FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

leaf

Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

leaf

Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

leaf

Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:ROBO1-HMCN1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ROBO1-HMCN1
FusionPDB ID: 75256
FusionGDB2.0 ID: 75256
HgeneTgene
Gene symbol

ROBO1

HMCN1

Gene ID

6091

83872

Gene nameroundabout guidance receptor 1hemicentin 1
SynonymsDUTT1|SAX3ARMD1|FBLN6|FIBL-6|FIBL6
Cytomap

3p12.3

1q25.3-q31.1

Type of geneprotein-codingprotein-coding
Descriptionroundabout homolog 1deleted in U twenty twentyroundabout, axon guidance receptor, homolog 1hemicentin-1LOC100507250/HMCN1 fusionfibulin-6
Modification date2020031320200313
UniProtAcc.

Q96RW7

Main function of 5'-partner protein: FUNCTION: Promotes cleavage furrow maturation during cytokinesis in preimplantation embryos. May play a role in the architecture of adhesive and flexible epithelial cell junctions. May play a role during myocardial remodeling by imparting an effect on cardiac fibroblast migration. {ECO:0000250|UniProtKB:D3YXG0}.
Ensembl transtripts involved in fusion geneENST idsENST00000436010, ENST00000464233, 
ENST00000467549, ENST00000495273, 
ENST00000466906, 
ENST00000485744, 
ENST00000271588, ENST00000367492, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 16 X 7=201611 X 10 X 5=550
# samples 1812
** MAII scorelog2(18/2016*10)=-3.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/550*10)=-2.1963972128035
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ROBO1 [Title/Abstract] AND HMCN1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ROBO1 [Title/Abstract] AND HMCN1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ROBO1(78987751)-HMCN1(185966561), # samples:2
Anticipated loss of major functional domain due to fusion event.ROBO1-HMCN1 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.
ROBO1-HMCN1 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.
ROBO1-HMCN1 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.
ROBO1-HMCN1 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.
ROBO1-HMCN1 seems lost the major protein functional domain in Hgene 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
HgeneROBO1

GO:0007156

homophilic cell adhesion via plasma membrane adhesion molecules

12504588

HgeneROBO1

GO:0021836

chemorepulsion involved in postnatal olfactory bulb interneuron migration

15207848

HgeneROBO1

GO:0050772

positive regulation of axonogenesis

12504588

HgeneROBO1

GO:0050925

negative regulation of negative chemotaxis

11748139



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/chr3:78987751/chr1:185966561)
- 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 ROBO1 (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 HMCN1 (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)
ENST00000436010ROBO1chr378987751-ENST00000271588HMCN1chr1185966561+155811380998145094503
ENST00000436010ROBO1chr378987751-ENST00000367492HMCN1chr1185966561+152341380998141584386
ENST00000495273ROBO1chr378987751-ENST00000271588HMCN1chr1185966561+15137936554140654503
ENST00000495273ROBO1chr378987751-ENST00000367492HMCN1chr1185966561+14790936554137144386
ENST00000467549ROBO1chr378987751-ENST00000271588HMCN1chr1185966561+1466646583135944503
ENST00000467549ROBO1chr378987751-ENST00000367492HMCN1chr1185966561+1431946583132434386

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
ENST00000436010ENST00000271588ROBO1chr378987751-HMCN1chr1185966561+0.000589280.99941075
ENST00000436010ENST00000367492ROBO1chr378987751-HMCN1chr1185966561+0.0015178180.99848217
ENST00000495273ENST00000271588ROBO1chr378987751-HMCN1chr1185966561+0.0003530450.9996469
ENST00000495273ENST00000367492ROBO1chr378987751-HMCN1chr1185966561+0.0008658360.99913424
ENST00000467549ENST00000271588ROBO1chr378987751-HMCN1chr1185966561+0.0002023060.99979776
ENST00000467549ENST00000367492ROBO1chr378987751-HMCN1chr1185966561+0.0004917430.99950826

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

Top

Fusion Protein Breakpoint Sequences for ROBO1-HMCN1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ROBO1chr378987751HMCN1chr118596656113801134LQISIAEKSDAALYSCVASNVAGTAK
ROBO1chr378987751HMCN1chr11859665611380128EAVSHNASLEVAKPPTVEDLEPPYNT
ROBO1chr378987751HMCN1chr118596656113801606NGHTLQIKEAQISDTGRYTCVASNIA
ROBO1chr378987751HMCN1chr11859665611380740WLKDDQPVNTAQGNLKIQSSGRVLQI
ROBO1chr378987751HMCN1chr11859665611380852RGQIIDIESAQISDAGIYKCVAINSA
ROBO1chr378987751HMCN1chr11859665614651134LQISIAEKSDAALYSCVASNVAGTAK
ROBO1chr378987751HMCN1chr1185966561465128EAVSHNASLEVAKPPTVEDLEPPYNT
ROBO1chr378987751HMCN1chr11859665614651606NGHTLQIKEAQISDTGRYTCVASNIA
ROBO1chr378987751HMCN1chr1185966561465740WLKDDQPVNTAQGNLKIQSSGRVLQI
ROBO1chr378987751HMCN1chr1185966561465852RGQIIDIESAQISDAGIYKCVAINSA
ROBO1chr378987751HMCN1chr11859665619361134LQISIAEKSDAALYSCVASNVAGTAK
ROBO1chr378987751HMCN1chr1185966561936128EAVSHNASLEVAKPPTVEDLEPPYNT
ROBO1chr378987751HMCN1chr11859665619361606NGHTLQIKEAQISDTGRYTCVASNIA
ROBO1chr378987751HMCN1chr1185966561936740WLKDDQPVNTAQGNLKIQSSGRVLQI
ROBO1chr378987751HMCN1chr1185966561936852RGQIIDIESAQISDAGIYKCVAINSA

Top

Potential FusionNeoAntigen Information of ROBO1-HMCN1 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.
ROBO1-HMCN1_78987751_185966561.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)
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:03AEKSDAALY0.99860.7995514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B18:01AEKSDAALY0.94350.5282514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B45:01AEKSDAALY0.59540.6168514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:03IAEKSDAALY0.73230.7851414
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:03SIAEKSDAALY0.81150.7376314
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:26AEKSDAALY0.99860.7995514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:07AEKSDAALY0.99860.7995514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:13AEKSDAALY0.99860.7995514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B18:04AEKSDAALY0.97280.5473514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B15:135AEKSDAALY0.95720.5342514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B18:05AEKSDAALY0.94350.5282514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B18:06AEKSDAALY0.93580.5316514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B15:50AEKSDAALY0.90340.5743514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B18:03AEKSDAALY0.87440.5146514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B18:11AEKSDAALY0.80780.5371514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B15:12AEKSDAALY0.7930.5588514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B35:28AEKSDAALY0.59010.607514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B35:20AEKSDAALY0.56240.6326514
ROBO1-HMCN1chr378987751chr11859665611380HLA-B48:02AEKSDAALY0.0880.5835514
ROBO1-HMCN1chr378987751chr11859665611380HLA-A02:03ALYSCVASNV0.99930.6511121
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:07IAEKSDAALY0.73230.7851414
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:13IAEKSDAALY0.73230.7851414
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:26IAEKSDAALY0.73230.7851414
ROBO1-HMCN1chr378987751chr11859665611380HLA-B15:53SIAEKSDAALY0.99910.5392314
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:26SIAEKSDAALY0.81150.7376314
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:13SIAEKSDAALY0.81150.7376314
ROBO1-HMCN1chr378987751chr11859665611380HLA-B44:07SIAEKSDAALY0.81150.7376314

Top

Potential FusionNeoAntigen Information of ROBO1-HMCN1 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)

Top

Fusion breakpoint peptide structures of ROBO1-HMCN1

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
1866EKSDAALYSCVASNROBO1HMCN1chr378987751chr11859665611380

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ROBO1-HMCN1

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-B14:023BVN1866EKSDAALYSCVASN-7.9962-8.1096
HLA-B14:023BVN1866EKSDAALYSCVASN-5.70842-6.74372
HLA-B52:013W391866EKSDAALYSCVASN-6.83737-6.95077
HLA-B52:013W391866EKSDAALYSCVASN-4.4836-5.5189
HLA-A11:014UQ21866EKSDAALYSCVASN-10.0067-10.1201
HLA-A11:014UQ21866EKSDAALYSCVASN-9.03915-10.0745
HLA-A24:025HGA1866EKSDAALYSCVASN-6.56204-6.67544
HLA-A24:025HGA1866EKSDAALYSCVASN-5.42271-6.45801
HLA-B44:053DX81866EKSDAALYSCVASN-7.85648-8.89178
HLA-B44:053DX81866EKSDAALYSCVASN-5.3978-5.5112
HLA-A02:016TDR1866EKSDAALYSCVASN-3.37154-4.40684

Top

Vaccine Design for the FusionNeoAntigens of ROBO1-HMCN1

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
ROBO1-HMCN1chr378987751chr11859665611121ALYSCVASNVTAGCCAAACCACCCACAGTGGAAGATCTAG
ROBO1-HMCN1chr378987751chr1185966561314SIAEKSDAALYTGAGCCACAATGCATCGCTGGAAGTAGCCAAAC
ROBO1-HMCN1chr378987751chr1185966561414IAEKSDAALYGCCACAATGCATCGCTGGAAGTAGCCAAAC
ROBO1-HMCN1chr378987751chr1185966561514AEKSDAALYACAATGCATCGCTGGAAGTAGCCAAAC

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

Top

Information of the samples that have these potential fusion neoantigens of ROBO1-HMCN1

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
SKCMROBO1-HMCN1chr378987751ENST00000436010chr1185966561ENST00000271588TCGA-ER-A3EV-06A

Top

Potential target of CAR-T therapy development for ROBO1-HMCN1

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

Top

Related Drugs to ROBO1-HMCN1

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to ROBO1-HMCN1

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