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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:AUTS2-SEMA3A (FusionGDB2 ID:HG26053TG10371)

Fusion Gene Summary for AUTS2-SEMA3A

check button Fusion gene summary
Fusion gene informationFusion gene name: AUTS2-SEMA3A
Fusion gene ID: hg26053tg10371
HgeneTgene
Gene symbol

AUTS2

SEMA3A

Gene ID

26053

10371

Gene nameactivator of transcription and developmental regulator AUTS2semaphorin 3A
SynonymsFBRSL2|MRD26COLL1|HH16|Hsema-I|Hsema-III|SEMA1|SEMAD|SEMAIII|SEMAL|SemD|coll-1
Cytomap('AUTS2')('SEMA3A')

7q11.22

7q21.11

Type of geneprotein-codingprotein-coding
Descriptionautism susceptibility gene 2 proteinAUTS2, activator of transcription and developmental regulatorautism susceptibility candidate 2autism-related protein 1semaphorin-3Acollapsin 1sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Asemaphorin Dsemaphorin IIIsemaphorin L
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000489774, ENST00000342771, 
ENST00000406775, ENST00000403018, 
Fusion gene scores* DoF score29 X 23 X 8=53366 X 5 X 5=150
# samples 306
** MAII scorelog2(30/5336*10)=-4.1527242606887
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/150*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AUTS2 [Title/Abstract] AND SEMA3A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAUTS2(70163606)-SEMA3A(83689874), # samples:2
Anticipated loss of major functional domain due to fusion event.AUTS2-SEMA3A seems lost the major protein functional domain in Hgene 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
HgeneAUTS2

GO:0045944

positive regulation of transcription by RNA polymerase II

25519132

HgeneAUTS2

GO:0051571

positive regulation of histone H3-K4 methylation

25519132

HgeneAUTS2

GO:2000620

positive regulation of histone H4-K16 acetylation

25519132

TgeneSEMA3A

GO:0048841

regulation of axon extension involved in axon guidance

18053124



check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4SARCTCGA-DX-A1L1-01AAUTS2chr7

70163606

-SEMA3Achr7

83689874

-
ChimerDB4SARCTCGA-DX-A1L1-01AAUTS2chr7

70163606

+SEMA3Achr7

83689874

-


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Fusion Gene ORF analysis for AUTS2-SEMA3A

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
3UTR-3CDSENST00000489774ENST00000265362AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
3UTR-3CDSENST00000489774ENST00000436949AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
3UTR-intronENST00000489774ENST00000471474AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
5CDS-intronENST00000342771ENST00000471474AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
5CDS-intronENST00000406775ENST00000471474AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
Frame-shiftENST00000342771ENST00000265362AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
Frame-shiftENST00000342771ENST00000436949AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
Frame-shiftENST00000406775ENST00000265362AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
Frame-shiftENST00000406775ENST00000436949AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
intron-3CDSENST00000403018ENST00000265362AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
intron-3CDSENST00000403018ENST00000436949AUTS2chr7

70163606

+SEMA3Achr7

83689874

-
intron-intronENST00000403018ENST00000471474AUTS2chr7

70163606

+SEMA3Achr7

83689874

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

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

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Fusion Genomic Features for AUTS2-SEMA3A


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for AUTS2-SEMA3A


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/:70163606/:83689874)
- 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 buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for AUTS2-SEMA3A


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for AUTS2-SEMA3A


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for AUTS2-SEMA3A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for AUTS2-SEMA3A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAUTS2C0036341Schizophrenia2PSYGENET
HgeneAUTS2C0006413Burkitt Lymphoma1ORPHANET
HgeneAUTS2C0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
HgeneAUTS2C0014544Epilepsy1CTD_human
HgeneAUTS2C0086237Epilepsy, Cryptogenic1CTD_human
HgeneAUTS2C0236018Aura1CTD_human
HgeneAUTS2C0751111Awakening Epilepsy1CTD_human
HgeneAUTS2C1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
HgeneAUTS2C2677504AUTISM, SUSCEPTIBILITY TO, 151GENOMICS_ENGLAND
HgeneAUTS2C4014435MENTAL RETARDATION, AUTOSOMAL DOMINANT 261CTD_human;ORPHANET
TgeneC0036341Schizophrenia3PSYGENET
TgeneC3554021HYPOGONADOTROPIC HYPOGONADISM 16 WITH OR WITHOUT ANOSMIA3CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0162809Kallmann Syndrome1ORPHANET