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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:AXIN1-TMEM207

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: AXIN1-TMEM207
FusionPDB ID: 8568
FusionGDB2.0 ID: 8568
HgeneTgene
Gene symbol

AXIN1

TMEM207

Gene ID

8312

131920

Gene nameaxin 1transmembrane protein 207
SynonymsAXIN|PPP1R49UNQ846
Cytomap

16p13.3

3q28

Type of geneprotein-codingprotein-coding
Descriptionaxin-1axis inhibition protein 1axis inhibitor 1fused, mouse, homolog ofprotein phosphatase 1, regulatory subunit 49transmembrane protein 207SRSR846
Modification date2020032220200313
UniProtAcc

O15169

Main function of 5'-partner protein: FUNCTION: Component of the beta-catenin destruction complex required for regulating CTNNB1 levels through phosphorylation and ubiquitination, and modulating Wnt-signaling (PubMed:12192039, PubMed:27098453). Controls dorsoventral patterning via two opposing effects; down-regulates CTNNB1 to inhibit the Wnt signaling pathway and ventralize embryos, but also dorsalizes embryos by activating a Wnt-independent JNK signaling pathway (PubMed:12192039). In Wnt signaling, probably facilitates the phosphorylation of CTNNB1 and APC by GSK3B (PubMed:12192039). Likely to function as a tumor suppressor. Enhances TGF-beta signaling by recruiting the RNF111 E3 ubiquitin ligase and promoting the degradation of inhibitory SMAD7 (PubMed:16601693). Also component of the AXIN1-HIPK2-TP53 complex which controls cell growth, apoptosis and development (PubMed:17210684). Facilitates the phosphorylation of TP53 by HIPK2 upon ultraviolet irradiation (PubMed:17210684). {ECO:0000269|PubMed:12192039, ECO:0000269|PubMed:16601693, ECO:0000269|PubMed:17210684, ECO:0000269|PubMed:27098453}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000481769, ENST00000262320, 
ENST00000354866, 
ENST00000354905, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 10 X 9=14404 X 2 X 2=16
# samples 234
** MAII scorelog2(23/1440*10)=-2.6463630453853
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/16*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: AXIN1 [Title/Abstract] AND TMEM207 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: AXIN1 [Title/Abstract] AND TMEM207 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)AXIN1(354304)-TMEM207(190165616), # samples:2
Anticipated loss of major functional domain due to fusion event.AXIN1-TMEM207 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.
AXIN1-TMEM207 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.
AXIN1-TMEM207 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.
AXIN1-TMEM207 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
HgeneAXIN1

GO:0001934

positive regulation of protein phosphorylation

9601641

HgeneAXIN1

GO:0032147

activation of protein kinase activity

9601641

HgeneAXIN1

GO:0034622

cellular protein-containing complex assembly

16601693

HgeneAXIN1

GO:0045732

positive regulation of protein catabolic process

9601641

HgeneAXIN1

GO:0090090

negative regulation of canonical Wnt signaling pathway

10644691



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/chr16:354304/chr3:190165616)
- 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 AXIN1 (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 TMEM207 (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)
ENST00000262320AXIN1chr16354304-ENST00000354905TMEM207chr3190165616-29321626211991656
ENST00000354866AXIN1chr16354304-ENST00000354905TMEM207chr3190165616-27221416151781588

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
ENST00000262320ENST00000354905AXIN1chr16354304-TMEM207chr3190165616-0.0067678890.99323213
ENST00000354866ENST00000354905AXIN1chr16354304-TMEM207chr3190165616-0.0055180230.99448204

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 AXIN1-TMEM207

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
AXIN1chr16354304TMEM207chr31901656161416462RTREAEEKLEERLKRVRMLVLSDLPC
AXIN1chr16354304TMEM207chr31901656161626530RTREAEEKLEERLKRVRMLVLSDLPC

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Potential FusionNeoAntigen Information of AXIN1-TMEM207 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.
AXIN1-TMEM207_354304_190165616.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)
AXIN1-TMEM207chr16354304chr31901656161626HLA-B14:02ERLKRVRM0.99820.61491018
AXIN1-TMEM207chr16354304chr31901656161626HLA-B14:01ERLKRVRM0.99820.61491018
AXIN1-TMEM207chr16354304chr31901656161626HLA-B14:02ERLKRVRML0.99510.53161019
AXIN1-TMEM207chr16354304chr31901656161626HLA-B14:01ERLKRVRML0.99510.53161019
AXIN1-TMEM207chr16354304chr31901656161626HLA-A30:08RLKRVRMLV0.97780.70741120
AXIN1-TMEM207chr16354304chr31901656161626HLA-B14:01LKRVRMLVL0.96980.62781221
AXIN1-TMEM207chr16354304chr31901656161626HLA-B14:02LKRVRMLVL0.96980.62781221
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:22KLEERLKRV0.94850.6853716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:60KLEERLKRV0.92850.7139716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:67KLEERLKRV0.9280.7244716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:24KLEERLKRV0.9280.7244716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:30KLEERLKRV0.9280.7244716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:11KLEERLKRV0.91930.73716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:27KLEERLKRV0.91690.6923716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:13KLEERLKRV0.90650.7007716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:38KLEERLKRV0.90520.7318716
AXIN1-TMEM207chr16354304chr31901656161626HLA-B08:01EERLKRVRM0.89510.5027918
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:29KLEERLKRV0.74260.7255716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:20KLEERLKRV0.70930.7312716
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:19KLEERLKRV0.68640.617716
AXIN1-TMEM207chr16354304chr31901656161626HLA-B13:02RLKRVRMLV0.0110.56331120
AXIN1-TMEM207chr16354304chr31901656161626HLA-C07:95ERLKRVRML0.97230.62321019
AXIN1-TMEM207chr16354304chr31901656161626HLA-C07:05ERLKRVRML0.95870.95281019
AXIN1-TMEM207chr16354304chr31901656161626HLA-C07:27ERLKRVRML0.9570.93961019
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:01KLEERLKRV0.9280.7244716
AXIN1-TMEM207chr16354304chr31901656161626HLA-B39:12ERLKRVRML0.89190.84271019
AXIN1-TMEM207chr16354304chr31901656161626HLA-C07:19ERLKRVRML0.84290.66121019
AXIN1-TMEM207chr16354304chr31901656161626HLA-B14:03ERLKRVRML0.41440.74991019
AXIN1-TMEM207chr16354304chr31901656161626HLA-C12:16ERLKRVRML0.19360.95871019
AXIN1-TMEM207chr16354304chr31901656161626HLA-B27:06ERLKRVRML0.99890.58141019
AXIN1-TMEM207chr16354304chr31901656161626HLA-B27:10ERLKRVRML0.99850.75411019
AXIN1-TMEM207chr16354304chr31901656161626HLA-A30:01RLKRVRMLV0.98080.83951120
AXIN1-TMEM207chr16354304chr31901656161626HLA-C07:01ERLKRVRML0.97860.59751019
AXIN1-TMEM207chr16354304chr31901656161626HLA-A02:03KLEERLKRV0.96440.7582716
AXIN1-TMEM207chr16354304chr31901656161626HLA-B39:31ERLKRVRML0.90950.84191019
AXIN1-TMEM207chr16354304chr31901656161626HLA-B08:18EERLKRVRM0.89510.5027918
AXIN1-TMEM207chr16354304chr31901656161626HLA-B18:06EERLKRVRM0.84530.9363918
AXIN1-TMEM207chr16354304chr31901656161626HLA-B18:08EERLKRVRM0.80890.9335918
AXIN1-TMEM207chr16354304chr31901656161626HLA-B18:03EERLKRVRM0.75280.9054918
AXIN1-TMEM207chr16354304chr31901656161626HLA-C06:08ERLKRVRML0.72810.97391019
AXIN1-TMEM207chr16354304chr31901656161626HLA-C07:22ERLKRVRML0.72490.78331019
AXIN1-TMEM207chr16354304chr31901656161626HLA-C06:17ERLKRVRML0.19060.98721019
AXIN1-TMEM207chr16354304chr31901656161626HLA-C06:02ERLKRVRML0.19060.98721019

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Potential FusionNeoAntigen Information of AXIN1-TMEM207 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 AXIN1-TMEM207

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
1845EKLEERLKRVRMLVAXIN1TMEM207chr16354304chr31901656161626

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AXIN1-TMEM207

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-B14:023BVN1845EKLEERLKRVRMLV-7.15543-7.26883
HLA-B14:023BVN1845EKLEERLKRVRMLV-4.77435-5.80965
HLA-B52:013W391845EKLEERLKRVRMLV-6.80875-6.92215
HLA-B52:013W391845EKLEERLKRVRMLV-4.20386-5.23916
HLA-A11:014UQ21845EKLEERLKRVRMLV-7.5194-8.5547
HLA-A11:014UQ21845EKLEERLKRVRMLV-6.9601-7.0735
HLA-A24:025HGA1845EKLEERLKRVRMLV-7.52403-7.63743
HLA-A24:025HGA1845EKLEERLKRVRMLV-5.82433-6.85963
HLA-B27:056PYJ1845EKLEERLKRVRMLV-3.28285-4.31815
HLA-B44:053DX81845EKLEERLKRVRMLV-5.91172-6.94702
HLA-B44:053DX81845EKLEERLKRVRMLV-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of AXIN1-TMEM207

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
AXIN1-TMEM207chr16354304chr31901656161018ERLKRVRMGTGCGCATGTTGGTGCTCTCGGAC
AXIN1-TMEM207chr16354304chr31901656161019ERLKRVRMLGTGCGCATGTTGGTGCTCTCGGACCTA
AXIN1-TMEM207chr16354304chr31901656161120RLKRVRMLVCGCATGTTGGTGCTCTCGGACCTACCA
AXIN1-TMEM207chr16354304chr31901656161221LKRVRMLVLATGTTGGTGCTCTCGGACCTACCATGC
AXIN1-TMEM207chr16354304chr3190165616716KLEERLKRVCTGAAGCGCGTGCGCATGTTGGTGCTC
AXIN1-TMEM207chr16354304chr3190165616918EERLKRVRMCGCGTGCGCATGTTGGTGCTCTCGGAC

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 AXIN1-TMEM207

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
LUSCAXIN1-TMEM207chr16354304ENST00000262320chr3190165616ENST00000354905TCGA-77-8008-01A

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Potential target of CAR-T therapy development for AXIN1-TMEM207

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
TgeneTMEM207chr16:354304chr3:190165616ENST000003549050552_720147.0TransmembraneHelical

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 AXIN1-TMEM207

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 AXIN1-TMEM207

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