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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:KRR1-KCNC2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KRR1-KCNC2
FusionPDB ID: 43466
FusionGDB2.0 ID: 43466
HgeneTgene
Gene symbol

KRR1

KCNC2

Gene ID

11103

3747

Gene nameKRR1 small subunit processome component homologpotassium voltage-gated channel subfamily C member 2
SynonymsHRB2|RIP-1KV3.2
Cytomap

12q21.2

12q21.1

Type of geneprotein-codingprotein-coding
DescriptionKRR1 small subunit processome component homologHIV-1 Rev-binding protein 2HIV-1 rev binding protein 2KRR-R motif-containing protein 1KRR1, small subunit (SSU) processome component, homologRev interacting proteinrev-interacting protein 1potassium voltage-gated channel subfamily C member 2potassium channel, voltage gated Shaw related subfamily C, member 2potassium voltage-gated channel, Shaw-related subfamily, member 2shaw-like potassium channelvoltage-gated potassium channel Kv3.2
Modification date2020032720200313
UniProtAcc

Q13601

Main function of 5'-partner protein: FUNCTION: Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly (By similarity). {ECO:0000250}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000229214, ENST00000438169, 
ENST00000548243, ENST00000298972, 
ENST00000341669, ENST00000350228, 
ENST00000393288, ENST00000540018, 
ENST00000548513, ENST00000549446, 
ENST00000550433, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 4 X 2=3215 X 5 X 6=450
# samples 416
** MAII scorelog2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(16/450*10)=-1.49185309632967
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: KRR1 [Title/Abstract] AND KCNC2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: KRR1 [Title/Abstract] AND KCNC2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KRR1(75900562)-KCNC2(75445097), # samples:1
Anticipated loss of major functional domain due to fusion event.KRR1-KCNC2 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.
KRR1-KCNC2 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.
KRR1-KCNC2 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.
KRR1-KCNC2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:75900562/chr12:75445097)
- 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 KRR1 (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 KCNC2 (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)
ENST00000229214KRR1chr1275900562-ENST00000550433KCNC2chr1275445097-2640417181619533
ENST00000229214KRR1chr1275900562-ENST00000548513KCNC2chr1275445097-2735417181571517
ENST00000229214KRR1chr1275900562-ENST00000549446KCNC2chr1275445097-4674417181646542
ENST00000229214KRR1chr1275900562-ENST00000298972KCNC2chr1275445097-2696417181571517
ENST00000229214KRR1chr1275900562-ENST00000341669KCNC2chr1275445097-2601417181619533
ENST00000229214KRR1chr1275900562-ENST00000350228KCNC2chr1275445097-2530417181406462
ENST00000229214KRR1chr1275900562-ENST00000540018KCNC2chr1275445097-1626417181481487
ENST00000229214KRR1chr1275900562-ENST00000393288KCNC2chr1275445097-1967417181586522
ENST00000438169KRR1chr1275900562-ENST00000550433KCNC2chr1275445097-261639301595531
ENST00000438169KRR1chr1275900562-ENST00000548513KCNC2chr1275445097-271139301547515
ENST00000438169KRR1chr1275900562-ENST00000549446KCNC2chr1275445097-465039301622540
ENST00000438169KRR1chr1275900562-ENST00000298972KCNC2chr1275445097-267239301547515
ENST00000438169KRR1chr1275900562-ENST00000341669KCNC2chr1275445097-257739301595531
ENST00000438169KRR1chr1275900562-ENST00000350228KCNC2chr1275445097-250639301382460
ENST00000438169KRR1chr1275900562-ENST00000540018KCNC2chr1275445097-160239301457485
ENST00000438169KRR1chr1275900562-ENST00000393288KCNC2chr1275445097-194339301562520

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
ENST00000229214ENST00000550433KRR1chr1275900562-KCNC2chr1275445097-0.0002899170.99971
ENST00000229214ENST00000548513KRR1chr1275900562-KCNC2chr1275445097-0.0002665550.9997334
ENST00000229214ENST00000549446KRR1chr1275900562-KCNC2chr1275445097-0.0002601250.9997398
ENST00000229214ENST00000298972KRR1chr1275900562-KCNC2chr1275445097-0.0002695240.9997304
ENST00000229214ENST00000341669KRR1chr1275900562-KCNC2chr1275445097-0.0002949380.999705
ENST00000229214ENST00000350228KRR1chr1275900562-KCNC2chr1275445097-0.0002828870.99971706
ENST00000229214ENST00000540018KRR1chr1275900562-KCNC2chr1275445097-0.0006887180.9993113
ENST00000229214ENST00000393288KRR1chr1275900562-KCNC2chr1275445097-0.0004081730.9995919
ENST00000438169ENST00000550433KRR1chr1275900562-KCNC2chr1275445097-0.0002710780.99972886
ENST00000438169ENST00000548513KRR1chr1275900562-KCNC2chr1275445097-0.0002494470.99975055
ENST00000438169ENST00000549446KRR1chr1275900562-KCNC2chr1275445097-0.0002483060.99975175
ENST00000438169ENST00000298972KRR1chr1275900562-KCNC2chr1275445097-0.0002521790.9997478
ENST00000438169ENST00000341669KRR1chr1275900562-KCNC2chr1275445097-0.0002746060.9997254
ENST00000438169ENST00000350228KRR1chr1275900562-KCNC2chr1275445097-0.0002647740.9997352
ENST00000438169ENST00000540018KRR1chr1275900562-KCNC2chr1275445097-0.0005850520.9994149
ENST00000438169ENST00000393288KRR1chr1275900562-KCNC2chr1275445097-0.0003639750.99963605

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 KRR1-KCNC2

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

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Potential FusionNeoAntigen Information of KRR1-KCNC2 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of KRR1-KCNC2 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 KRR1-KCNC2

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KRR1-KCNC2

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score

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Vaccine Design for the FusionNeoAntigens of KRR1-KCNC2

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

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

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Information of the samples that have these potential fusion neoantigens of KRR1-KCNC2

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample

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Potential target of CAR-T therapy development for KRR1-KCNC2

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
TgeneKCNC2chr12:75900562chr12:75445097ENST0000029897216230_2500599.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000029897216284_3030599.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000029897216314_3340599.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000029897216346_3680599.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000029897216382_4020599.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000029897216453_4730599.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNC2chr12:75900562chr12:75445097ENST0000034166915230_2500630.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000034166915284_3030630.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000034166915314_3340630.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000034166915346_3680630.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000034166915382_4020630.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000034166915453_4730630.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNC2chr12:75900562chr12:75445097ENST0000035022815230_2500543.6666666666666TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000035022815284_3030543.6666666666666TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000035022815314_3340543.6666666666666TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000035022815346_3680543.6666666666666TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000035022815382_4020543.6666666666666TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000035022815453_4730543.6666666666666TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNC2chr12:75900562chr12:75445097ENST0000039328815230_2500619.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000039328815284_3030619.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000039328815314_3340619.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000039328815346_3680619.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000039328815382_4020619.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000039328815453_4730619.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054001814230_2500584.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054001814284_3030584.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054001814314_3340584.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054001814346_3680584.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054001814382_4020584.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054001814453_4730584.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054851305230_2500477.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054851305284_3030477.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054851305314_3340477.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054851305346_3680477.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054851305382_4020477.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054851305453_4730477.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054944615230_2500639.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054944615284_3030639.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054944615314_3340639.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054944615346_3680639.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054944615382_4020639.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000054944615453_4730639.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNC2chr12:75900562chr12:75445097ENST0000055043304230_2500630.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNC2chr12:75900562chr12:75445097ENST0000055043304284_3030630.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNC2chr12:75900562chr12:75445097ENST0000055043304314_3340630.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNC2chr12:75900562chr12:75445097ENST0000055043304346_3680630.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNC2chr12:75900562chr12:75445097ENST0000055043304382_4020630.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNC2chr12:75900562chr12:75445097ENST0000055043304453_4730630.0TransmembraneHelical%3B Name%3DSegment S6

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 KRR1-KCNC2

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 KRR1-KCNC2

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