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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:ATAD3A-CPSF3L (FusionGDB2 ID:HG55210TG54973)

Fusion Gene Summary for ATAD3A-CPSF3L

check button Fusion gene summary
Fusion gene informationFusion gene name: ATAD3A-CPSF3L
Fusion gene ID: hg55210tg54973
HgeneTgene
Gene symbol

ATAD3A

CPSF3L

Gene ID

55210

54973

Gene nameATPase family AAA domain containing 3Aintegrator complex subunit 11
SynonymsHAYOSCPSF3L|CPSF73L|INT11|RC-68|RC68
Cytomap('ATAD3A')('CPSF3L')

1p36.33

1p36.33

Type of geneprotein-codingprotein-coding
DescriptionATPase family AAA domain-containing protein 3Aintegrator complex subunit 11CPSF3-like proteincleavage and polyadenylation specific factor 3-likecleavage and polyadenylation-specific factor 3-like proteinprotein related to CPSF subunits of 68 kDarelated to CPSF subunits 68 kDa
Modification date2020032020200313
UniProtAcc

Q9NVI7

.
Ensembl transtripts involved in fusion geneENST00000378755, ENST00000378756, 
ENST00000536055, 
Fusion gene scores* DoF score4 X 4 X 3=488 X 8 X 6=384
# samples 410
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/384*10)=-1.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATAD3A [Title/Abstract] AND CPSF3L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATAD3A(1447853)-CPSF3L(1250998), # samples:1
Anticipated loss of major functional domain due to fusion event.ATAD3A-CPSF3L 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
TgeneCPSF3L

GO:0016180

snRNA processing

16239144



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
ChimerDB4ESCATCGA-L5-A891ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-


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Fusion Gene ORF analysis for ATAD3A-CPSF3L

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
5CDS-5UTRENST00000378755ENST00000419704ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-5UTRENST00000378755ENST00000421495ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-5UTRENST00000378755ENST00000462432ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-5UTRENST00000378755ENST00000540437ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-5UTRENST00000378756ENST00000419704ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-5UTRENST00000378756ENST00000421495ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-5UTRENST00000378756ENST00000462432ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-5UTRENST00000378756ENST00000540437ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-intronENST00000378755ENST00000450926ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-intronENST00000378755ENST00000545578ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-intronENST00000378756ENST00000450926ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
5CDS-intronENST00000378756ENST00000545578ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
Frame-shiftENST00000378755ENST00000411962ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
Frame-shiftENST00000378755ENST00000435064ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
Frame-shiftENST00000378756ENST00000411962ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
Frame-shiftENST00000378756ENST00000435064ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-3CDSENST00000536055ENST00000411962ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-3CDSENST00000536055ENST00000435064ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-5UTRENST00000536055ENST00000419704ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-5UTRENST00000536055ENST00000421495ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-5UTRENST00000536055ENST00000462432ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-5UTRENST00000536055ENST00000540437ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-intronENST00000536055ENST00000450926ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-
intron-intronENST00000536055ENST00000545578ATAD3Achr1

1447853

+CPSF3Lchr1

1250998

-

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 ATAD3A-CPSF3L


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 ATAD3A-CPSF3L


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/:1447853/:1250998)
- 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
ATAD3A

Q9NVI7

.
FUNCTION: Essential for mitochondrial network organization, mitochondrial metabolism and cell growth at organism and cellular level. May play an important role in mitochondrial protein synthesis. May also participate in mitochondrial DNA replication. May bind to mitochondrial DNA D-loops and contribute to nucleoid stability. Required for enhanced channeling of cholesterol for hormone-dependent steroidogenesis. Involved in mitochondrial-mediated antiviral innate immunity (PubMed:31522117). {ECO:0000269|PubMed:17210950, ECO:0000269|PubMed:20154147, ECO:0000269|PubMed:22453275, ECO:0000269|PubMed:31522117}.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 ATAD3A-CPSF3L


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 ATAD3A-CPSF3L


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 ATAD3A-CPSF3L


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 ATAD3A-CPSF3L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATAD3AC4310677HAREL-YOON SYNDROME4CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneATAD3AC0001125Acidosis, Lactic1GENOMICS_ENGLAND
HgeneATAD3AC0007194Hypertrophic Cardiomyopathy1GENOMICS_ENGLAND
HgeneATAD3AC0026847Spinal Muscular Atrophy1GENOMICS_ENGLAND
HgeneATAD3AC0029124Optic Atrophy1GENOMICS_ENGLAND
HgeneATAD3AC0033578Prostatic Neoplasms1CTD_human
HgeneATAD3AC0036439Scoliosis, unspecified1GENOMICS_ENGLAND
HgeneATAD3AC0266470Cerebellar Hypoplasia1GENOMICS_ENGLAND
HgeneATAD3AC0376358Malignant neoplasm of prostate1CTD_human