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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:CDK14-PUM2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CDK14-PUM2
FusionPDB ID: 15181
FusionGDB2.0 ID: 15181
HgeneTgene
Gene symbol

CDK14

PUM2

Gene ID

5218

23369

Gene namecyclin dependent kinase 14pumilio RNA binding family member 2
SynonymsPFTAIRE1|PFTK1PUMH2|PUML2
Cytomap

7q21.13

2p24.1

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase 14PFTAIRE protein kinase 1cell division protein kinase 14serine/threonine-protein kinase PFTAIRE-1pumilio homolog 2pumilio-2
Modification date2020031320200313
UniProtAcc

O94921

Main function of 5'-partner protein: FUNCTION: Serine/threonine-protein kinase involved in the control of the eukaryotic cell cycle, whose activity is controlled by an associated cyclin. Acts as a cell-cycle regulator of Wnt signaling pathway during G2/M phase by mediating the phosphorylation of LRP6 at 'Ser-1490', leading to the activation of the Wnt signaling pathway. Acts as a regulator of cell cycle progression and cell proliferation via its interaction with CCDN3. Phosphorylates RB1 in vitro, however the relevance of such result remains to be confirmed in vivo. May also play a role in meiosis, neuron differentiation and may indirectly act as a negative regulator of insulin-responsive glucose transport. {ECO:0000269|PubMed:16461467, ECO:0000269|PubMed:17517622, ECO:0000269|PubMed:19524571, ECO:0000269|PubMed:20059949}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000265741, ENST00000380050, 
ENST00000406263, ENST00000436577, 
ENST00000496279, 
ENST00000420234, 
ENST00000319801, ENST00000338086, 
ENST00000361078, ENST00000403432, 
ENST00000536417, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 13 X 8=176811 X 9 X 5=495
# samples 1813
** MAII scorelog2(18/1768*10)=-3.29604946306176
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/495*10)=-1.92891690193852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CDK14 [Title/Abstract] AND PUM2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CDK14 [Title/Abstract] AND PUM2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CDK14(90547039)-PUM2(20483247), # samples:1
Anticipated loss of major functional domain due to fusion event.CDK14-PUM2 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.
CDK14-PUM2 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.
CDK14-PUM2 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.
CDK14-PUM2 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
HgeneCDK14

GO:0000086

G2/M transition of mitotic cell cycle

20059949

HgeneCDK14

GO:0060828

regulation of canonical Wnt signaling pathway

20059949

TgenePUM2

GO:0010608

posttranscriptional regulation of gene expression

25100735

TgenePUM2

GO:0043488

regulation of mRNA stability

26724866

TgenePUM2

GO:0051983

regulation of chromosome segregation

26724866

TgenePUM2

GO:1900246

positive regulation of RIG-I signaling pathway

25340845



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/chr7:90547039/chr2:20483247)
- 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 CDK14 (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 PUM2 (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)
ENST00000380050CDK14chr790547039+ENST00000338086PUM2chr220483247-5755957772860927
ENST00000380050CDK14chr790547039+ENST00000319801PUM2chr220483247-5523957772629850
ENST00000380050CDK14chr790547039+ENST00000361078PUM2chr220483247-5760957772866929
ENST00000380050CDK14chr790547039+ENST00000536417PUM2chr220483247-3136957772860927
ENST00000380050CDK14chr790547039+ENST00000403432PUM2chr220483247-3136957772860927
ENST00000265741CDK14chr790547039+ENST00000338086PUM2chr220483247-57149161442819891
ENST00000265741CDK14chr790547039+ENST00000319801PUM2chr220483247-54829161442588814
ENST00000265741CDK14chr790547039+ENST00000361078PUM2chr220483247-57199161442825893
ENST00000265741CDK14chr790547039+ENST00000536417PUM2chr220483247-30959161442819891
ENST00000265741CDK14chr790547039+ENST00000403432PUM2chr220483247-30959161442819891
ENST00000406263CDK14chr790547039+ENST00000338086PUM2chr220483247-592811304423033863
ENST00000406263CDK14chr790547039+ENST00000319801PUM2chr220483247-569611304422802786
ENST00000406263CDK14chr790547039+ENST00000361078PUM2chr220483247-593311304423039865
ENST00000406263CDK14chr790547039+ENST00000536417PUM2chr220483247-330911304423033863
ENST00000406263CDK14chr790547039+ENST00000403432PUM2chr220483247-330911304423033863
ENST00000436577CDK14chr790547039+ENST00000338086PUM2chr220483247-55027042562607783
ENST00000436577CDK14chr790547039+ENST00000319801PUM2chr220483247-52707042562376706
ENST00000436577CDK14chr790547039+ENST00000361078PUM2chr220483247-55077042562613785
ENST00000436577CDK14chr790547039+ENST00000536417PUM2chr220483247-28837042562607783
ENST00000436577CDK14chr790547039+ENST00000403432PUM2chr220483247-28837042562607783

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
ENST00000380050ENST00000338086CDK14chr790547039+PUM2chr220483247-0.0002312250.9997688
ENST00000380050ENST00000319801CDK14chr790547039+PUM2chr220483247-0.0002714820.9997285
ENST00000380050ENST00000361078CDK14chr790547039+PUM2chr220483247-0.0001934220.9998066
ENST00000380050ENST00000536417CDK14chr790547039+PUM2chr220483247-0.0038054560.9961946
ENST00000380050ENST00000403432CDK14chr790547039+PUM2chr220483247-0.0038054560.9961946
ENST00000265741ENST00000338086CDK14chr790547039+PUM2chr220483247-0.000133440.9998665
ENST00000265741ENST00000319801CDK14chr790547039+PUM2chr220483247-0.0001493350.99985063
ENST00000265741ENST00000361078CDK14chr790547039+PUM2chr220483247-0.0001261450.9998739
ENST00000265741ENST00000536417CDK14chr790547039+PUM2chr220483247-0.0026559350.9973441
ENST00000265741ENST00000403432CDK14chr790547039+PUM2chr220483247-0.0026559350.9973441
ENST00000406263ENST00000338086CDK14chr790547039+PUM2chr220483247-0.0001507370.9998492
ENST00000406263ENST00000319801CDK14chr790547039+PUM2chr220483247-0.0001111560.9998888
ENST00000406263ENST00000361078CDK14chr790547039+PUM2chr220483247-0.000126740.9998733
ENST00000406263ENST00000536417CDK14chr790547039+PUM2chr220483247-0.0021955170.99780446
ENST00000406263ENST00000403432CDK14chr790547039+PUM2chr220483247-0.0021955170.99780446
ENST00000436577ENST00000338086CDK14chr790547039+PUM2chr220483247-0.0007775060.9992225
ENST00000436577ENST00000319801CDK14chr790547039+PUM2chr220483247-0.0005914580.9994086
ENST00000436577ENST00000361078CDK14chr790547039+PUM2chr220483247-0.0006576030.9993424
ENST00000436577ENST00000536417CDK14chr790547039+PUM2chr220483247-0.0098503680.9901496
ENST00000436577ENST00000403432CDK14chr790547039+PUM2chr220483247-0.0098503680.9901496

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 CDK14-PUM2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CDK14chr790547039PUM2chr2204832471130229LISDTGELKLADFGYQVLAPTAYYDQ
CDK14chr790547039PUM2chr220483247704149LISDTGELKLADFGYQVLAPTAYYDQ
CDK14chr790547039PUM2chr220483247916257LISDTGELKLADFGYQVLAPTAYYDQ
CDK14chr790547039PUM2chr220483247957293LISDTGELKLADFGYQVLAPTAYYDQ

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Potential FusionNeoAntigen Information of CDK14-PUM2 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.
CDK14-PUM2_90547039_20483247.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)
CDK14-PUM2chr790547039chr220483247916HLA-A02:22KLADFGYQV0.99950.6882817
CDK14-PUM2chr790547039chr220483247916HLA-A02:60KLADFGYQV0.99940.7261817
CDK14-PUM2chr790547039chr220483247916HLA-A02:67KLADFGYQV0.99940.7521817
CDK14-PUM2chr790547039chr220483247916HLA-A02:11KLADFGYQV0.99940.7914817
CDK14-PUM2chr790547039chr220483247916HLA-A02:30KLADFGYQV0.99940.7521817
CDK14-PUM2chr790547039chr220483247916HLA-A02:24KLADFGYQV0.99940.7521817
CDK14-PUM2chr790547039chr220483247916HLA-A02:21KLADFGYQV0.99930.8358817
CDK14-PUM2chr790547039chr220483247916HLA-A02:16KLADFGYQV0.99930.753817
CDK14-PUM2chr790547039chr220483247916HLA-A02:27KLADFGYQV0.99920.736817
CDK14-PUM2chr790547039chr220483247916HLA-A02:38KLADFGYQV0.9990.717817
CDK14-PUM2chr790547039chr220483247916HLA-A02:13KLADFGYQV0.9990.8028817
CDK14-PUM2chr790547039chr220483247916HLA-A02:19KLADFGYQV0.99840.5016817
CDK14-PUM2chr790547039chr220483247916HLA-A02:04KLADFGYQV0.99580.9331817
CDK14-PUM2chr790547039chr220483247916HLA-A02:17KLADFGYQV0.99510.8376817
CDK14-PUM2chr790547039chr220483247916HLA-A02:35KLADFGYQV0.99370.7796817
CDK14-PUM2chr790547039chr220483247916HLA-A02:29KLADFGYQV0.9910.7577817
CDK14-PUM2chr790547039chr220483247916HLA-A02:20KLADFGYQV0.98010.7592817
CDK14-PUM2chr790547039chr220483247916HLA-B35:03LADFGYQVL0.96350.9743918
CDK14-PUM2chr790547039chr220483247916HLA-B45:01ADFGYQVLA0.92480.88091019
CDK14-PUM2chr790547039chr220483247916HLA-B50:02ADFGYQVLA0.88760.83281019
CDK14-PUM2chr790547039chr220483247916HLA-B15:02ELKLADFGY0.8780.8375615
CDK14-PUM2chr790547039chr220483247916HLA-B35:04LADFGYQVL0.85060.9882918
CDK14-PUM2chr790547039chr220483247916HLA-B35:02LADFGYQVL0.85060.9882918
CDK14-PUM2chr790547039chr220483247916HLA-B50:01ADFGYQVLA0.60910.95681019
CDK14-PUM2chr790547039chr220483247916HLA-A32:13KLADFGYQV0.58510.9747817
CDK14-PUM2chr790547039chr220483247916HLA-B41:01ADFGYQVLA0.51740.95011019
CDK14-PUM2chr790547039chr220483247916HLA-B13:02KLADFGYQV0.30660.9953817
CDK14-PUM2chr790547039chr220483247916HLA-B13:01KLADFGYQV0.2760.9984817
CDK14-PUM2chr790547039chr220483247916HLA-A02:22KLADFGYQVL0.99880.6441818
CDK14-PUM2chr790547039chr220483247916HLA-B44:03GELKLADFGY0.99830.9407515
CDK14-PUM2chr790547039chr220483247916HLA-A02:13KLADFGYQVL0.99820.8247818
CDK14-PUM2chr790547039chr220483247916HLA-A02:24KLADFGYQVL0.99760.7249818
CDK14-PUM2chr790547039chr220483247916HLA-A02:67KLADFGYQVL0.99760.7249818
CDK14-PUM2chr790547039chr220483247916HLA-A02:30KLADFGYQVL0.99760.7249818
CDK14-PUM2chr790547039chr220483247916HLA-A02:11KLADFGYQVL0.99760.7578818
CDK14-PUM2chr790547039chr220483247916HLA-A02:60KLADFGYQVL0.99750.7128818
CDK14-PUM2chr790547039chr220483247916HLA-A02:04KLADFGYQVL0.99730.8779818
CDK14-PUM2chr790547039chr220483247916HLA-A02:17KLADFGYQVL0.99720.7683818
CDK14-PUM2chr790547039chr220483247916HLA-A02:27KLADFGYQVL0.99710.7384818
CDK14-PUM2chr790547039chr220483247916HLA-A02:16KLADFGYQVL0.99630.6507818
CDK14-PUM2chr790547039chr220483247916HLA-A02:38KLADFGYQVL0.99240.7592818
CDK14-PUM2chr790547039chr220483247916HLA-A02:35KLADFGYQVL0.95520.7492818
CDK14-PUM2chr790547039chr220483247916HLA-A02:22LKLADFGYQV0.88960.6428717
CDK14-PUM2chr790547039chr220483247916HLA-A02:29KLADFGYQVL0.88040.7305818
CDK14-PUM2chr790547039chr220483247916HLA-A02:20KLADFGYQVL0.86010.7309818
CDK14-PUM2chr790547039chr220483247916HLA-A02:60LKLADFGYQV0.85090.6429717
CDK14-PUM2chr790547039chr220483247916HLA-A02:16LKLADFGYQV0.84890.6923717
CDK14-PUM2chr790547039chr220483247916HLA-A02:30LKLADFGYQV0.84760.6335717
CDK14-PUM2chr790547039chr220483247916HLA-A02:67LKLADFGYQV0.84760.6335717
CDK14-PUM2chr790547039chr220483247916HLA-A02:24LKLADFGYQV0.84760.6335717
CDK14-PUM2chr790547039chr220483247916HLA-A02:11LKLADFGYQV0.81030.6586717
CDK14-PUM2chr790547039chr220483247916HLA-A02:35LKLADFGYQV0.73120.6495717
CDK14-PUM2chr790547039chr220483247916HLA-A02:29LKLADFGYQV0.70930.638717
CDK14-PUM2chr790547039chr220483247916HLA-A02:20LKLADFGYQV0.70820.6437717
CDK14-PUM2chr790547039chr220483247916HLA-A02:27LKLADFGYQV0.65570.6894717
CDK14-PUM2chr790547039chr220483247916HLA-A02:19LKLADFGYQV0.64280.6452717
CDK14-PUM2chr790547039chr220483247916HLA-A02:22KLADFGYQVLA0.99850.6587819
CDK14-PUM2chr790547039chr220483247916HLA-A02:24KLADFGYQVLA0.99830.698819
CDK14-PUM2chr790547039chr220483247916HLA-A02:67KLADFGYQVLA0.99830.698819
CDK14-PUM2chr790547039chr220483247916HLA-A02:30KLADFGYQVLA0.99830.698819
CDK14-PUM2chr790547039chr220483247916HLA-A02:60KLADFGYQVLA0.99830.6973819
CDK14-PUM2chr790547039chr220483247916HLA-B15:01FGYQVLAPTAY0.99680.95261223
CDK14-PUM2chr790547039chr220483247916HLA-B15:25FGYQVLAPTAY0.98480.94791223
CDK14-PUM2chr790547039chr220483247916HLA-B15:02FGYQVLAPTAY0.97130.95171223
CDK14-PUM2chr790547039chr220483247916HLA-B46:01FGYQVLAPTAY0.95760.77611223
CDK14-PUM2chr790547039chr220483247916HLA-A02:29KLADFGYQVLA0.83640.7028819
CDK14-PUM2chr790547039chr220483247916HLA-A02:20KLADFGYQVLA0.82440.7057819
CDK14-PUM2chr790547039chr220483247916HLA-C05:09LADFGYQV10.9948917
CDK14-PUM2chr790547039chr220483247916HLA-C08:15ADFGYQVL0.99990.99441018
CDK14-PUM2chr790547039chr220483247916HLA-C08:15LADFGYQV0.99980.9967917
CDK14-PUM2chr790547039chr220483247916HLA-C08:13LADFGYQV0.96190.9981917
CDK14-PUM2chr790547039chr220483247916HLA-C08:04LADFGYQV0.96190.9981917
CDK14-PUM2chr790547039chr220483247916HLA-C08:03LADFGYQV0.94220.9984917
CDK14-PUM2chr790547039chr220483247916HLA-C04:10LADFGYQVL0.99990.9768918
CDK14-PUM2chr790547039chr220483247916HLA-C04:07LADFGYQVL0.99990.9738918
CDK14-PUM2chr790547039chr220483247916HLA-C08:15LADFGYQVL0.99990.9955918
CDK14-PUM2chr790547039chr220483247916HLA-C05:09LADFGYQVL0.99990.9941918
CDK14-PUM2chr790547039chr220483247916HLA-C01:17LADFGYQVL0.99970.9799918
CDK14-PUM2chr790547039chr220483247916HLA-A02:02KLADFGYQV0.99950.6245817
CDK14-PUM2chr790547039chr220483247916HLA-A02:05KLADFGYQV0.99940.7068817
CDK14-PUM2chr790547039chr220483247916HLA-C03:07LADFGYQVL0.99940.9939918
CDK14-PUM2chr790547039chr220483247916HLA-A02:01KLADFGYQV0.99940.7521817
CDK14-PUM2chr790547039chr220483247916HLA-A02:07KLADFGYQV0.99940.7804817
CDK14-PUM2chr790547039chr220483247916HLA-C03:19LADFGYQVL0.99940.9969918
CDK14-PUM2chr790547039chr220483247916HLA-C03:08LADFGYQVL0.99880.9767918
CDK14-PUM2chr790547039chr220483247916HLA-C05:09KLADFGYQV0.99790.9925817
CDK14-PUM2chr790547039chr220483247916HLA-C01:30LADFGYQVL0.99640.9796918
CDK14-PUM2chr790547039chr220483247916HLA-C15:06LADFGYQVL0.99610.985918
CDK14-PUM2chr790547039chr220483247916HLA-C04:06LADFGYQVL0.98730.9899918
CDK14-PUM2chr790547039chr220483247916HLA-C08:13LADFGYQVL0.98290.997918
CDK14-PUM2chr790547039chr220483247916HLA-C08:04LADFGYQVL0.98290.997918
CDK14-PUM2chr790547039chr220483247916HLA-C04:06KLADFGYQV0.97270.9819817
CDK14-PUM2chr790547039chr220483247916HLA-B40:06ADFGYQVLA0.94870.9581019
CDK14-PUM2chr790547039chr220483247916HLA-C08:03LADFGYQVL0.92920.9976918
CDK14-PUM2chr790547039chr220483247916HLA-C03:14LADFGYQVL0.92810.994918
CDK14-PUM2chr790547039chr220483247916HLA-C04:14LADFGYQVL0.92460.978918
CDK14-PUM2chr790547039chr220483247916HLA-C04:14KLADFGYQV0.86560.9616817
CDK14-PUM2chr790547039chr220483247916HLA-B35:12LADFGYQVL0.85060.9882918
CDK14-PUM2chr790547039chr220483247916HLA-C02:06LADFGYQVL0.78180.993918
CDK14-PUM2chr790547039chr220483247916HLA-B15:31ELKLADFGY0.76160.7068615
CDK14-PUM2chr790547039chr220483247916HLA-C02:06KLADFGYQV0.66220.9939817
CDK14-PUM2chr790547039chr220483247916HLA-C05:09KLADFGYQVL0.99970.9864818
CDK14-PUM2chr790547039chr220483247916HLA-A02:05KLADFGYQVL0.99830.5924818
CDK14-PUM2chr790547039chr220483247916HLA-C08:15KLADFGYQVL0.99820.9894818
CDK14-PUM2chr790547039chr220483247916HLA-A02:07KLADFGYQVL0.99780.7439818
CDK14-PUM2chr790547039chr220483247916HLA-A02:01KLADFGYQVL0.99760.7249818
CDK14-PUM2chr790547039chr220483247916HLA-A02:02LKLADFGYQV0.88910.5857717
CDK14-PUM2chr790547039chr220483247916HLA-A02:01LKLADFGYQV0.84760.6335717
CDK14-PUM2chr790547039chr220483247916HLA-A02:01KLADFGYQVLA0.99830.698819
CDK14-PUM2chr790547039chr220483247916HLA-B15:07FGYQVLAPTAY0.99350.84611223
CDK14-PUM2chr790547039chr220483247916HLA-B15:05FGYQVLAPTAY0.94630.88311223
CDK14-PUM2chr790547039chr220483247916HLA-B15:31FGYQVLAPTAY0.92830.89191223
CDK14-PUM2chr790547039chr220483247916HLA-C05:01LADFGYQV10.9948917
CDK14-PUM2chr790547039chr220483247916HLA-C04:03LADFGYQV10.9809917
CDK14-PUM2chr790547039chr220483247916HLA-C08:02ADFGYQVL0.99990.99441018
CDK14-PUM2chr790547039chr220483247916HLA-C08:02LADFGYQV0.99980.9967917
CDK14-PUM2chr790547039chr220483247916HLA-C08:01LADFGYQV0.94220.9984917
CDK14-PUM2chr790547039chr220483247916HLA-C01:03LADFGYQVL0.99990.9662918
CDK14-PUM2chr790547039chr220483247916HLA-C04:03LADFGYQVL0.99990.9785918
CDK14-PUM2chr790547039chr220483247916HLA-C08:02LADFGYQVL0.99990.9955918
CDK14-PUM2chr790547039chr220483247916HLA-C04:01LADFGYQVL0.99990.9738918
CDK14-PUM2chr790547039chr220483247916HLA-C05:01LADFGYQVL0.99990.9941918
CDK14-PUM2chr790547039chr220483247916HLA-C18:01LADFGYQVL0.99990.9793918
CDK14-PUM2chr790547039chr220483247916HLA-C01:02LADFGYQVL0.99970.9798918
CDK14-PUM2chr790547039chr220483247916HLA-C03:04LADFGYQVL0.99940.9959918
CDK14-PUM2chr790547039chr220483247916HLA-C03:03LADFGYQVL0.99940.9959918
CDK14-PUM2chr790547039chr220483247916HLA-A02:14KLADFGYQV0.99930.8241817
CDK14-PUM2chr790547039chr220483247916HLA-A02:06KLADFGYQV0.99930.8358817
CDK14-PUM2chr790547039chr220483247916HLA-A02:03KLADFGYQV0.99920.8173817
CDK14-PUM2chr790547039chr220483247916HLA-C03:17LADFGYQVL0.99880.9897918
CDK14-PUM2chr790547039chr220483247916HLA-C03:67LADFGYQVL0.99870.994918
CDK14-PUM2chr790547039chr220483247916HLA-C03:05LADFGYQVL0.99870.9697918
CDK14-PUM2chr790547039chr220483247916HLA-C05:01KLADFGYQV0.99790.9925817
CDK14-PUM2chr790547039chr220483247916HLA-C04:03KLADFGYQV0.99690.9577817
CDK14-PUM2chr790547039chr220483247916HLA-C15:05LADFGYQVL0.99480.9888918
CDK14-PUM2chr790547039chr220483247916HLA-C03:02LADFGYQVL0.99070.99918
CDK14-PUM2chr790547039chr220483247916HLA-C15:02KLADFGYQV0.99050.9633817
CDK14-PUM2chr790547039chr220483247916HLA-C15:05KLADFGYQV0.98830.9638817
CDK14-PUM2chr790547039chr220483247916HLA-C03:06LADFGYQVL0.9880.9954918
CDK14-PUM2chr790547039chr220483247916HLA-C18:01KLADFGYQV0.98640.9552817
CDK14-PUM2chr790547039chr220483247916HLA-C04:04LADFGYQVL0.98030.9896918
CDK14-PUM2chr790547039chr220483247916HLA-B35:13LADFGYQVL0.96090.9766918
CDK14-PUM2chr790547039chr220483247916HLA-C16:01LADFGYQVL0.9550.9919918
CDK14-PUM2chr790547039chr220483247916HLA-C08:01LADFGYQVL0.92920.9976918
CDK14-PUM2chr790547039chr220483247916HLA-B35:22LADFGYQVL0.92150.715918
CDK14-PUM2chr790547039chr220483247916HLA-C04:04KLADFGYQV0.91320.9803817
CDK14-PUM2chr790547039chr220483247916HLA-B51:05LADFGYQVL0.89780.6636918
CDK14-PUM2chr790547039chr220483247916HLA-C07:04LADFGYQVL0.87610.9837918
CDK14-PUM2chr790547039chr220483247916HLA-B35:09LADFGYQVL0.85060.9882918
CDK14-PUM2chr790547039chr220483247916HLA-A69:01KLADFGYQV0.81810.8617817
CDK14-PUM2chr790547039chr220483247916HLA-B51:06LADFGYQVL0.80840.8471918
CDK14-PUM2chr790547039chr220483247916HLA-C17:01LADFGYQVL0.80280.9895918
CDK14-PUM2chr790547039chr220483247916HLA-C17:01KLADFGYQV0.790.9778817
CDK14-PUM2chr790547039chr220483247916HLA-A32:01KLADFGYQV0.73350.9895817
CDK14-PUM2chr790547039chr220483247916HLA-B50:04ADFGYQVLA0.60910.95681019
CDK14-PUM2chr790547039chr220483247916HLA-B50:05ADFGYQVLA0.60910.95681019
CDK14-PUM2chr790547039chr220483247916HLA-B07:13LADFGYQVL0.33420.9051918
CDK14-PUM2chr790547039chr220483247916HLA-C07:04KLADFGYQV0.1380.9665817
CDK14-PUM2chr790547039chr220483247916HLA-B40:21KLADFGYQV0.12710.7547817
CDK14-PUM2chr790547039chr220483247916HLA-C05:01KLADFGYQVL0.99970.9864818
CDK14-PUM2chr790547039chr220483247916HLA-A02:03KLADFGYQVL0.99850.7909818
CDK14-PUM2chr790547039chr220483247916HLA-B44:13GELKLADFGY0.99830.9407515
CDK14-PUM2chr790547039chr220483247916HLA-B44:07GELKLADFGY0.99830.9407515
CDK14-PUM2chr790547039chr220483247916HLA-B44:26GELKLADFGY0.99830.9407515
CDK14-PUM2chr790547039chr220483247916HLA-C08:02KLADFGYQVL0.99820.9894818
CDK14-PUM2chr790547039chr220483247916HLA-A02:14KLADFGYQVL0.99670.796818
CDK14-PUM2chr790547039chr220483247916HLA-B15:73KLADFGYQVL0.99320.987818
CDK14-PUM2chr790547039chr220483247916HLA-B15:30KLADFGYQVL0.98150.9738818
CDK14-PUM2chr790547039chr220483247916HLA-B40:21KLADFGYQVL0.46340.768818
CDK14-PUM2chr790547039chr220483247916HLA-B15:34FGYQVLAPTAY0.99680.95261223
CDK14-PUM2chr790547039chr220483247916HLA-B15:33FGYQVLAPTAY0.99680.95261223
CDK14-PUM2chr790547039chr220483247916HLA-B15:125FGYQVLAPTAY0.99680.95261223
CDK14-PUM2chr790547039chr220483247916HLA-B15:27FGYQVLAPTAY0.99640.95911223
CDK14-PUM2chr790547039chr220483247916HLA-B15:135FGYQVLAPTAY0.99590.9691223
CDK14-PUM2chr790547039chr220483247916HLA-B15:50FGYQVLAPTAY0.99450.94911223
CDK14-PUM2chr790547039chr220483247916HLA-B15:35FGYQVLAPTAY0.99280.96411223
CDK14-PUM2chr790547039chr220483247916HLA-B15:12FGYQVLAPTAY0.98710.96161223
CDK14-PUM2chr790547039chr220483247916HLA-B15:39FGYQVLAPTAY0.98470.9251223
CDK14-PUM2chr790547039chr220483247916HLA-B15:20FGYQVLAPTAY0.95140.89831223
CDK14-PUM2chr790547039chr220483247916HLA-B35:28FGYQVLAPTAY0.93210.90061223

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Potential FusionNeoAntigen Information of CDK14-PUM2 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.
CDK14-PUM2_90547039_20483247.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)
CDK14-PUM2chr790547039chr220483247916DRB1-1216DFGYQVLAPTAYYDQ1126
CDK14-PUM2chr790547039chr220483247916DRB1-1216ADFGYQVLAPTAYYD1025
CDK14-PUM2chr790547039chr220483247916DRB1-1222DFGYQVLAPTAYYDQ1126
CDK14-PUM2chr790547039chr220483247916DRB1-1222ADFGYQVLAPTAYYD1025
CDK14-PUM2chr790547039chr220483247916DRB1-1222LADFGYQVLAPTAYY924

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Fusion breakpoint peptide structures of CDK14-PUM2

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
1907ELKLADFGYQVLAPCDK14PUM2chr790547039chr220483247916

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDK14-PUM2

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-B14:023BVN1907ELKLADFGYQVLAP-7.15543-7.26883
HLA-B14:023BVN1907ELKLADFGYQVLAP-4.77435-5.80965
HLA-B52:013W391907ELKLADFGYQVLAP-6.80875-6.92215
HLA-B52:013W391907ELKLADFGYQVLAP-4.20386-5.23916
HLA-A11:014UQ21907ELKLADFGYQVLAP-7.5194-8.5547
HLA-A11:014UQ21907ELKLADFGYQVLAP-6.9601-7.0735
HLA-A24:025HGA1907ELKLADFGYQVLAP-7.52403-7.63743
HLA-A24:025HGA1907ELKLADFGYQVLAP-5.82433-6.85963
HLA-B27:056PYJ1907ELKLADFGYQVLAP-3.28285-4.31815
HLA-B44:053DX81907ELKLADFGYQVLAP-5.91172-6.94702
HLA-B44:053DX81907ELKLADFGYQVLAP-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of CDK14-PUM2

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
CDK14-PUM2chr790547039chr2204832471018ADFGYQVLCAGATTTCGGCTATCAAGTACTAG
CDK14-PUM2chr790547039chr2204832471019ADFGYQVLACAGATTTCGGCTATCAAGTACTAGCTC
CDK14-PUM2chr790547039chr2204832471223FGYQVLAPTAYTCGGCTATCAAGTACTAGCTCCAACTGCCTATT
CDK14-PUM2chr790547039chr220483247515GELKLADFGYGGGAGTTAAAGCTGGCAGATTTCGGCTATC
CDK14-PUM2chr790547039chr220483247615ELKLADFGYAGTTAAAGCTGGCAGATTTCGGCTATC
CDK14-PUM2chr790547039chr220483247717LKLADFGYQVTAAAGCTGGCAGATTTCGGCTATCAAGTAC
CDK14-PUM2chr790547039chr220483247817KLADFGYQVAGCTGGCAGATTTCGGCTATCAAGTAC
CDK14-PUM2chr790547039chr220483247818KLADFGYQVLAGCTGGCAGATTTCGGCTATCAAGTACTAG
CDK14-PUM2chr790547039chr220483247819KLADFGYQVLAAGCTGGCAGATTTCGGCTATCAAGTACTAGCTC
CDK14-PUM2chr790547039chr220483247917LADFGYQVTGGCAGATTTCGGCTATCAAGTAC
CDK14-PUM2chr790547039chr220483247918LADFGYQVLTGGCAGATTTCGGCTATCAAGTACTAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
CDK14-PUM2chr790547039chr2204832471025ADFGYQVLAPTAYYDCAGATTTCGGCTATCAAGTACTAGCTCCAACTGCCTATTATGATC
CDK14-PUM2chr790547039chr2204832471126DFGYQVLAPTAYYDQATTTCGGCTATCAAGTACTAGCTCCAACTGCCTATTATGATCAGA
CDK14-PUM2chr790547039chr220483247924LADFGYQVLAPTAYYTGGCAGATTTCGGCTATCAAGTACTAGCTCCAACTGCCTATTATG

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Information of the samples that have these potential fusion neoantigens of CDK14-PUM2

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
STADCDK14-PUM2chr790547039ENST00000265741chr220483247ENST00000319801TCGA-CD-A486-01A

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Potential target of CAR-T therapy development for CDK14-PUM2

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 CDK14-PUM2

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 CDK14-PUM2

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