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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:PAX5-AUTS2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PAX5-AUTS2
FusionPDB ID: 62946
FusionGDB2.0 ID: 62946
HgeneTgene
Gene symbol

PAX5

AUTS2

Gene ID

5079

26053

Gene namepaired box 5activator of transcription and developmental regulator AUTS2
SynonymsALL3|BSAPFBRSL2|MRD26
Cytomap

9p13.2

7q11.22

Type of geneprotein-codingprotein-coding
Descriptionpaired box protein Pax-5B-cell lineage specific activatorpaired box homeotic gene 5paired domain gene 5transcription factor PAX 5autism susceptibility gene 2 proteinAUTS2, activator of transcription and developmental regulatorautism susceptibility candidate 2autism-related protein 1
Modification date2020031320200313
UniProtAcc

Q02548

Main function of 5'-partner protein: FUNCTION: Transcription factor that plays an essential role in commitment of lymphoid progenitors to the B-lymphocyte lineage (PubMed:10811620, PubMed:27181361). Fulfills a dual role by repressing B-lineage inappropriate genes and simultaneously activating B-lineage-specific genes (PubMed:10811620, PubMed:27181361). In turn, regulates cell adhesion and migration, induces V(H)-to-D(H)J(H) recombination, facilitates pre-B-cell receptor signaling and promotes development to the mature B-cell stage (PubMed:32612238). Repression of the cohesin-release factor WAPL causes global changes of the chromosomal architecture in pro-B cells to facilitate the generation of a diverse antibody repertoire (PubMed:32612238). {ECO:0000269|PubMed:10811620, ECO:0000269|PubMed:27181361, ECO:0000269|PubMed:32612238}.; FUNCTION: (Microbial infection) Plays an essential role in the maintenance of Epstein-Barr virus genome copy number within the host cell by promoting EBNA1/oriP-dependent binding and transcription (PubMed:31941781). Participates also in the inhibition of lytic EBV reactivation by modulating viral BZLF1 activity (PubMed:23678172). {ECO:0000269|PubMed:23678172, ECO:0000269|PubMed:31941781}.

Q8WXX7

Main function of 5'-partner protein: FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility (PubMed:25519132). The PRC1-like complex that contains PCGF5, RNF2, CSNK2B, RYBP and AUTS2 has decreased histone H2A ubiquitination activity, due to the phosphorylation of RNF2 by CSNK2B (PubMed:25519132). As a consequence, the complex mediates transcriptional activation (PubMed:25519132). In the cytoplasm, plays a role in axon and dendrite elongation and in neuronal migration during embryonic brain development. Promotes reorganization of the actin cytoskeleton, lamellipodia formation and neurite elongation via its interaction with RAC guanine nucleotide exchange factors, which then leads to the activation of RAC1 (By similarity). {ECO:0000250|UniProtKB:A0A087WPF7, ECO:0000269|PubMed:25519132}.
Ensembl transtripts involved in fusion geneENST idsENST00000358127, ENST00000377847, 
ENST00000377852, ENST00000377853, 
ENST00000414447, ENST00000446742, 
ENST00000520154, ENST00000520281, 
ENST00000522003, ENST00000523145, 
ENST00000523241, 		ENST00000489774, 
ENST00000342771, ENST00000403018, 
ENST00000406775, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 15 X 7=157525 X 24 X 10=6000
# samples 1027
** MAII scorelog2(10/1575*10)=-3.97727992349992
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(27/6000*10)=-4.47393118833241
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PAX5 [Title/Abstract] AND AUTS2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PAX5 [Title/Abstract] AND AUTS2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PAX5(36966583)-AUTS2(69599518), # samples:1
PAX5(36966546)-AUTS2(69599518), # samples:1
Anticipated loss of major functional domain due to fusion event.PAX5-AUTS2 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.
PAX5-AUTS2 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.
PAX5-AUTS2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
PAX5-AUTS2 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
PAX5-AUTS2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PAX5-AUTS2 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneAUTS2

GO:0045944

positive regulation of transcription by RNA polymerase II

25519132

TgeneAUTS2

GO:0051571

positive regulation of histone H3-K4 methylation

25519132

TgeneAUTS2

GO:2000620

positive regulation of histone H4-K16 acetylation

25519132



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/chr9:36966583/chr7:69599518)
- 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 PAX5 (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 AUTS2 (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)
ENST00000358127PAX5chr936966546-ENST00000406775AUTS2chr769599518+54468557539381287
ENST00000358127PAX5chr936966546-ENST00000342771AUTS2chr769599518+60838557540101311
ENST00000358127PAX5chr936966546-ENST00000403018AUTS2chr769599518+1145855751031318
ENST00000523241PAX5chr936966546-ENST00000406775AUTS2chr769599518+53817901038731287
ENST00000523241PAX5chr936966546-ENST00000342771AUTS2chr769599518+60187901039451311
ENST00000523241PAX5chr936966546-ENST00000403018AUTS2chr769599518+108079010966318
ENST00000520154PAX5chr936966546-ENST00000406775AUTS2chr769599518+53817901038731287
ENST00000520154PAX5chr936966546-ENST00000342771AUTS2chr769599518+60187901039451311
ENST00000520154PAX5chr936966546-ENST00000403018AUTS2chr769599518+108079010966318
ENST00000377852PAX5chr936966546-ENST00000406775AUTS2chr769599518+53817901038731287
ENST00000377852PAX5chr936966546-ENST00000342771AUTS2chr769599518+60187901039451311
ENST00000377852PAX5chr936966546-ENST00000403018AUTS2chr769599518+108079010966318
ENST00000377853PAX5chr936966546-ENST00000406775AUTS2chr769599518+53817901038731287
ENST00000377853PAX5chr936966546-ENST00000342771AUTS2chr769599518+60187901039451311
ENST00000377853PAX5chr936966546-ENST00000403018AUTS2chr769599518+108079010966318
ENST00000520281PAX5chr936966546-ENST00000406775AUTS2chr769599518+5242651037341244
ENST00000520281PAX5chr936966546-ENST00000342771AUTS2chr769599518+5879651038061268
ENST00000520281PAX5chr936966546-ENST00000403018AUTS2chr769599518+9416510827275
ENST00000414447PAX5chr936966546-ENST00000406775AUTS2chr769599518+5242651037341244
ENST00000414447PAX5chr936966546-ENST00000342771AUTS2chr769599518+5879651038061268
ENST00000414447PAX5chr936966546-ENST00000403018AUTS2chr769599518+9416510827275
ENST00000446742PAX5chr936966546-ENST00000406775AUTS2chr769599518+5173582036651221
ENST00000446742PAX5chr936966546-ENST00000342771AUTS2chr769599518+5810582037371245
ENST00000446742PAX5chr936966546-ENST00000403018AUTS2chr769599518+8725820758252
ENST00000377847PAX5chr936966546-ENST00000406775AUTS2chr769599518+5371780038631287
ENST00000377847PAX5chr936966546-ENST00000342771AUTS2chr769599518+6008780039351311
ENST00000377847PAX5chr936966546-ENST00000403018AUTS2chr769599518+10707800956318

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
ENST00000358127ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0016091930.9983908
ENST00000358127ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0013101730.99868983
ENST00000358127ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0077848010.9922152
ENST00000523241ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0016315570.99836844
ENST00000523241ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0012909630.9987091
ENST00000523241ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0087864450.9912136
ENST00000520154ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0016315570.99836844
ENST00000520154ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0012909630.9987091
ENST00000520154ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0087864450.9912136
ENST00000377852ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0016315570.99836844
ENST00000377852ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0012909630.9987091
ENST00000377852ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0087864450.9912136
ENST00000377853ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0016315570.99836844
ENST00000377853ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0012909630.9987091
ENST00000377853ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0087864450.9912136
ENST00000520281ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0015870460.99841297
ENST00000520281ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0012326380.9987674
ENST00000520281ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0044964630.9955036
ENST00000414447ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0015870460.99841297
ENST00000414447ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0012326380.9987674
ENST00000414447ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0044964630.9955036
ENST00000446742ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.0021178160.9978822
ENST00000446742ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0015778460.99842215
ENST00000446742ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0096797960.99032015
ENST00000377847ENST00000406775PAX5chr936966546-AUTS2chr769599518+0.001651410.9983486
ENST00000377847ENST00000342771PAX5chr936966546-AUTS2chr769599518+0.0012963790.9987036
ENST00000377847ENST00000403018PAX5chr936966546-AUTS2chr769599518+0.0087393760.9912606

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 PAX5-AUTS2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PAX5chr936966546AUTS2chr769599518582193SDIFTTTEPIKPEQSSAPSSLGTGYF
PAX5chr936966546AUTS2chr769599518651216SDIFTTTEPIKPEQSSAPSSLGTGYF
PAX5chr936966546AUTS2chr769599518780259SDIFTTTEPIKPEQSSAPSSLGTGYF
PAX5chr936966546AUTS2chr769599518790259SDIFTTTEPIKPEQSSAPSSLGTGYF
PAX5chr936966546AUTS2chr769599518855259SDIFTTTEPIKPEQSSAPSSLGTGYF

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Potential FusionNeoAntigen Information of PAX5-AUTS2 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.
PAX5-AUTS2_36966546_69599518.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)
PAX5-AUTS2chr936966546chr769599518855HLA-B39:01EQSSAPSSL0.98440.92951221
PAX5-AUTS2chr936966546chr769599518855HLA-B39:13EQSSAPSSL0.97650.95551221
PAX5-AUTS2chr936966546chr769599518855HLA-B38:02EQSSAPSSL0.96510.971221
PAX5-AUTS2chr936966546chr769599518855HLA-B38:01EQSSAPSSL0.96130.96041221
PAX5-AUTS2chr936966546chr769599518855HLA-B14:02EQSSAPSSL0.94770.88871221
PAX5-AUTS2chr936966546chr769599518855HLA-B14:01EQSSAPSSL0.94770.88871221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:10EQSSAPSSL0.90620.5691221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:18EQSSAPSSL0.79790.72391221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:37EQSSAPSSL0.66040.55611221
PAX5-AUTS2chr936966546chr769599518855HLA-B13:01EQSSAPSSL0.55190.91721221
PAX5-AUTS2chr936966546chr769599518855HLA-B45:01TEPIKPEQSSA0.99910.9757617
PAX5-AUTS2chr936966546chr769599518855HLA-B50:02TEPIKPEQSSA0.99830.7856617
PAX5-AUTS2chr936966546chr769599518855HLA-B41:01TEPIKPEQSSA0.9960.985617
PAX5-AUTS2chr936966546chr769599518855HLA-B50:01TEPIKPEQSSA0.99580.9217617
PAX5-AUTS2chr936966546chr769599518855HLA-B39:09EQSSAPSSL0.98590.74481221
PAX5-AUTS2chr936966546chr769599518855HLA-B39:12EQSSAPSSL0.97810.93021221
PAX5-AUTS2chr936966546chr769599518855HLA-B39:05EQSSAPSSL0.97290.91951221
PAX5-AUTS2chr936966546chr769599518855HLA-B39:08EQSSAPSSL0.95030.85591221
PAX5-AUTS2chr936966546chr769599518855HLA-B14:03EQSSAPSSL0.75910.89731221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:21EQSSAPSSL0.73070.92231221
PAX5-AUTS2chr936966546chr769599518855HLA-B51:07EQSSAPSSL0.05810.80011221
PAX5-AUTS2chr936966546chr769599518855HLA-B54:01EPIKPEQSSA0.96560.6343717
PAX5-AUTS2chr936966546chr769599518855HLA-B78:01EPIKPEQSSA0.40850.6608717
PAX5-AUTS2chr936966546chr769599518855HLA-B42:02KPEQSSAPSSL0.96860.62851021
PAX5-AUTS2chr936966546chr769599518855HLA-B42:01KPEQSSAPSSL0.95230.62071021
PAX5-AUTS2chr936966546chr769599518855HLA-B39:10KPEQSSAPSSL0.930.93961021
PAX5-AUTS2chr936966546chr769599518855HLA-B39:02EQSSAPSSL0.98770.94991221
PAX5-AUTS2chr936966546chr769599518855HLA-B39:31EQSSAPSSL0.98560.92841221
PAX5-AUTS2chr936966546chr769599518855HLA-B38:05EQSSAPSSL0.96130.96041221
PAX5-AUTS2chr936966546chr769599518855HLA-B39:11EQSSAPSSL0.93750.84361221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:73EQSSAPSSL0.79980.89091221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:30EQSSAPSSL0.76370.85531221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:09EQSSAPSSL0.74580.57951221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:53EQSSAPSSL0.71450.85721221
PAX5-AUTS2chr936966546chr769599518855HLA-B35:20EQSSAPSSL0.62470.94291221
PAX5-AUTS2chr936966546chr769599518855HLA-B15:12EQSSAPSSL0.46210.92531221
PAX5-AUTS2chr936966546chr769599518855HLA-B56:05EPIKPEQSSA0.73520.5708717
PAX5-AUTS2chr936966546chr769599518855HLA-B78:02EPIKPEQSSA0.33450.7748717
PAX5-AUTS2chr936966546chr769599518855HLA-B50:05TEPIKPEQSSA0.99580.9217617
PAX5-AUTS2chr936966546chr769599518855HLA-B50:04TEPIKPEQSSA0.99580.9217617
PAX5-AUTS2chr936966546chr769599518855HLA-B15:73KPEQSSAPSSL0.97880.8661021
PAX5-AUTS2chr936966546chr769599518855HLA-B35:13KPEQSSAPSSL0.97370.81391021
PAX5-AUTS2chr936966546chr769599518855HLA-B15:30KPEQSSAPSSL0.97060.82231021
PAX5-AUTS2chr936966546chr769599518855HLA-B67:01KPEQSSAPSSL0.92980.86941021

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Potential FusionNeoAntigen Information of PAX5-AUTS2 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 PAX5-AUTS2

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
9313TEPIKPEQSSAPSSPAX5AUTS2chr936966546chr769599518855

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PAX5-AUTS2

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-B14:023BVN9313TEPIKPEQSSAPSS-7.9962-8.1096
HLA-B14:023BVN9313TEPIKPEQSSAPSS-5.70842-6.74372
HLA-B52:013W399313TEPIKPEQSSAPSS-6.83737-6.95077
HLA-B52:013W399313TEPIKPEQSSAPSS-4.4836-5.5189
HLA-A11:014UQ29313TEPIKPEQSSAPSS-10.0067-10.1201
HLA-A11:014UQ29313TEPIKPEQSSAPSS-9.03915-10.0745
HLA-A24:025HGA9313TEPIKPEQSSAPSS-6.56204-6.67544
HLA-A24:025HGA9313TEPIKPEQSSAPSS-5.42271-6.45801
HLA-B44:053DX89313TEPIKPEQSSAPSS-7.85648-8.89178
HLA-B44:053DX89313TEPIKPEQSSAPSS-5.3978-5.5112
HLA-A02:016TDR9313TEPIKPEQSSAPSS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PAX5-AUTS2

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
PAX5-AUTS2chr936966546chr7695995181021KPEQSSAPSSLCCCGAGCAGAGTTCAGCTCCTTCCAGCTTGGGA
PAX5-AUTS2chr936966546chr7695995181221EQSSAPSSLCAGAGTTCAGCTCCTTCCAGCTTGGGA
PAX5-AUTS2chr936966546chr769599518617TEPIKPEQSSAGAGCCCATCAAGCCCGAGCAGAGTTCAGCTCCT
PAX5-AUTS2chr936966546chr769599518717EPIKPEQSSACCCATCAAGCCCGAGCAGAGTTCAGCTCCT

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 PAX5-AUTS2

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
N/APAX5-AUTS2chr936966546ENST00000358127chr769599518ENST00000342771EU784146

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Potential target of CAR-T therapy development for PAX5-AUTS2

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 PAX5-AUTS2

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 PAX5-AUTS2

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
HgenePAX5C0006413Burkitt Lymphoma4ORPHANET
HgenePAX5C1292769Precursor B-cell lymphoblastic leukemia4ORPHANET
HgenePAX5C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma2CTD_human
HgenePAX5C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma2CGI;CTD_human;UNIPROT
HgenePAX5C0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
HgenePAX5C0023453L2 Acute Lymphoblastic Leukemia1CTD_human
HgenePAX5C1535926Neurodevelopmental Disorders1CTD_human