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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:GGA3-ATF7 (FusionGDB2 ID:33006)

Fusion Gene Summary for GGA3-ATF7

check button Fusion gene summary
Fusion gene informationFusion gene name: GGA3-ATF7
Fusion gene ID: 33006
HgeneTgene
Gene symbol

GGA3

ATF7

Gene ID

23163

11016

Gene namegolgi associated, gamma adaptin ear containing, ARF binding protein 3activating transcription factor 7
Synonyms-ATFA
Cytomap

17q25.1

12q13.13

Type of geneprotein-codingprotein-coding
DescriptionADP-ribosylation factor-binding protein GGA3Golgi-localized, gamma ear-containing, ARF-binding protein 3cyclic AMP-dependent transcription factor ATF-7transcription factor ATF-A
Modification date2020031320200313
UniProtAcc

Q9NZ52

Q5U623

Ensembl transtripts involved in fusion geneENST00000245541, ENST00000351904, 
ENST00000538886, ENST00000578348, 
ENST00000582486, ENST00000582717, 
ENST00000537686, ENST00000579743, 
ENST00000548446, ENST00000328463, 
ENST00000415113, ENST00000420353, 
ENST00000456903, ENST00000546661, 
ENST00000548118, ENST00000591397, 
Fusion gene scores* DoF score4 X 4 X 4=6417 X 13 X 6=1326
# samples 519
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1326*10)=-2.80300945178164
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GGA3 [Title/Abstract] AND ATF7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGGA3(73235870)-ATF7(53901811), # samples:3
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
HgeneGGA3

GO:0031647

regulation of protein stability

17553422|20484053

HgeneGGA3

GO:0031648

protein destabilization

20484053

HgeneGGA3

GO:1902430

negative regulation of amyloid-beta formation

17553422

TgeneATF7

GO:0006355

regulation of transcription, DNA-templated

8288576


check buttonFusion gene breakpoints across GGA3 (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 ATF7 (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
ChimerDB4BRCATCGA-GM-A2DL-01AGGA3chr17

73235870

-ATF7chr12

53901811

-


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Fusion Gene ORF analysis for GGA3-ATF7

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-3UTRENST00000245541ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-3UTRENST00000351904ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-3UTRENST00000538886ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-3UTRENST00000578348ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-3UTRENST00000582486ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-3UTRENST00000582717ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000245541ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000245541ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000245541ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000245541ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000245541ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000245541ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000245541ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000351904ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000351904ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000351904ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000351904ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000351904ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000351904ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000351904ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000538886ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000538886ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000538886ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000538886ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000538886ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000538886ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000538886ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000578348ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000578348ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000578348ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000578348ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000578348ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000578348ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000578348ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582486ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582486ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582486ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582486ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582486ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582486ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582486ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582717ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582717ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582717ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582717ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582717ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582717ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
5CDS-intronENST00000582717ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-3UTRENST00000537686ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-3UTRENST00000579743ENST00000548446GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000537686ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000537686ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000537686ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000537686ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000537686ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000537686ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000537686ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000579743ENST00000328463GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000579743ENST00000415113GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000579743ENST00000420353GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000579743ENST00000456903GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000579743ENST00000546661GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000579743ENST00000548118GGA3chr17

73235870

-ATF7chr12

53901811

-
intron-intronENST00000579743ENST00000591397GGA3chr17

73235870

-ATF7chr12

53901811

-

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 GGA3-ATF7


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)

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 GGA3-ATF7


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/:73235870/:53901811)
- 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
GGA3

Q9NZ52

ATF7

Q5U623

FUNCTION: Plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes. Mediates the ARF-dependent recruitment of clathrin to the TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster-dileucine (DXXLL) motif (PubMed:11301005). Mediates export of the GPCR receptor ADRA2B to the cell surface (PubMed:26811329). nvolved in BACE1 transport and sorting as well as regulation of BACE1 protein levels (PubMed:17553422, PubMed:15615712, PubMed:20484053). Regulates retrograde transport of BACE1 from endosomes to the trans-Golgi network via interaction through the VHS motif and dependent of BACE1 phosphorylation (PubMed:15615712). Modulates BACE1 protein levels independently of the interaction between VHS domain and DXXLL motif through recognition of ubiquitination (PubMed:20484053). Key player in a novel DXXLL-mediated endosomal sorting machinery to the recycling pathway that targets NTRK1 to the plasma membrane (By similarity). {ECO:0000250|UniProtKB:A0A0G2JV04, ECO:0000269|PubMed:11301005, ECO:0000269|PubMed:15615712, ECO:0000269|PubMed:17553422, ECO:0000269|PubMed:20484053, ECO:0000269|PubMed:26811329}.FUNCTION: Recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation. Can both act as an activator or a repressor depending on the context. Mediates MBD1-dependent transcriptional repression, probably by recruiting complexes containing SETDB1. The complex formed with MBD1 and SETDB1 represses transcription and probably couples DNA methylation and histone H3 'Lys-9' trimethylation (H3K9me3) activity (Probable). {ECO:0000305}.

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 GGA3-ATF7


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 GGA3-ATF7


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 GGA3-ATF7


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 GGA3-ATF7


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource