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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:CDC6-CCR7

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CDC6-CCR7
FusionPDB ID: 14930
FusionGDB2.0 ID: 14930
HgeneTgene
Gene symbol

CDC6

CCR7

Gene ID

990

1236

Gene namecell division cycle 6C-C motif chemokine receptor 7
SynonymsCDC18L|HsCDC18|HsCDC6|MGORS5BLR2|CC-CKR-7|CCR-7|CD197|CDw197|CMKBR7|EBI1
Cytomap

17q21.2

17q21.2

Type of geneprotein-codingprotein-coding
Descriptioncell division control protein 6 homologCDC6 cell division cycle 6 homologCDC6-related proteincdc18-related proteincell division cycle 6 homologp62(cdc6)C-C chemokine receptor type 7Bukitt's lymphoma receptor 2CC chemokine receptor 7EBV-induced G protein-coupled receptor 1Epstein-Barr virus induced gene 1Epstein-Barr virus-induced G-protein coupled receptor 1MIP-3 beta receptorchemokine (C-C motif)
Modification date2020031320200322
UniProtAcc

Q99741

Main function of 5'-partner protein: FUNCTION: Involved in the initiation of DNA replication. Also participates in checkpoint controls that ensure DNA replication is completed before mitosis is initiated.		.
Ensembl transtripts involved in fusion geneENST idsENST00000209728, ENST00000579344, 
ENST00000246657, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 12 X 6=8647 X 2 X 7=98
# samples 129
** MAII scorelog2(12/864*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/98*10)=-0.122856747785533
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CDC6 [Title/Abstract] AND CCR7 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CDC6 [Title/Abstract] AND CCR7 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CDC6(38451708)-CCR7(38715194), # samples:2
Anticipated loss of major functional domain due to fusion event.CDC6-CCR7 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CDC6-CCR7 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CDC6-CCR7 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CDC6-CCR7 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgeneCDC6

GO:0051984

positive regulation of chromosome segregation

21041660

TgeneCCR7

GO:0002408

myeloid dendritic cell chemotaxis

11602640

TgeneCCR7

GO:0071345

cellular response to cytokine stimulus

11602640

TgeneCCR7

GO:0090023

positive regulation of neutrophil chemotaxis

21051556



check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:38451708/chr17:38715194)
- 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 CDC6 (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 CCR7 (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)
ENST00000209728CDC6chr1738453019+ENST00000246657CCR7chr1738715194-382017203632846827

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
ENST00000209728ENST00000246657CDC6chr1738453019+CCR7chr1738715194-0.0025087390.99749124

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 CDC6-CCR7

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CDC6chr1738453019CCR7chr17387151941720453VKSQTILKPLSEWKPMKSVLVVALLV

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Potential FusionNeoAntigen Information of CDC6-CCR7 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.
CDC6-CCR7_38453019_38715194.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)
CDC6-CCR7chr1738453019chr17387151941720HLA-B45:01SEWKPMKSV0.99870.92181019
CDC6-CCR7chr1738453019chr17387151941720HLA-B50:02SEWKPMKSV0.99850.73011019
CDC6-CCR7chr1738453019chr17387151941720HLA-B13:01SEWKPMKSV0.98740.90541019
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:03SEWKPMKSV0.9480.93371019
CDC6-CCR7chr1738453019chr17387151941720HLA-B41:01SEWKPMKSV0.77170.89891019
CDC6-CCR7chr1738453019chr17387151941720HLA-B08:01EWKPMKSVL0.7490.51351120
CDC6-CCR7chr1738453019chr17387151941720HLA-B18:01SEWKPMKSV0.69940.94971019
CDC6-CCR7chr1738453019chr17387151941720HLA-B50:01SEWKPMKSV0.37140.77761019
CDC6-CCR7chr1738453019chr17387151941720HLA-B39:13SEWKPMKSV0.12920.93271019
CDC6-CCR7chr1738453019chr17387151941720HLA-B52:01SEWKPMKSV0.01750.97321019
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:03SEWKPMKSVL0.94320.92681020
CDC6-CCR7chr1738453019chr17387151941720HLA-B47:01SEWKPMKSVL0.90870.53971020
CDC6-CCR7chr1738453019chr17387151941720HLA-B39:13SEWKPMKSVL0.80640.8611020
CDC6-CCR7chr1738453019chr17387151941720HLA-B40:06SEWKPMKSV0.99980.61321019
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:09SEWKPMKSV0.93940.50381019
CDC6-CCR7chr1738453019chr17387151941720HLA-B42:02KPLSEWKPM0.69290.6578716
CDC6-CCR7chr1738453019chr17387151941720HLA-B42:01KPLSEWKPM0.63540.6515716
CDC6-CCR7chr1738453019chr17387151941720HLA-B39:08SEWKPMKSV0.42290.91781019
CDC6-CCR7chr1738453019chr17387151941720HLA-B51:07SEWKPMKSV0.00730.89841019
CDC6-CCR7chr1738453019chr17387151941720HLA-B40:06SEWKPMKSVL0.99750.50181020
CDC6-CCR7chr1738453019chr17387151941720HLA-B39:08SEWKPMKSVL0.82760.83871020
CDC6-CCR7chr1738453019chr17387151941720HLA-B40:04SEWKPMKSV0.99860.71151019
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:26SEWKPMKSV0.9480.93371019
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:13SEWKPMKSV0.9480.93371019
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:07SEWKPMKSV0.9480.93371019
CDC6-CCR7chr1738453019chr17387151941720HLA-B41:03SEWKPMKSV0.86990.55761019
CDC6-CCR7chr1738453019chr17387151941720HLA-B08:18EWKPMKSVL0.7490.51351120
CDC6-CCR7chr1738453019chr17387151941720HLA-B18:08SEWKPMKSV0.71010.9381019
CDC6-CCR7chr1738453019chr17387151941720HLA-B18:05SEWKPMKSV0.69940.94971019
CDC6-CCR7chr1738453019chr17387151941720HLA-B67:01KPLSEWKPM0.67610.9107716
CDC6-CCR7chr1738453019chr17387151941720HLA-B18:06SEWKPMKSV0.65650.95291019
CDC6-CCR7chr1738453019chr17387151941720HLA-B18:03SEWKPMKSV0.63340.94551019
CDC6-CCR7chr1738453019chr17387151941720HLA-B18:11SEWKPMKSV0.56220.8831019
CDC6-CCR7chr1738453019chr17387151941720HLA-B08:12EWKPMKSVL0.54620.64351120
CDC6-CCR7chr1738453019chr17387151941720HLA-B50:05SEWKPMKSV0.37140.77761019
CDC6-CCR7chr1738453019chr17387151941720HLA-B50:04SEWKPMKSV0.37140.77761019
CDC6-CCR7chr1738453019chr17387151941720HLA-B39:02SEWKPMKSV0.11290.93371019
CDC6-CCR7chr1738453019chr17387151941720HLA-B40:04SEWKPMKSVL0.98670.62941020
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:26SEWKPMKSVL0.94320.92681020
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:13SEWKPMKSVL0.94320.92681020
CDC6-CCR7chr1738453019chr17387151941720HLA-B44:07SEWKPMKSVL0.94320.92681020
CDC6-CCR7chr1738453019chr17387151941720HLA-B39:02SEWKPMKSVL0.87730.86321020

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Potential FusionNeoAntigen Information of CDC6-CCR7 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.
CDC6-CCR7_38453019_38715194.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)
CDC6-CCR7chr1738453019chr17387151941720DRB1-0101PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0101LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0103PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0103LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0103SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-0105PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0105LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0107PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0107LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0109PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0109LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0111PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0111LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0111SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-0113PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0113LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0115PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0115LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0115SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-0117PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0117LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0117KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-0117SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-0119PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0119LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0121PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0121LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0125PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0125LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0127PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0127LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0129PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0129LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0129SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-0129KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-0131PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0131LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-0704PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0709PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0711PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0819PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0825PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-0834PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1216PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1216LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1222PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1222LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1511PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1515PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1527PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1527LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1527KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1527SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1531PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1534PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1534LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1601PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1601LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1601KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1601SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1602PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1602LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1602KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1602SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1603PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1603LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1603KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1603SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1604PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1604LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1604KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1604SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1605PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1605LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1605KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1605SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1607PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1607LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1607KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1607SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1608PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1608LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1608KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1608SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1609PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1609LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1609SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1609KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1610PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1610LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1610KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1610SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1611PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1611LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1611KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1611SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1612PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1612LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1612KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1612SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1614PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1614LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1614KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1614SEWKPMKSVLVVALL1025
CDC6-CCR7chr1738453019chr17387151941720DRB1-1616PLSEWKPMKSVLVVA823
CDC6-CCR7chr1738453019chr17387151941720DRB1-1616LSEWKPMKSVLVVAL924
CDC6-CCR7chr1738453019chr17387151941720DRB1-1616KPLSEWKPMKSVLVV722
CDC6-CCR7chr1738453019chr17387151941720DRB1-1616SEWKPMKSVLVVALL1025

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Fusion breakpoint peptide structures of CDC6-CCR7

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
5172LKPLSEWKPMKSVLCDC6CCR7chr1738453019chr17387151941720

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDC6-CCR7

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-B14:023BVN5172LKPLSEWKPMKSVL-7.9962-8.1096
HLA-B14:023BVN5172LKPLSEWKPMKSVL-5.70842-6.74372
HLA-B52:013W395172LKPLSEWKPMKSVL-6.83737-6.95077
HLA-B52:013W395172LKPLSEWKPMKSVL-4.4836-5.5189
HLA-A11:014UQ25172LKPLSEWKPMKSVL-10.0067-10.1201
HLA-A11:014UQ25172LKPLSEWKPMKSVL-9.03915-10.0745
HLA-A24:025HGA5172LKPLSEWKPMKSVL-6.56204-6.67544
HLA-A24:025HGA5172LKPLSEWKPMKSVL-5.42271-6.45801
HLA-B44:053DX85172LKPLSEWKPMKSVL-7.85648-8.89178
HLA-B44:053DX85172LKPLSEWKPMKSVL-5.3978-5.5112
HLA-A02:016TDR5172LKPLSEWKPMKSVL-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of CDC6-CCR7

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
CDC6-CCR7chr1738453019chr17387151941019SEWKPMKSVTGTCTGAATGGAAACCAATGAAAAGCG
CDC6-CCR7chr1738453019chr17387151941020SEWKPMKSVLTGTCTGAATGGAAACCAATGAAAAGCGTGC
CDC6-CCR7chr1738453019chr17387151941120EWKPMKSVLCTGAATGGAAACCAATGAAAAGCGTGC
CDC6-CCR7chr1738453019chr1738715194716KPLSEWKPMTCAAACCACTGTCTGAATGGAAACCAA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
CDC6-CCR7chr1738453019chr17387151941025SEWKPMKSVLVVALLTGTCTGAATGGAAACCAATGAAAAGCGTGCTGGTGGTGGCTCTCC
CDC6-CCR7chr1738453019chr1738715194722KPLSEWKPMKSVLVVTCAAACCACTGTCTGAATGGAAACCAATGAAAAGCGTGCTGGTGG
CDC6-CCR7chr1738453019chr1738715194823PLSEWKPMKSVLVVAAACCACTGTCTGAATGGAAACCAATGAAAAGCGTGCTGGTGGTGG
CDC6-CCR7chr1738453019chr1738715194924LSEWKPMKSVLVVALCACTGTCTGAATGGAAACCAATGAAAAGCGTGCTGGTGGTGGCTC

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Information of the samples that have these potential fusion neoantigens of CDC6-CCR7

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
STADCDC6-CCR7chr1738453019ENST00000209728chr1738715194ENST00000246657TCGA-EQ-8122-01A

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Potential target of CAR-T therapy development for CDC6-CCR7

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
TgeneCCR7chr17:38453019chr17:38715194ENST0000024665703131_1520379.0TransmembraneHelical%3B Name%3D3
TgeneCCR7chr17:38453019chr17:38715194ENST0000024665703171_1910379.0TransmembraneHelical%3B Name%3D4
TgeneCCR7chr17:38453019chr17:38715194ENST0000024665703220_2470379.0TransmembraneHelical%3B Name%3D5
TgeneCCR7chr17:38453019chr17:38715194ENST0000024665703264_2890379.0TransmembraneHelical%3B Name%3D6
TgeneCCR7chr17:38453019chr17:38715194ENST0000024665703314_3310379.0TransmembraneHelical%3B Name%3D7
TgeneCCR7chr17:38453019chr17:38715194ENST000002466570360_860379.0TransmembraneHelical%3B Name%3D1
TgeneCCR7chr17:38453019chr17:38715194ENST000002466570396_1160379.0TransmembraneHelical%3B Name%3D2

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 CDC6-CCR7

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 CDC6-CCR7

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