00000588502MRPL4chr1910368897+84052268742224
ENST00000535915LDLRchr1911218190+ENST00000307422MRPL4chr1910368897+1624903681393441
ENST00000535915LDLRchr1911218190+ENST00000253099MRPL4chr1910368897+1626903681393441
ENST00000535915LDLRchr1911218190+ENST00000590669MRPL4chr1910368897+1637903681249393
ENST00000535915LDLRchr1911218190+ENST00000393733MRPL4chr1910368897+2051903681531487
ENST00000535915LDLRchr1911218190+ENST00000588502MRPL4chr1910368897+1221903681123351
ENST00000545707LDLRchr1911218190+ENST00000307422MRPL4chr1910368897+1366645681135355
ENST00000545707LDLRchr1911218190+ENST00000253099MRPL4chr1910368897+1368645681135355
ENST00000545707LDLRchr1911218190+ENST00000590669MRPL4chr1910368897+137964568991307
ENST00000545707LDLRchr1911218190+ENST00000393733MRPL4chr1910368897+1793645681273401
ENST00000545707LDLRchr1911218190+ENST00000588502MRPL4chr1910368897+96364568865265
ENST00000558013LDLRchr1911218190+ENST00000307422MRPL4chr1910368897+17321011531501482
ENST00000558013LDLRchr1911218190+ENST00000253099MRPL4chr1910368897+17341011531501482
ENST00000558013LDLRchr1911218190+ENST00000590669MRPL4chr1910368897+17451011531357434
ENST00000558013LDLRchr1911218190+ENST00000393733MRPL4chr1910368897+21591011531639528
ENST00000558013LDLRchr1911218190+ENST00000588502MRPL4chr1910368897+13291011531231392
ENST00000558518LDLRchr1911218189+ENST00000307422MRPL4chr1910368897+184811271691617482
ENST00000558518LDLRchr1911218189+ENST00000253099MRPL4chr1910368897+185011271691617482
ENST00000558518LDLRchr1911218189+ENST00000590669MRPL4chr1910368897+186111271691473434
ENST00000558518LDLRchr1911218189+ENST00000393733MRPL4chr1910368897+227511271691755528
ENST00000558518LDLRchr1911218189+ENST00000588502MRPL4chr1910368897+144511271691347392
ENST00000557933LDLRchr1911218189+ENST00000307422MRPL4chr1910368897+17481027691517482
ENST00000557933LDLRchr1911218189+ENST00000253099MRPL4chr1910368897+17501027691517482
ENST00000557933LDLRchr1911218189+ENST00000590669MRPL4chr1910368897+17611027691373434
ENST00000557933LDLRchr1911218189+ENST00000393733MRPL4chr1910368897+21751027691655528
ENST00000557933LDLRchr1911218189+ENST00000588502MRPL4chr1910368897+13451027691247392
ENST00000455727LDLRchr1911218189+ENST00000307422MRPL4chr1910368897+1243522681012314
ENST00000455727LDLRchr1911218189+ENST00000253099MRPL4chr1910368897+1245522681012314
ENST00000455727LDLRchr1911218189+ENST00000590669MRPL4chr1910368897+125652268868266
ENST00000455727LDLRchr1911218189+ENST00000393733MRPL4chr1910368897+1670522681150360
ENST00000455727LDLRchr1911218189+ENST00000588502MRPL4chr1910368897+84052268742224
ENST00000535915LDLRchr1911218189+ENST00000307422MRPL4chr1910368897+1624903681393441
ENST00000535915LDLRchr1911218189+ENST00000253099MRPL4chr1910368897+1626903681393441
ENST00000535915LDLRchr1911218189+ENST00000590669MRPL4chr1910368897+1637903681249393
ENST00000535915LDLRchr1911218189+ENST00000393733MRPL4chr1910368897+2051903681531487
ENST00000535915LDLRchr1911218189+ENST00000588502MRPL4chr1910368897+1221903681123351
ENST00000545707LDLRchr1911218189+ENST00000307422MRPL4chr1910368897+1366645681135355
ENST00000545707LDLRchr1911218189+ENST00000253099MRPL4chr1910368897+1368645681135355
ENST00000545707LDLRchr1911218189+ENST00000590669MRPL4chr1910368897+137964568991307
ENST00000545707LDLRchr1911218189+ENST00000393733MRPL4chr1910368897+1793645681273401
ENST00000545707LDLRchr1911218189+ENST00000588502MRPL4chr1910368897+96364568865265
ENST00000558013LDLRchr1911218189+ENST00000307422MRPL4chr1910368897+17321011531501482
ENST00000558013LDLRchr1911218189+ENST00000253099MRPL4chr1910368897+17341011531501482
ENST00000558013LDLRchr1911218189+ENST00000590669MRPL4chr1910368897+17451011531357434
ENST00000558013LDLRchr1911218189+ENST00000393733MRPL4chr1910368897+21591011531639528
ENST00000558013LDLRchr1911218189+ENST00000588502MRPL4chr1910368897+13291011531231392

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
ENST00000558518ENST00000307422LDLRchr1911218190+MRPL4chr1910368898+0.0300157420.96998423
ENST00000558518ENST00000253099LDLRchr1911218190+MRPL4chr1910368898+0.0302685930.9697314
ENST00000558518ENST00000590669LDLRchr1911218190+MRPL4chr1910368898+0.0181817920.98181826
ENST00000558518ENST00000393733LDLRchr1911218190+MRPL4chr1910368898+0.062543380.93745667
ENST00000558518ENST00000588502LDLRchr1911218190+MRPL4chr1910368898+0.0213034640.9786966
ENST00000557933ENST00000307422LDLRchr1911218190+MRPL4chr1910368898+0.0309661680.96903384
ENST00000557933ENST00000253099LDLRchr1911218190+MRPL4chr1910368898+0.031260790.96873915
ENST00000557933ENST00000590669LDLRchr1911218190+MRPL4chr1910368898+0.0188106450.98118937
ENST00000557933ENST00000393733LDLRchr1911218190+MRPL4chr1910368898+0.0637379660.936262
ENST00000557933ENST00000588502LDLRchr1911218190+MRPL4chr1910368898+0.0219260830.9780739
ENST00000455727ENST00000307422LDLRchr1911218190+MRPL4chr1910368898+0.088527980.911472
ENST00000455727ENST00000253099LDLRchr1911218190+MRPL4chr1910368898+0.08816930.91183066
ENST00000455727ENST00000590669LDLRchr1911218190+MRPL4chr1910368898+0.042153830.95784616
ENST00000455727ENST00000393733LDLRchr1911218190+MRPL4chr1910368898+0.227077710.77292234
ENST00000455727ENST00000588502LDLRchr1911218190+MRPL4chr1910368898+0.0315204520.9684796
ENST00000535915ENST00000307422LDLRchr1911218190+MRPL4chr1910368898+0.031777020.9682229
ENST00000535915ENST00000253099LDLRchr1911218190+MRPL4chr1910368898+0.0321103820.9678896
ENST00000535915ENST00000590669LDLRchr1911218190+MRPL4chr1910368898+0.0194187460.9805813
ENST00000535915ENST00000393733LDLRchr1911218190+MRPL4chr1910368898+0.085000830.9149992
ENST00000535915ENST00000588502LDLRchr1911218190+MRPL4chr1910368898+0.0194183870.98058164
ENST00000545707ENST00000307422LDLRchr1911218190+MRPL4chr1910368898+0.037289670.9627103
ENST00000545707ENST00000253099LDLRchr1911218190+MRPL4chr1910368898+0.037459870.9625401
ENST00000545707ENST00000590669LDLRchr1911218190+MRPL4chr1910368898+0.0223110710.9776889
ENST00000545707ENST00000393733LDLRchr1911218190+MRPL4chr1910368898+0.20243310.79756695
ENST00000545707ENST00000588502LDLRchr1911218190+MRPL4chr1910368898+0.0220663920.97793365
ENST00000558013ENST00000307422LDLRchr1911218190+MRPL4chr1910368898+0.0311579460.96884197
ENST00000558013ENST00000253099LDLRchr1911218190+MRPL4chr1910368898+0.0314641330.96853584
ENST00000558013ENST00000590669LDLRchr1911218190+MRPL4chr1910368898+0.0187173820.9812826
ENST00000558013ENST00000393733LDLRchr1911218190+MRPL4chr1910368898+0.0641571950.93584275
ENST00000558013ENST00000588502LDLRchr1911218190+MRPL4chr1910368898+0.0214059130.97859406
ENST00000558518ENST00000307422LDLRchr1911218190+MRPL4chr1910368897+0.0300157420.96998423
ENST00000558518ENST00000253099LDLRchr1911218190+MRPL4chr1910368897+0.0302685930.9697314
ENST00000558518ENST00000590669LDLRchr1911218190+MRPL4chr1910368897+0.0181817920.98181826
ENST00000558518ENST00000393733LDLRchr1911218190+MRPL4chr1910368897+0.062543380.93745667
ENST00000558518ENST00000588502LDLRchr1911218190+MRPL4chr1910368897+0.0213034640.9786966
ENST00000557933ENST00000307422LDLRchr1911218190+MRPL4chr1910368897+0.0309661680.96903384
ENST00000557933ENST00000253099LDLRchr1911218190+MRPL4chr1910368897+0.031260790.96873915
ENST00000557933ENST00000590669LDLRchr1911218190+MRPL4chr1910368897+0.0188106450.98118937
ENST00000557933ENST00000393733LDLRchr1911218190+MRPL4chr1910368897+0.0637379660.936262
ENST00000557933ENST00000588502LDLRchr1911218190+MRPL4chr1910368897+0.0219260830.9780739
ENST00000455727ENST00000307422LDLRchr1911218190+MRPL4chr1910368897+0.088527980.911472
ENST00000455727ENST00000253099LDLRchr1911218190+MRPL4chr1910368897+0.08816930.91183066
ENST00000455727ENST00000590669LDLRchr1911218190+MRPL4chr1910368897+0.042153830.95784616
ENST00000455727ENST00000393733LDLRchr1911218190+MRPL4chr1910368897+0.227077710.77292234
ENST00000455727ENST00000588502LDLRchr1911218190+MRPL4chr1910368897+0.0315204520.9684796
ENST00000535915ENST00000307422LDLRchr1911218190+MRPL4chr1910368897+0.031777020.9682229
ENST00000535915ENST00000253099LDLRchr1911218190+MRPL4chr1910368897+0.0321103820.9678896
ENST00000535915ENST00000590669LDLRchr1911218190+MRPL4chr1910368897+0.0194187460.9805813
ENST00000535915ENST00000393733LDLRchr1911218190+MRPL4chr1910368897+0.085000830.9149992
ENST00000535915ENST00000588502LDLRchr1911218190+MRPL4chr1910368897+0.0194183870.98058164
ENST00000545707ENST00000307422LDLRchr1911218190+MRPL4chr1910368897+0.037289670.9627103
ENST00000545707ENST00000253099LDLRchr1911218190+MRPL4chr1910368897+0.037459870.9625401
ENST00000545707ENST00000590669LDLRchr1911218190+MRPL4chr1910368897+0.0223110710.9776889
ENST00000545707ENST00000393733LDLRchr1911218190+MRPL4chr1910368897+0.20243310.79756695
ENST00000545707ENST00000588502LDLRchr1911218190+MRPL4chr1910368897+0.0220663920.97793365
ENST00000558013ENST00000307422LDLRchr1911218190+MRPL4chr1910368897+0.0311579460.96884197
ENST00000558013ENST00000253099LDLRchr1911218190+MRPL4chr1910368897+0.0314641330.96853584
ENST00000558013ENST00000590669LDLRchr1911218190+MRPL4chr1910368897+0.0187173820.9812826
ENST00000558013ENST00000393733LDLRchr1911218190+MRPL4chr1910368897+0.0641571950.93584275
ENST00000558013ENST00000588502LDLRchr1911218190+MRPL4chr1910368897+0.0214059130.97859406
ENST00000558518ENST00000307422LDLRchr1911218189+MRPL4chr1910368897+0.0300157420.96998423
ENST00000558518ENST00000253099LDLRchr1911218189+MRPL4chr1910368897+0.0302685930.9697314
ENST00000558518ENST00000590669LDLRchr1911218189+MRPL4chr1910368897+0.0181817920.98181826
ENST00000558518ENST00000393733LDLRchr1911218189+MRPL4chr1910368897+0.062543380.93745667
ENST00000558518ENST00000588502LDLRchr1911218189+MRPL4chr1910368897+0.0213034640.9786966
ENST00000557933ENST00000307422LDLRchr1911218189+MRPL4chr1910368897+0.0309661680.96903384
ENST00000557933ENST00000253099LDLRchr1911218189+MRPL4chr1910368897+0.031260790.96873915
ENST00000557933ENST00000590669LDLRchr1911218189+MRPL4chr1910368897+0.0188106450.98118937
ENST00000557933ENST00000393733LDLRchr1911218189+MRPL4chr1910368897+0.0637379660.936262
ENST00000557933ENST00000588502LDLRchr1911218189+MRPL4chr1910368897+0.0219260830.9780739
ENST00000455727ENST00000307422LDLRchr1911218189+MRPL4chr1910368897+0.088527980.911472
ENST00000455727ENST00000253099LDLRchr1911218189+MRPL4chr1910368897+0.08816930.91183066
ENST00000455727ENST00000590669LDLRchr1911218189+MRPL4chr1910368897+0.042153830.95784616
ENST00000455727ENST00000393733LDLRchr1911218189+MRPL4chr1910368897+0.227077710.77292234
ENST00000455727ENST00000588502LDLRchr1911218189+MRPL4chr1910368897+0.0315204520.9684796
ENST00000535915ENST00000307422LDLRchr1911218189+MRPL4chr1910368897+0.031777020.9682229
ENST00000535915ENST00000253099LDLRchr1911218189+MRPL4chr1910368897+0.0321103820.9678896
ENST00000535915ENST00000590669LDLRchr1911218189+MRPL4chr1910368897+0.0194187460.9805813
ENST00000535915ENST00000393733LDLRchr1911218189+MRPL4chr1910368897+0.085000830.9149992
ENST00000535915ENST00000588502LDLRchr1911218189+MRPL4chr1910368897+0.0194183870.98058164
ENST00000545707ENST00000307422LDLRchr1911218189+MRPL4chr1910368897+0.037289670.9627103
ENST00000545707ENST00000253099LDLRchr1911218189+MRPL4chr1910368897+0.037459870.9625401
ENST00000545707ENST00000590669LDLRchr1911218189+MRPL4chr1910368897+0.0223110710.9776889
ENST00000545707ENST00000393733LDLRchr1911218189+MRPL4chr1910368897+0.20243310.79756695
ENST00000545707ENST00000588502LDLRchr1911218189+MRPL4chr1910368897+0.0220663920.97793365
ENST00000558013ENST00000307422LDLRchr1911218189+MRPL4chr1910368897+0.0311579460.96884197
ENST00000558013ENST00000253099LDLRchr1911218189+MRPL4chr1910368897+0.0314641330.96853584
ENST00000558013ENST00000590669LDLRchr1911218189+MRPL4chr1910368897+0.0187173820.9812826
ENST00000558013ENST00000393733LDLRchr1911218189+MRPL4chr1910368897+0.0641571950.93584275
ENST00000558013ENST00000588502LDLRchr1911218189+MRPL4chr1910368897+0.0214059130.97859406

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 LDLR-MRPL4

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
LDLRchr1911218189MRPL4chr19103688971011319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218189MRPL4chr19103688971027319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218189MRPL4chr19103688971127319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218189MRPL4chr1910368897522151DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218189MRPL4chr1910368897645192DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218189MRPL4chr1910368897903278DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr19103688971011319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr19103688971027319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr19103688971127319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr1910368897522151DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr1910368897645192DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr1910368897903278DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr19103688981011319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr19103688981027319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr19103688981127319DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr1910368898522151DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr1910368898645192DCRDWSDEPIKECGGVAHGPRGPTSY
LDLRchr1911218190MRPL4chr1910368898903278DCRDWSDEPIKECGGVAHGPRGPTSY

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Potential FusionNeoAntigen Information of LDLR-MRPL4 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 LDLR-MRPL4 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 LDLR-MRPL4

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 LDLR-MRPL4

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 LDLR-MRPL4

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 LDLR-MRPL4

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 LDLR-MRPL4

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 LDLR-MRPL4

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 LDLR-MRPL4

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