FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:GTF2A2-CTDSPL2 (FusionGDB2 ID:35160)

Fusion Gene Summary for GTF2A2-CTDSPL2

check button Fusion gene summary
Fusion gene informationFusion gene name: GTF2A2-CTDSPL2
Fusion gene ID: 35160
HgeneTgene
Gene symbol

GTF2A2

CTDSPL2

Gene ID

2958

51496

Gene namegeneral transcription factor IIA subunit 2CTD small phosphatase like 2
SynonymsHsT18745|T18745|TF2A2|TFIIA|TFIIA-12|TFIIA-gamma|TFIIASHSPC058|HSPC129|SCP4
Cytomap

15q22.2

15q15.3-q21.1

Type of geneprotein-codingprotein-coding
Descriptiontranscription initiation factor IIA subunit 2TFIIA gamma subunitTFIIA p12 subunitgeneral transcription factor IIA 2general transcription factor IIA, 2, 12kDatranscription initiation factor IIA gamma chainCTD small phosphatase-like protein 2CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2CTDSP-like 2
Modification date2020031320200313
UniProtAcc

P52657

Q05D32

Ensembl transtripts involved in fusion geneENST00000267869, ENST00000396060, 
ENST00000396063, ENST00000396064, 
ENST00000484743, ENST00000396061, 
ENST00000260327, ENST00000396780, 
ENST00000558966, ENST00000558373, 
ENST00000561189, 
Fusion gene scores* DoF score6 X 5 X 3=908 X 10 X 4=320
# samples 611
** MAII scorelog2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/320*10)=-1.5405683813627
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GTF2A2 [Title/Abstract] AND CTDSPL2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGTF2A2(59949605)-CTDSPL2(44751189), # 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
HgeneGTF2A2

GO:0006366

transcription by RNA polymerase II

7724559|7958900|8626665|27193682

HgeneGTF2A2

GO:0045944

positive regulation of transcription by RNA polymerase II

7958899

HgeneGTF2A2

GO:0051091

positive regulation of DNA-binding transcription factor activity

8626665

HgeneGTF2A2

GO:0051123

RNA polymerase II preinitiation complex assembly

7958899|8626665


check buttonFusion gene breakpoints across GTF2A2 (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 CTDSPL2 (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
ChimerDB4STADTCGA-BR-A4QI-01AGTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+


Top

Fusion Gene ORF analysis for GTF2A2-CTDSPL2

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-5UTRENST00000267869ENST00000260327GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000267869ENST00000396780GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000267869ENST00000558966GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396060ENST00000260327GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396060ENST00000396780GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396060ENST00000558966GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396063ENST00000260327GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396063ENST00000396780GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396063ENST00000558966GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396064ENST00000260327GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396064ENST00000396780GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000396064ENST00000558966GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000484743ENST00000260327GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000484743ENST00000396780GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-5UTRENST00000484743ENST00000558966GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000267869ENST00000558373GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000267869ENST00000561189GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000396060ENST00000558373GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000396060ENST00000561189GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000396063ENST00000558373GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000396063ENST00000561189GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000396064ENST00000558373GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000396064ENST00000561189GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000484743ENST00000558373GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
5UTR-intronENST00000484743ENST00000561189GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
intron-5UTRENST00000396061ENST00000260327GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
intron-5UTRENST00000396061ENST00000396780GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
intron-5UTRENST00000396061ENST00000558966GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
intron-intronENST00000396061ENST00000558373GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+
intron-intronENST00000396061ENST00000561189GTF2A2chr15

59949605

-CTDSPL2chr15

44751189

+

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

Top

Fusion Genomic Features for GTF2A2-CTDSPL2


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)
GTF2A2chr1559949604-CTDSPL2chr1544751188+0.0047897930.99521023
GTF2A2chr1559949604-CTDSPL2chr1544751188+0.0047897930.99521023

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.
genomic feature of top 1%

Top

Fusion Protein Features for GTF2A2-CTDSPL2


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/:59949605/:44751189)
- 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
GTF2A2

P52657

CTDSPL2

Q05D32

FUNCTION: TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity. {ECO:0000269|PubMed:11030333}.FUNCTION: Probable phosphatase. {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


Top

Fusion Gene Sequence for GTF2A2-CTDSPL2


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.

Top

Fusion Gene PPI Analysis for GTF2A2-CTDSPL2


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


Top

Related Drugs for GTF2A2-CTDSPL2


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

Top

Related Diseases for GTF2A2-CTDSPL2


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