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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:CALR-QSOX1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CALR-QSOX1
FusionPDB ID: 12613
FusionGDB2.0 ID: 12613
HgeneTgene
Gene symbol

CALR

QSOX1

Gene ID

811

5768

Gene namecalreticulinquiescin sulfhydryl oxidase 1
SynonymsCRT|HEL-S-99n|RO|SSA|cC1qRQ6|QSCN6
Cytomap

19p13.13

1q25.2

Type of geneprotein-codingprotein-coding
DescriptioncalreticulinCRP55ERp60HACBPSicca syndrome antigen A (autoantigen Ro; calreticulin)calregulinendoplasmic reticulum resident protein 60epididymis secretory sperm binding protein Li 99ngrp60sulfhydryl oxidase 1quiescin Q6 sulfhydryl oxidase 1testis tissue sperm-binding protein Li 62nthiol oxidase 1
Modification date2020032920200313
UniProtAcc

Q96L12

Main function of 5'-partner protein: FUNCTION: During spermatogenesis, may act as a lectin-independent chaperone for specific client proteins such as ADAM3. Required for sperm fertility (By similarity). CALR3 capacity for calcium-binding may be absent or much lower than that of CALR. {ECO:0000250, ECO:0000269|PubMed:21590275}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000316448, ENST00000367600, 
ENST00000367602, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 17 X 9=27548 X 9 X 3=216
# samples 249
** MAII scorelog2(24/2754*10)=-3.52042224852645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/216*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CALR [Title/Abstract] AND QSOX1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CALR [Title/Abstract] AND QSOX1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CALR(13051468)-QSOX1(180165396), # samples:1
Anticipated loss of major functional domain due to fusion event.CALR-QSOX1 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.
CALR-QSOX1 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.
CALR-QSOX1 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.
CALR-QSOX1 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.
CALR-QSOX1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CALR-QSOX1 seems lost the major protein functional domain in Hgene partner, which is a CGC 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
HgeneCALR

GO:0000122

negative regulation of transcription by RNA polymerase II

8107809

HgeneCALR

GO:0006611

protein export from nucleus

11149926

HgeneCALR

GO:0017148

negative regulation of translation

14726956

HgeneCALR

GO:0033144

negative regulation of intracellular steroid hormone receptor signaling pathway

8107809

HgeneCALR

GO:0034504

protein localization to nucleus

15998798

HgeneCALR

GO:0045665

negative regulation of neuron differentiation

8107809

HgeneCALR

GO:0045892

negative regulation of transcription, DNA-templated

8107809

HgeneCALR

GO:0048387

negative regulation of retinoic acid receptor signaling pathway

8107809



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/chr19:13051468/chr1:180165396)
- 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 CALR (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 QSOX1 (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)
ENST00000316448CALRchr1913051468+ENST00000367602QSOX1chr1180165396+8658889521176374

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
ENST00000316448ENST00000367602CALRchr1913051468+QSOX1chr1180165396+0.0020338680.9979662

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 CALR-QSOX1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CALRchr1913051468QSOX1chr1180165396889279EWEPPVIQNPEYKVPPARTPSSPRCS

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Potential FusionNeoAntigen Information of CALR-QSOX1 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.
CALR-QSOX1_13051468_180165396.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)
CALR-QSOX1chr1913051468chr1180165396889HLA-B52:01IQNPEYKV0.95970.9236614
CALR-QSOX1chr1913051468chr1180165396889HLA-B08:09NPEYKVPPA0.91990.61817
CALR-QSOX1chr1913051468chr1180165396889HLA-B78:01NPEYKVPPA0.56630.5287817
CALR-QSOX1chr1913051468chr1180165396889HLA-B78:02NPEYKVPPA0.45130.657817

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Potential FusionNeoAntigen Information of CALR-QSOX1 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.
CALR-QSOX1_13051468_180165396.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)
CALR-QSOX1chr1913051468chr1180165396889DRB1-0303EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-0324EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-0338EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-0338WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-0338EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-0338PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB1-0825EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1114EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1120EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1168EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1182EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1220EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1222EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1302EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1323EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1329EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1331EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1331WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1331EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1331PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB1-1334EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1336EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1339EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1341EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1341WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1343EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1354EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1367EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1373EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1374EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1377EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1396EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1396WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1397EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1399EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1401EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1404EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1404WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1416EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1416WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1424EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1426EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1428EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1428WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1431EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1431WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1432EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1432WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1435EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1437EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1438EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1438WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1439EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1439WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1439EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1439PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB1-1447EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1448EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1448WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1448EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1448PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB1-1449EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1449WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1450EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1450WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1450EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1454EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1455EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1455WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1458EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1460EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1461EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1461WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1462EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1468EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1470EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1470WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1470EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1470PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB1-1471EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1471WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1475EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1476EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1476WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1479EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1479WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1482EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1482WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1486EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1487EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1488EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1490EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1493EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1493WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1497EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1499EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1503EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1503WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1503PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB1-1503EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1523EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1523WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1523PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB1-1523EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1525EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB1-1525WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB1-1525EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB1-1525PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB3-0109EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0109WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0109EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB3-0201EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0201WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0204EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0204WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0204PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB3-0204EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB3-0209EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0209WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0214EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0214WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0216EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0216WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0221EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0221WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0224EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0224WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0301EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0301WEPPVIQNPEYKVPP116
CALR-QSOX1chr1913051468chr1180165396889DRB3-0301EWEPPVIQNPEYKVP015
CALR-QSOX1chr1913051468chr1180165396889DRB3-0301PPVIQNPEYKVPPAR318
CALR-QSOX1chr1913051468chr1180165396889DRB3-0303EPPVIQNPEYKVPPA217
CALR-QSOX1chr1913051468chr1180165396889DRB3-0303WEPPVIQNPEYKVPP116

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Fusion breakpoint peptide structures of CALR-QSOX1

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
3925IQNPEYKVPPARTPCALRQSOX1chr1913051468chr1180165396889

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CALR-QSOX1

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-B14:023BVN3925IQNPEYKVPPARTP-7.15543-7.26883
HLA-B14:023BVN3925IQNPEYKVPPARTP-4.77435-5.80965
HLA-B52:013W393925IQNPEYKVPPARTP-6.80875-6.92215
HLA-B52:013W393925IQNPEYKVPPARTP-4.20386-5.23916
HLA-A11:014UQ23925IQNPEYKVPPARTP-7.5194-8.5547
HLA-A11:014UQ23925IQNPEYKVPPARTP-6.9601-7.0735
HLA-A24:025HGA3925IQNPEYKVPPARTP-7.52403-7.63743
HLA-A24:025HGA3925IQNPEYKVPPARTP-5.82433-6.85963
HLA-B27:056PYJ3925IQNPEYKVPPARTP-3.28285-4.31815
HLA-B44:053DX83925IQNPEYKVPPARTP-5.91172-6.94702
HLA-B44:053DX83925IQNPEYKVPPARTP-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of CALR-QSOX1

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
CALR-QSOX1chr1913051468chr1180165396614IQNPEYKVATTCAGAACCCTGAGTACAAGGTG
CALR-QSOX1chr1913051468chr1180165396817NPEYKVPPAAACCCTGAGTACAAGGTGCCCCCAGCG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
CALR-QSOX1chr1913051468chr1180165396015EWEPPVIQNPEYKVPGAGTGGGAACCCCCAGTGATTCAGAACCCTGAGTACAAGGTGCCC
CALR-QSOX1chr1913051468chr1180165396116WEPPVIQNPEYKVPPTGGGAACCCCCAGTGATTCAGAACCCTGAGTACAAGGTGCCCCCA
CALR-QSOX1chr1913051468chr1180165396217EPPVIQNPEYKVPPAGAACCCCCAGTGATTCAGAACCCTGAGTACAAGGTGCCCCCAGCG
CALR-QSOX1chr1913051468chr1180165396318PPVIQNPEYKVPPARCCCCCAGTGATTCAGAACCCTGAGTACAAGGTGCCCCCAGCGAGG

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Information of the samples that have these potential fusion neoantigens of CALR-QSOX1

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
OVCALR-QSOX1chr1913051468ENST00000316448chr1180165396ENST00000367602TCGA-13-0919

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Potential target of CAR-T therapy development for CALR-QSOX1

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
TgeneQSOX1chr19:13051468chr1:180165396ENST000003676001013710_7300605.0TransmembraneHelical
TgeneQSOX1chr19:13051468chr1:180165396ENST000003676021012710_7300748.0TransmembraneHelical

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 CALR-QSOX1

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 CALR-QSOX1

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