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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:TREX1-ATRIP (FusionGDB2 ID:93298)

Fusion Gene Summary for TREX1-ATRIP

check button Fusion gene summary
Fusion gene informationFusion gene name: TREX1-ATRIP
Fusion gene ID: 93298
HgeneTgene
Gene symbol

TREX1

ATRIP

Gene ID

11277

84126

Gene namethree prime repair exonuclease 1ATR interacting protein
SynonymsAGS1|CRV|DRN3|HERNS-
Cytomap

3p21.31

3p21.31

Type of geneprotein-codingprotein-coding
Descriptionthree-prime repair exonuclease 13' repair exonuclease 13'-5' exonuclease TREX1DNase IIIdeoxyribonuclease IIIATR-interacting proteinATM and Rad3-related-interacting protein
Modification date2020031320200313
UniProtAcc.

Q8WXE1

Ensembl transtripts involved in fusion geneENST00000296443, ENST00000433541, 
ENST00000422277, ENST00000436480, 
ENST00000444177, ENST00000456089, 
ENST00000492235, 		ENST00000320211, 
ENST00000346691, ENST00000357105, 
ENST00000412052, 
Fusion gene scores* DoF score1 X 1 X 1=12 X 2 X 2=8
# samples 12
** MAII scorelog2(1/1*10)=3.32192809488736log2(2/8*10)=1.32192809488736
Context

PubMed: TREX1 [Title/Abstract] AND ATRIP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTREX1(48507708)-ATRIP(48505144), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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 buttonFusion gene breakpoints across TREX1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ATRIP (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4UCECTCGA-BS-A0TI-01ATREX1chr3

48507708

+ATRIPchr3

48505144

+


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Fusion Gene ORF analysis for TREX1-ATRIP

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
5UTR-3CDSENST00000296443ENST00000320211TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000296443ENST00000346691TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000296443ENST00000357105TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000296443ENST00000412052TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000433541ENST00000320211TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000433541ENST00000346691TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000433541ENST00000357105TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000433541ENST00000412052TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000422277ENST00000320211TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000422277ENST00000346691TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000422277ENST00000357105TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000422277ENST00000412052TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000436480ENST00000320211TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000436480ENST00000346691TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000436480ENST00000357105TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000436480ENST00000412052TREX1chr3

48507708

+ATRIPchr3

48505144

+
intron-3CDSENST00000444177ENST00000320211TREX1chr3

48507708

+ATRIPchr3

48505144

+
intron-3CDSENST00000444177ENST00000346691TREX1chr3

48507708

+ATRIPchr3

48505144

+
intron-3CDSENST00000444177ENST00000357105TREX1chr3

48507708

+ATRIPchr3

48505144

+
intron-3CDSENST00000444177ENST00000412052TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000456089ENST00000320211TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000456089ENST00000346691TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000456089ENST00000357105TREX1chr3

48507708

+ATRIPchr3

48505144

+
5UTR-3CDSENST00000456089ENST00000412052TREX1chr3

48507708

+ATRIPchr3

48505144

+
3UTR-3CDSENST00000492235ENST00000320211TREX1chr3

48507708

+ATRIPchr3

48505144

+
3UTR-3CDSENST00000492235ENST00000346691TREX1chr3

48507708

+ATRIPchr3

48505144

+
3UTR-3CDSENST00000492235ENST00000357105TREX1chr3

48507708

+ATRIPchr3

48505144

+
3UTR-3CDSENST00000492235ENST00000412052TREX1chr3

48507708

+ATRIPchr3

48505144

+

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 TREX1-ATRIP


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)
TREX1chr348507708+ATRIPchr348505143+0.3856450.61435497
TREX1chr348507708+ATRIPchr348505143+0.3856450.61435497

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for TREX1-ATRIP


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.ATRIP

Q8WXE1

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Required for checkpoint signaling after DNA damage. Required for ATR expression, possibly by stabilizing the protein. {ECO:0000269|PubMed:12791985}.

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 TREX1-ATRIP


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 TREX1-ATRIP


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 TREX1-ATRIP


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 TREX1-ATRIP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTREX1C0796126AICARDI-GOUTIERES SYNDROME 114CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTREX1C1860518Vasculopathy, Retinal, With Cerebral Leukodystrophy8CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneTREX1C0024141Lupus Erythematosus, Systemic5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneTREX1C0024145Chilblain lupus 14CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTREX1C0393591AICARDI-GOUTIERES SYNDROME4CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneTREX1C0006111Brain Diseases1CTD_human
HgeneTREX1C0013421Dystonia1GENOMICS_ENGLAND
HgeneTREX1C0021368Inflammation1CTD_human
HgeneTREX1C0021400Influenza1CTD_human
HgeneTREX1C0022658Kidney Diseases1GENOMICS_ENGLAND
HgeneTREX1C0035309Retinal Diseases1GENOMICS_ENGLAND
HgeneTREX1C0036572Seizures1GENOMICS_ENGLAND
HgeneTREX1C0085584Encephalopathies1CTD_human
HgeneTREX1C0242380Libman-Sacks Disease1CTD_human
HgeneTREX1C1962966Retinopathy, CTCAE1GENOMICS_ENGLAND
HgeneTREX1C3489724Aicardi-Goutieres Syndrome 21CTD_human
HgeneTREX1C3489725Pseudo-TORCH syndrome1CTD_human
HgeneTREX1C3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneTREX1C3860213Autoinflammatory disorder1GENOMICS_ENGLAND
HgeneTREX1C4303791Cerebroretinal vasculopathy1GENOMICS_ENGLAND
TgeneATRIPC0265202Seckel syndrome1GENOMICS_ENGLAND;ORPHANET