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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:RCCD1-BLM

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RCCD1-BLM
FusionPDB ID: 73298
FusionGDB2.0 ID: 73298
HgeneTgene
Gene symbol

RCCD1

BLM

Gene ID

91433

641

Gene nameRCC1 domain containing 1BLM RecQ like helicase
Synonyms-BS|MGRISCE1|RECQ2|RECQL2|RECQL3
Cytomap

15q26.1

15q26.1

Type of geneprotein-codingprotein-coding
DescriptionRCC1 domain-containing protein 1Bloom syndrome proteinBloom syndrome RecQ like helicaseBloom syndrome, RecQ helicase-likeDNA helicase, RecQ-like type 2recQ protein-like 3
Modification date2020031320200313
UniProtAcc.

Q13867

Main function of 5'-partner protein: FUNCTION: The normal physiological role of BLM hydrolase is unknown, but it catalyzes the inactivation of the antitumor drug BLM (a glycopeptide) by hydrolyzing the carboxamide bond of its B-aminoalaninamide moiety thus protecting normal and malignant cells from BLM toxicity. {ECO:0000250}.
Ensembl transtripts involved in fusion geneENST idsENST00000556774, ENST00000394258, 
ENST00000555155, ENST00000556618, 
ENST00000355112, ENST00000560509, 
ENST00000560136, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score2 X 8 X 2=327 X 13 X 3=273
# samples 38
** MAII scorelog2(3/32*10)=-0.0931094043914815
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/273*10)=-1.77082904603249
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: RCCD1 [Title/Abstract] AND BLM [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: RCCD1 [Title/Abstract] AND BLM [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RCCD1(91498178)-BLM(91326052), # samples:2
Anticipated loss of major functional domain due to fusion event.RCCD1-BLM 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.
RCCD1-BLM 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.
RCCD1-BLM 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.
RCCD1-BLM 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.
RCCD1-BLM seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
RCCD1-BLM seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
RCCD1-BLM 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
TgeneBLM

GO:0000729

DNA double-strand break processing

21325134

TgeneBLM

GO:0006974

cellular response to DNA damage stimulus

23509288

TgeneBLM

GO:0007095

mitotic G2 DNA damage checkpoint

11309417

TgeneBLM

GO:0010165

response to X-ray

11309417

TgeneBLM

GO:0031297

replication fork processing

17115688

TgeneBLM

GO:0032508

DNA duplex unwinding

11735402|24816114|25901030

TgeneBLM

GO:0044806

G-quadruplex DNA unwinding

11735402

TgeneBLM

GO:0045893

positive regulation of transcription, DNA-templated

11781842

TgeneBLM

GO:0051259

protein complex oligomerization

28228481

TgeneBLM

GO:0051260

protein homooligomerization

28228481

TgeneBLM

GO:0061820

telomeric D-loop disassembly

19734539

TgeneBLM

GO:0071479

cellular response to ionizing radiation

23509288

TgeneBLM

GO:0072711

cellular response to hydroxyurea

23509288

TgeneBLM

GO:0072757

cellular response to camptothecin

23509288



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/chr15:91498178/chr15:91326052)
- 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 RCCD1 (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 BLM (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)
ENST00000394258RCCD1chr1591500955+ENST00000355112BLMchr1591328150+2656881192472817
ENST00000394258RCCD1chr1591500955+ENST00000560509BLMchr1591328150+2134881192079686
ENST00000555155RCCD1chr1591500955+ENST00000355112BLMchr1591328150+264587082461817
ENST00000555155RCCD1chr1591500955+ENST00000560509BLMchr1591328150+212387082068686
ENST00000556618RCCD1chr1591500955+ENST00000355112BLMchr1591328150+25768011222392756
ENST00000556618RCCD1chr1591500955+ENST00000560509BLMchr1591328150+20548011221999625
ENST00000394258RCCD1chr1591500955+ENST00000355112BLMchr1591328151+2656881192472817
ENST00000394258RCCD1chr1591500955+ENST00000560509BLMchr1591328151+2134881192079686
ENST00000555155RCCD1chr1591500955+ENST00000355112BLMchr1591328151+264587082461817
ENST00000555155RCCD1chr1591500955+ENST00000560509BLMchr1591328151+212387082068686
ENST00000556618RCCD1chr1591500955+ENST00000355112BLMchr1591328151+25768011222392756
ENST00000556618RCCD1chr1591500955+ENST00000560509BLMchr1591328151+20548011221999625
ENST00000394258RCCD1chr1591500733+ENST00000355112BLMchr1591326052+2641759192457812
ENST00000394258RCCD1chr1591500733+ENST00000560509BLMchr1591326052+2119759192064681
ENST00000555155RCCD1chr1591500733+ENST00000355112BLMchr1591326052+263074882446812
ENST00000555155RCCD1chr1591500733+ENST00000560509BLMchr1591326052+210874882053681
ENST00000556618RCCD1chr1591500733+ENST00000355112BLMchr1591326052+25616791222377751
ENST00000556618RCCD1chr1591500733+ENST00000560509BLMchr1591326052+20396791221984620
ENST00000394258RCCD1chr1591500954+ENST00000355112BLMchr1591328150+2656881192472817
ENST00000394258RCCD1chr1591500954+ENST00000560509BLMchr1591328150+2134881192079686
ENST00000555155RCCD1chr1591500954+ENST00000355112BLMchr1591328150+264587082461817
ENST00000555155RCCD1chr1591500954+ENST00000560509BLMchr1591328150+212387082068686
ENST00000556618RCCD1chr1591500954+ENST00000355112BLMchr1591328150+25768011222392756
ENST00000556618RCCD1chr1591500954+ENST00000560509BLMchr1591328150+20548011221999625

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
ENST00000394258ENST00000355112RCCD1chr1591500955+BLMchr1591328150+0.0019756060.99802446
ENST00000394258ENST00000560509RCCD1chr1591500955+BLMchr1591328150+0.0100234320.9899766
ENST00000555155ENST00000355112RCCD1chr1591500955+BLMchr1591328150+0.0020194620.99798054
ENST00000555155ENST00000560509RCCD1chr1591500955+BLMchr1591328150+0.0103169140.98968303
ENST00000556618ENST00000355112RCCD1chr1591500955+BLMchr1591328150+0.0021976110.99780244
ENST00000556618ENST00000560509RCCD1chr1591500955+BLMchr1591328150+0.0113788190.9886212
ENST00000394258ENST00000355112RCCD1chr1591500955+BLMchr1591328151+0.0019756060.99802446
ENST00000394258ENST00000560509RCCD1chr1591500955+BLMchr1591328151+0.0100234320.9899766
ENST00000555155ENST00000355112RCCD1chr1591500955+BLMchr1591328151+0.0020194620.99798054
ENST00000555155ENST00000560509RCCD1chr1591500955+BLMchr1591328151+0.0103169140.98968303
ENST00000556618ENST00000355112RCCD1chr1591500955+BLMchr1591328151+0.0021976110.99780244
ENST00000556618ENST00000560509RCCD1chr1591500955+BLMchr1591328151+0.0113788190.9886212
ENST00000394258ENST00000355112RCCD1chr1591500733+BLMchr1591326052+0.0016132630.99838674
ENST00000394258ENST00000560509RCCD1chr1591500733+BLMchr1591326052+0.0065977430.9934023
ENST00000555155ENST00000355112RCCD1chr1591500733+BLMchr1591326052+0.0016416980.9983583
ENST00000555155ENST00000560509RCCD1chr1591500733+BLMchr1591326052+0.0067661580.99323386
ENST00000556618ENST00000355112RCCD1chr1591500733+BLMchr1591326052+0.0017634730.99823654
ENST00000556618ENST00000560509RCCD1chr1591500733+BLMchr1591326052+0.0076647550.99233526
ENST00000394258ENST00000355112RCCD1chr1591500954+BLMchr1591328150+0.0019756060.99802446
ENST00000394258ENST00000560509RCCD1chr1591500954+BLMchr1591328150+0.0100234320.9899766
ENST00000555155ENST00000355112RCCD1chr1591500954+BLMchr1591328150+0.0020194620.99798054
ENST00000555155ENST00000560509RCCD1chr1591500954+BLMchr1591328150+0.0103169140.98968303
ENST00000556618ENST00000355112RCCD1chr1591500954+BLMchr1591328150+0.0021976110.99780244
ENST00000556618ENST00000560509RCCD1chr1591500954+BLMchr1591328150+0.0113788190.9886212

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 RCCD1-BLM

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RCCD1chr1591500733BLMchr1591326052679180EHALLLDAAGQVFSWGGGRFSMSFNR
RCCD1chr1591500733BLMchr1591326052748241EHALLLDAAGQVFSWGGGRFSMSFNR
RCCD1chr1591500733BLMchr1591326052759241EHALLLDAAGQVFSWGGGRFSMSFNR
RCCD1chr1591500954BLMchr1591328150801226EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500954BLMchr1591328150870287EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500954BLMchr1591328150881287EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500955BLMchr1591328150801226EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500955BLMchr1591328150870287EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500955BLMchr1591328150881287EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500955BLMchr1591328151801226EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500955BLMchr1591328151870287EVAAGGWHSVCVSDDSGIIYCLSRRE
RCCD1chr1591500955BLMchr1591328151881287EVAAGGWHSVCVSDDSGIIYCLSRRE

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Potential FusionNeoAntigen Information of RCCD1-BLM 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.
RCCD1-BLM_91500733_91326052.msa
RCCD1-BLM_91500954_91328150.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)
RCCD1-BLMchr1591500733chr1591326052759HLA-B58:01AAGQVFSW0.99870.9795715
RCCD1-BLMchr1591500733chr1591326052759HLA-B53:01DAAGQVFSW0.98740.5687615
RCCD1-BLMchr1591500733chr1591326052759HLA-B35:01DAAGQVFSW0.97940.7529615
RCCD1-BLMchr1591500733chr1591326052759HLA-A74:09QVFSWGGGR0.97330.50971019
RCCD1-BLMchr1591500733chr1591326052759HLA-A74:03QVFSWGGGR0.97330.50971019
RCCD1-BLMchr1591500733chr1591326052759HLA-A74:11QVFSWGGGR0.97330.50971019
RCCD1-BLMchr1591500733chr1591326052759HLA-A26:02DAAGQVFSW0.96810.5772615
RCCD1-BLMchr1591500733chr1591326052759HLA-B58:01DAAGQVFSW0.96720.9209615
RCCD1-BLMchr1591500733chr1591326052759HLA-A26:14DAAGQVFSW0.92920.5979615
RCCD1-BLMchr1591500733chr1591326052759HLA-A26:15DAAGQVFSW0.92920.5979615
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:01DAAGQVFSW0.90340.9571615
RCCD1-BLMchr1591500733chr1591326052759HLA-B58:02DAAGQVFSW0.84160.9306615
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:01LDAAGQVFSW0.9990.9815515
RCCD1-BLMchr1591500733chr1591326052759HLA-B58:02LDAAGQVFSW0.99550.9647515
RCCD1-BLMchr1591500733chr1591326052759HLA-B58:01LDAAGQVFSW0.99520.9673515
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:03LDAAGQVFSW0.9850.9922515
RCCD1-BLMchr1591500733chr1591326052759HLA-B53:01LDAAGQVFSW0.96150.7378515
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:01LLDAAGQVFSW0.99990.9822415
RCCD1-BLMchr1591500733chr1591326052759HLA-B58:01LLDAAGQVFSW0.99860.9734415
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:03LLDAAGQVFSW0.9980.9935415
RCCD1-BLMchr1591500733chr1591326052759HLA-A26:01DAAGQVFSW0.92920.5979615
RCCD1-BLMchr1591500733chr1591326052759HLA-B44:08DAAGQVFSW0.6380.756615
RCCD1-BLMchr1591500733chr1591326052759HLA-C15:04FSWGGGRFSM0.99980.97411222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:08FSWGGGRFSM0.99980.91721222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:07FSWGGGRFSM0.99970.98581222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:19FSWGGGRFSM0.99970.98391222
RCCD1-BLMchr1591500733chr1591326052759HLA-C12:12FSWGGGRFSM0.99870.96321222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:14FSWGGGRFSM0.99780.98841222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:02FSWGGGRF0.99960.9581220
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:04AAGQVFSW0.99930.79715
RCCD1-BLMchr1591500733chr1591326052759HLA-B53:02DAAGQVFSW0.99620.5396615
RCCD1-BLMchr1591500733chr1591326052759HLA-B35:24DAAGQVFSW0.99170.7403615
RCCD1-BLMchr1591500733chr1591326052759HLA-A25:01DAAGQVFSW0.99070.8968615
RCCD1-BLMchr1591500733chr1591326052759HLA-B35:77DAAGQVFSW0.97940.7529615
RCCD1-BLMchr1591500733chr1591326052759HLA-B35:23DAAGQVFSW0.97840.7958615
RCCD1-BLMchr1591500733chr1591326052759HLA-A74:01QVFSWGGGR0.97330.50971019
RCCD1-BLMchr1591500733chr1591326052759HLA-B15:13DAAGQVFSW0.93830.9359615
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:04DAAGQVFSW0.92630.7274615
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:02DAAGQVFSW0.92220.9528615
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:10DAAGQVFSW0.90340.9571615
RCCD1-BLMchr1591500733chr1591326052759HLA-B51:06DAAGQVFSW0.80920.7087615
RCCD1-BLMchr1591500733chr1591326052759HLA-C14:02VFSWGGGRF0.13370.92621120
RCCD1-BLMchr1591500733chr1591326052759HLA-C14:03VFSWGGGRF0.13370.92621120
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:04FSWGGGRFSM0.99980.97911222
RCCD1-BLMchr1591500733chr1591326052759HLA-C15:09FSWGGGRFSM0.99980.97411222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:03FSWGGGRFSM0.99980.97911222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:02FSWGGGRFSM0.99980.96971222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:05FSWGGGRFSM0.99960.89691222
RCCD1-BLMchr1591500733chr1591326052759HLA-C03:17FSWGGGRFSM0.99950.95981222
RCCD1-BLMchr1591500733chr1591326052759HLA-C16:04FSWGGGRFSM0.99950.98131222
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:10LDAAGQVFSW0.9990.9815515
RCCD1-BLMchr1591500733chr1591326052759HLA-C16:01FSWGGGRFSM0.99830.97491222
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:04LDAAGQVFSW0.99670.8125515
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:02LDAAGQVFSW0.98420.9748515
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:10LLDAAGQVFSW0.99990.9822415
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:04LLDAAGQVFSW0.99980.8517415
RCCD1-BLMchr1591500733chr1591326052759HLA-B57:02LLDAAGQVFSW0.9990.981415
RCCD1-BLMchr1591500954chr1591328150881HLA-B35:08VSDDSGIIY0.71790.52011120
RCCD1-BLMchr1591500954chr1591328150881HLA-B35:01VSDDSGIIY0.5360.57391120
RCCD1-BLMchr1591500954chr1591328150881HLA-C05:09VSDDSGII10.87451119
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:15VSDDSGII0.99990.85351119
RCCD1-BLMchr1591500954chr1591328150881HLA-C04:07VSDDSGIIY0.96420.53821120
RCCD1-BLMchr1591500954chr1591328150881HLA-C04:10VSDDSGIIY0.96410.51131120
RCCD1-BLMchr1591500954chr1591328150881HLA-C05:09VSDDSGIIY0.96280.8081120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:15VSDDSGIIY0.78590.83351120
RCCD1-BLMchr1591500954chr1591328150881HLA-B15:05VSDDSGIIY0.75020.56181120
RCCD1-BLMchr1591500954chr1591328150881HLA-B15:21VSDDSGIIY0.58610.6621120
RCCD1-BLMchr1591500954chr1591328150881HLA-B15:31VSDDSGIIY0.56920.57331120
RCCD1-BLMchr1591500954chr1591328150881HLA-C15:04VSDDSGIIY0.47340.78531120
RCCD1-BLMchr1591500954chr1591328150881HLA-C04:06VSDDSGIIY0.29190.57341120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:13VSDDSGIIY0.1520.76551120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:04VSDDSGIIY0.1520.76551120
RCCD1-BLMchr1591500954chr1591328150881HLA-C03:14VSDDSGIIY0.02870.91591120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:03VSDDSGIIY0.00760.85821120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:15VSDDSGIIYCL10.90941122
RCCD1-BLMchr1591500954chr1591328150881HLA-C05:09VSDDSGIIYCL10.8761122
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:03VSDDSGIIYCL0.82740.92261122
RCCD1-BLMchr1591500954chr1591328150881HLA-C04:03VSDDSGII10.70721119
RCCD1-BLMchr1591500954chr1591328150881HLA-C05:01VSDDSGII10.87451119
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:02VSDDSGII0.99990.85351119
RCCD1-BLMchr1591500954chr1591328150881HLA-C04:01VSDDSGIIY0.96420.53821120
RCCD1-BLMchr1591500954chr1591328150881HLA-C04:03VSDDSGIIY0.9640.61731120
RCCD1-BLMchr1591500954chr1591328150881HLA-C05:01VSDDSGIIY0.96280.8081120
RCCD1-BLMchr1591500954chr1591328150881HLA-C18:01VSDDSGIIY0.95090.56481120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:02VSDDSGIIY0.78590.83351120
RCCD1-BLMchr1591500954chr1591328150881HLA-B35:28VSDDSGIIY0.6680.64531120
RCCD1-BLMchr1591500954chr1591328150881HLA-B35:11VSDDSGIIY0.57570.64411120
RCCD1-BLMchr1591500954chr1591328150881HLA-B35:77VSDDSGIIY0.5360.57391120
RCCD1-BLMchr1591500954chr1591328150881HLA-B35:23VSDDSGIIY0.53370.5831120
RCCD1-BLMchr1591500954chr1591328150881HLA-B35:20VSDDSGIIY0.52620.6571120
RCCD1-BLMchr1591500954chr1591328150881HLA-C15:09VSDDSGIIY0.47340.78531120
RCCD1-BLMchr1591500954chr1591328150881HLA-C03:02VSDDSGIIY0.41660.87341120
RCCD1-BLMchr1591500954chr1591328150881HLA-C07:17VSDDSGIIY0.26110.86771120
RCCD1-BLMchr1591500954chr1591328150881HLA-C16:01VSDDSGIIY0.09660.891120
RCCD1-BLMchr1591500954chr1591328150881HLA-C16:02VSDDSGIIY0.04270.951120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:01VSDDSGIIY0.00760.85821120
RCCD1-BLMchr1591500954chr1591328150881HLA-C12:02VSDDSGIIY0.00320.86781120
RCCD1-BLMchr1591500954chr1591328150881HLA-C02:02VSDDSGIIY0.00160.88331120
RCCD1-BLMchr1591500954chr1591328150881HLA-C02:10VSDDSGIIY0.00160.88331120
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:02VSDDSGIIYCL10.90941122
RCCD1-BLMchr1591500954chr1591328150881HLA-C04:03VSDDSGIIYCL10.83081122
RCCD1-BLMchr1591500954chr1591328150881HLA-C05:01VSDDSGIIYCL10.8761122
RCCD1-BLMchr1591500954chr1591328150881HLA-C08:01VSDDSGIIYCL0.82740.92261122

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Potential FusionNeoAntigen Information of RCCD1-BLM 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 RCCD1-BLM

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
982DAAGQVFSWGGGRFRCCD1BLMchr1591500733chr1591326052759
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
10473WHSVCVSDDSGIIYRCCD1BLMchr1591500954chr1591328150881

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RCCD1-BLM

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-B14:023BVN982DAAGQVFSWGGGRF-7.9962-8.1096
HLA-B14:023BVN982DAAGQVFSWGGGRF-5.70842-6.74372
HLA-B52:013W39982DAAGQVFSWGGGRF-6.83737-6.95077
HLA-B52:013W39982DAAGQVFSWGGGRF-4.4836-5.5189
HLA-A11:014UQ2982DAAGQVFSWGGGRF-10.0067-10.1201
HLA-A11:014UQ2982DAAGQVFSWGGGRF-9.03915-10.0745
HLA-A24:025HGA982DAAGQVFSWGGGRF-6.56204-6.67544
HLA-A24:025HGA982DAAGQVFSWGGGRF-5.42271-6.45801
HLA-B44:053DX8982DAAGQVFSWGGGRF-7.85648-8.89178
HLA-B44:053DX8982DAAGQVFSWGGGRF-5.3978-5.5112
HLA-A02:016TDR982DAAGQVFSWGGGRF-3.37154-4.40684
HLA-B14:023BVN10473WHSVCVSDDSGIIY-7.9962-8.1096
HLA-B14:023BVN10473WHSVCVSDDSGIIY-5.70842-6.74372
HLA-B52:013W3910473WHSVCVSDDSGIIY-6.83737-6.95077
HLA-B52:013W3910473WHSVCVSDDSGIIY-4.4836-5.5189
HLA-A11:014UQ210473WHSVCVSDDSGIIY-10.0067-10.1201
HLA-A11:014UQ210473WHSVCVSDDSGIIY-9.03915-10.0745
HLA-A24:025HGA10473WHSVCVSDDSGIIY-6.56204-6.67544
HLA-A24:025HGA10473WHSVCVSDDSGIIY-5.42271-6.45801
HLA-B44:053DX810473WHSVCVSDDSGIIY-7.85648-8.89178
HLA-B44:053DX810473WHSVCVSDDSGIIY-5.3978-5.5112
HLA-B35:011A1N10473WHSVCVSDDSGIIY-6.27422-6.38762
HLA-A02:016TDR10473WHSVCVSDDSGIIY-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of RCCD1-BLM

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
RCCD1-BLMchr1591500733chr15913260521019QVFSWGGGRCGGGGGCAGGTTTAGCATGAGCTTTAA
RCCD1-BLMchr1591500733chr15913260521120VFSWGGGRFGGGCAGGTTTAGCATGAGCTTTAACAG
RCCD1-BLMchr1591500733chr15913260521220FSWGGGRFCAGGTTTAGCATGAGCTTTAACAG
RCCD1-BLMchr1591500733chr15913260521222FSWGGGRFSMCAGGTTTAGCATGAGCTTTAACAGACATAA
RCCD1-BLMchr1591500733chr1591326052415LLDAAGQVFSWCCAGGTGTTCTCCTGGGGCGGGGGCAGGTTTAG
RCCD1-BLMchr1591500733chr1591326052515LDAAGQVFSWGGTGTTCTCCTGGGGCGGGGGCAGGTTTAG
RCCD1-BLMchr1591500733chr1591326052615DAAGQVFSWGTTCTCCTGGGGCGGGGGCAGGTTTAG
RCCD1-BLMchr1591500733chr1591326052715AAGQVFSWCTCCTGGGGCGGGGGCAGGTTTAG
RCCD1-BLMchr1591500954chr15913281501119VSDDSGIITGAGTGATGATTCAGGGATAATTT
RCCD1-BLMchr1591500954chr15913281501120VSDDSGIIYTGAGTGATGATTCAGGGATAATTTACT
RCCD1-BLMchr1591500954chr15913281501122VSDDSGIIYCLTGAGTGATGATTCAGGGATAATTTACTGCCTCT

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 RCCD1-BLM

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
LUADRCCD1-BLMchr1591500733ENST00000394258chr1591326052ENST00000355112TCGA-38-4630-01A
LUADRCCD1-BLMchr1591500954ENST00000394258chr1591328150ENST00000355112TCGA-38-4630-01A

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Potential target of CAR-T therapy development for RCCD1-BLM

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 RCCD1-BLM

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 RCCD1-BLM

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