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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:ATIC-RBM39

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ATIC-RBM39
FusionPDB ID: 7633
FusionGDB2.0 ID: 7633
HgeneTgene
Gene symbol

ATIC

RBM39

Gene ID

471

9584

Gene name5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseRNA binding motif protein 39
SynonymsAICAR|AICARFT|HEL-S-70p|IMPCHASE|PURHCAPER|CAPERalpha|FSAP59|HCC1|RNPC2
Cytomap

2q35

20q11.22

Type of geneprotein-codingprotein-coding
Descriptionbifunctional purine biosynthesis protein PURH5-aminoimidazole-4-carboxamide-1-beta-D-ribonucleotide transformylase/inosinicaseAICAR formyltransferase/IMP cyclohydrolase bifunctional enzymeAICARFT/IMPCHASEepididymis secretory sperm binding protein Li 7RNA-binding protein 39CAPER alphaRNA-binding region (RNP1, RRM) containing 2coactivator of activating protein-1 and estrogen receptorsepididymis secretory sperm binding proteinfunctional spliceosome-associated protein 59hepatocellular carcinoma prot
Modification date2020031320200327
UniProtAcc

P31939

Main function of 5'-partner protein: FUNCTION: Bifunctional enzyme that catalyzes the last two steps of purine biosynthesis (PubMed:11948179, PubMed:14756554). Acts as a transformylase that incorporates a formyl group to the AMP analog AICAR (5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide) to produce the intermediate formyl-AICAR (FAICAR) (PubMed:9378707, PubMed:11948179, PubMed:10985775). Can use both 10-formyldihydrofolate and 10-formyltetrahydrofolate as the formyl donor in this reaction (PubMed:10985775). Also catalyzes the cyclization of FAICAR to IMP (PubMed:11948179, PubMed:14756554). Is able to convert thio-AICAR to 6-mercaptopurine ribonucleotide, an inhibitor of purine biosynthesis used in the treatment of human leukemias (PubMed:10985775). Promotes insulin receptor/INSR autophosphorylation and is involved in INSR internalization (PubMed:25687571). {ECO:0000269|PubMed:10985775, ECO:0000269|PubMed:11948179, ECO:0000269|PubMed:14756554, ECO:0000269|PubMed:25687571, ECO:0000269|PubMed:9378707}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000236959, ENST00000435675, 
ENST00000540518, 
ENST00000397370, 
ENST00000407261, ENST00000463098, 
ENST00000253363, ENST00000361162, 
ENST00000528062, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 9 X 4=32424 X 16 X 12=4608
# samples 927
** MAII scorelog2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(27/4608*10)=-4.09310940439148
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ATIC [Title/Abstract] AND RBM39 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ATIC [Title/Abstract] AND RBM39 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATIC(216203630)-RBM39(34326939), # samples:1
Anticipated loss of major functional domain due to fusion event.ATIC-RBM39 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.
ATIC-RBM39 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.
ATIC-RBM39 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.
ATIC-RBM39 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/chr2:216203630/chr20:34326939)
- 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 ATIC (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 RBM39 (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)
ENST00000236959ATICchr2216203630+ENST00000253363RBM39chr2034326939-396615532663094942
ENST00000236959ATICchr2216203630+ENST00000361162RBM39chr2034326939-394815532663076936
ENST00000236959ATICchr2216203630+ENST00000528062RBM39chr2034326939-361215532663028920
ENST00000540518ATICchr2216203630+ENST00000253363RBM39chr2034326939-394015272793068929
ENST00000540518ATICchr2216203630+ENST00000361162RBM39chr2034326939-392215272793050923
ENST00000540518ATICchr2216203630+ENST00000528062RBM39chr2034326939-358615272793002907
ENST00000435675ATICchr2216203630+ENST00000253363RBM39chr2034326939-402816153913156921
ENST00000435675ATICchr2216203630+ENST00000361162RBM39chr2034326939-401016153913138915
ENST00000435675ATICchr2216203630+ENST00000528062RBM39chr2034326939-367416153913090899

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
ENST00000236959ENST00000253363ATICchr2216203630+RBM39chr2034326939-0.0006979610.999302
ENST00000236959ENST00000361162ATICchr2216203630+RBM39chr2034326939-0.0007713440.9992287
ENST00000236959ENST00000528062ATICchr2216203630+RBM39chr2034326939-0.0008732420.99912673
ENST00000540518ENST00000253363ATICchr2216203630+RBM39chr2034326939-0.0006757550.9993243
ENST00000540518ENST00000361162ATICchr2216203630+RBM39chr2034326939-0.0006931290.9993069
ENST00000540518ENST00000528062ATICchr2216203630+RBM39chr2034326939-0.0008140060.999186
ENST00000435675ENST00000253363ATICchr2216203630+RBM39chr2034326939-0.0003527910.99964726
ENST00000435675ENST00000361162ATICchr2216203630+RBM39chr2034326939-0.0003992980.9996007
ENST00000435675ENST00000528062ATICchr2216203630+RBM39chr2034326939-0.0004487910.99955124

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 ATIC-RBM39

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ATICchr2216203630RBM39chr20343269391527416KSLFSNVVTKNKDDENKLSSANGHEE
ATICchr2216203630RBM39chr20343269391553429KSLFSNVVTKNKDDENKLSSANGHEE
ATICchr2216203630RBM39chr20343269391615408KSLFSNVVTKNKDDENKLSSANGHEE

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Potential FusionNeoAntigen Information of ATIC-RBM39 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.
ATIC-RBM39_216203630_34326939.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)
ATIC-RBM39chr2216203630chr20343269391553HLA-B39:11NKDDENKL0.93310.61061018

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Potential FusionNeoAntigen Information of ATIC-RBM39 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.
ATIC-RBM39_216203630_34326939.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)
ATIC-RBM39chr2216203630chr20343269391553DRB3-0201KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0202KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0204KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0205KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0210KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0211KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0212KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0213KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0214KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0215KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0217KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0218KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0219KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0220KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0222KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0223KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0224KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB3-0225KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0101KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0102KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0103KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0104KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0105KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0108NKSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0112KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0113KSLFSNVVTKNKDDE015
ATIC-RBM39chr2216203630chr20343269391553DRB5-0114KSLFSNVVTKNKDDE015

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Fusion breakpoint peptide structures of ATIC-RBM39

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
10377VVTKNKDDENKLSSATICRBM39chr2216203630chr20343269391553

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATIC-RBM39

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-B14:023BVN10377VVTKNKDDENKLSS-7.9962-8.1096
HLA-B14:023BVN10377VVTKNKDDENKLSS-5.70842-6.74372
HLA-B52:013W3910377VVTKNKDDENKLSS-6.83737-6.95077
HLA-B52:013W3910377VVTKNKDDENKLSS-4.4836-5.5189
HLA-A11:014UQ210377VVTKNKDDENKLSS-10.0067-10.1201
HLA-A11:014UQ210377VVTKNKDDENKLSS-9.03915-10.0745
HLA-A24:025HGA10377VVTKNKDDENKLSS-6.56204-6.67544
HLA-A24:025HGA10377VVTKNKDDENKLSS-5.42271-6.45801
HLA-B44:053DX810377VVTKNKDDENKLSS-7.85648-8.89178
HLA-B44:053DX810377VVTKNKDDENKLSS-5.3978-5.5112
HLA-B35:011A1N10377VVTKNKDDENKLSS-6.27422-6.38762
HLA-B35:011A1N10377VVTKNKDDENKLSS-5.27424-6.30954
HLA-A02:016TDR10377VVTKNKDDENKLSS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ATIC-RBM39

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
ATIC-RBM39chr2216203630chr20343269391018NKDDENKLAATAAAGATGATGAGAACAAGTTG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ATIC-RBM39chr2216203630chr2034326939015KSLFSNVVTKNKDDEAAGTCATTATTTAGCAATGTTGTTACCAAAAATAAAGATGATGAG

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Information of the samples that have these potential fusion neoantigens of ATIC-RBM39

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
GBMATIC-RBM39chr2216203630ENST00000236959chr2034326939ENST00000253363TCGA-14-2554-01A

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Potential target of CAR-T therapy development for ATIC-RBM39

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 ATIC-RBM39

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 ATIC-RBM39

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
HgeneATICC0001787Osteoporosis, Age-Related1CTD_human
HgeneATICC0003873Rheumatoid Arthritis1CTD_human
HgeneATICC0013221Drug toxicity1CTD_human
HgeneATICC0029456Osteoporosis1CTD_human
HgeneATICC0029459Osteoporosis, Senile1CTD_human
HgeneATICC0041755Adverse reaction to drug1CTD_human
HgeneATICC0155003Blindness, Transient1CTD_human
HgeneATICC0221473Blindness, Hysterical1CTD_human
HgeneATICC0271215Blindness, Legal1CTD_human
HgeneATICC0339730Blindness, Acquired1CTD_human
HgeneATICC0376288Amaurosis1CTD_human
HgeneATICC0456909Blindness1CTD_human
HgeneATICC0750958Blindness, Monocular1CTD_human
HgeneATICC0751406Post-Traumatic Osteoporosis1CTD_human
HgeneATICC1837530AICAR Transformylase Inosine Monophosphate Cyclohydrolase Deficiency1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneATICC1879328Blindness both eyes NOS (disorder)1CTD_human
HgeneATICC3714756Intellectual Disability1GENOMICS_ENGLAND