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:CHTOP-ICA1 (FusionGDB2 ID:16751)

Fusion Gene Summary for CHTOP-ICA1

check button Fusion gene summary
Fusion gene informationFusion gene name: CHTOP-ICA1
Fusion gene ID: 16751
HgeneTgene
Gene symbol

CHTOP

ICA1

Gene ID

26097

3382

Gene namechromatin target of PRMT1islet cell autoantigen 1
SynonymsC10orf77|C1orf77|FL-SRAG|FOP|SRAG|SRAG-3|SRAG-5|pp7704ICA69|ICAp69
Cytomap

1q21.3

7p21.3

Type of geneprotein-codingprotein-coding
Descriptionchromatin target of PRMT1 proteinfriend of PRMT1 proteinsmall protein rich in arginine and glycineislet cell autoantigen 169 kDa islet cell autoantigendiabetes mellitus type I autoantigenislet cell autoantigen 1 isoformislet cell autoantigen 1, 69kDaislet cell autoantigen p69p69testicular tissue protein Li 162
Modification date2020031320200327
UniProtAcc

Q9Y3Y2

Q8NDH6

Ensembl transtripts involved in fusion geneENST00000495554, ENST00000368694, 
ENST00000403433, ENST00000368686, 
ENST00000368687, ENST00000368690, 
ENST00000265577, ENST00000396675, 
ENST00000401396, ENST00000402384, 
ENST00000406470, ENST00000407906, 
ENST00000422063, ENST00000476942, 
Fusion gene scores* DoF score7 X 8 X 5=28014 X 8 X 8=896
# samples 913
** MAII scorelog2(9/280*10)=-1.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/896*10)=-2.78498710902915
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHTOP [Title/Abstract] AND ICA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHTOP(153606819)-ICA1(8196844), # 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
HgeneCHTOP

GO:0006406

mRNA export from nucleus

23299939

HgeneCHTOP

GO:0032781

positive regulation of ATPase activity

23299939

HgeneCHTOP

GO:0051096

positive regulation of helicase activity

23299939


check buttonFusion gene breakpoints across CHTOP (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 ICA1 (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-7722-01ACHTOPchr1

153606819

+ICA1chr7

8196844

-


Top

Fusion Gene ORF analysis for CHTOP-ICA1

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-3CDSENST00000495554ENST00000265577CHTOPchr1

153606819

+ICA1chr7

8196844

-
3UTR-3CDSENST00000495554ENST00000396675CHTOPchr1

153606819

+ICA1chr7

8196844

-
3UTR-3CDSENST00000495554ENST00000401396CHTOPchr1

153606819

+ICA1chr7

8196844

-
3UTR-3CDSENST00000495554ENST00000402384CHTOPchr1

153606819

+ICA1chr7

8196844

-
3UTR-3CDSENST00000495554ENST00000406470CHTOPchr1

153606819

+ICA1chr7

8196844

-
3UTR-3CDSENST00000495554ENST00000407906CHTOPchr1

153606819

+ICA1chr7

8196844

-
3UTR-3CDSENST00000495554ENST00000422063CHTOPchr1

153606819

+ICA1chr7

8196844

-
3UTR-intronENST00000495554ENST00000476942CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000368694ENST00000265577CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000368694ENST00000396675CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000368694ENST00000401396CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000368694ENST00000402384CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000368694ENST00000406470CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000368694ENST00000407906CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000368694ENST00000422063CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000403433ENST00000265577CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000403433ENST00000396675CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000403433ENST00000401396CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000403433ENST00000402384CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000403433ENST00000406470CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000403433ENST00000407906CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-3CDSENST00000403433ENST00000422063CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-intronENST00000368694ENST00000476942CHTOPchr1

153606819

+ICA1chr7

8196844

-
5UTR-intronENST00000403433ENST00000476942CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368686ENST00000265577CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368686ENST00000396675CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368686ENST00000401396CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368686ENST00000402384CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368686ENST00000406470CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368686ENST00000407906CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368686ENST00000422063CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368687ENST00000265577CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368687ENST00000396675CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368687ENST00000401396CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368687ENST00000402384CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368687ENST00000406470CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368687ENST00000407906CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368687ENST00000422063CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368690ENST00000265577CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368690ENST00000396675CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368690ENST00000401396CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368690ENST00000402384CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368690ENST00000406470CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368690ENST00000407906CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-3CDSENST00000368690ENST00000422063CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-intronENST00000368686ENST00000476942CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-intronENST00000368687ENST00000476942CHTOPchr1

153606819

+ICA1chr7

8196844

-
intron-intronENST00000368690ENST00000476942CHTOPchr1

153606819

+ICA1chr7

8196844

-

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 CHTOP-ICA1


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.

Top

Fusion Protein Features for CHTOP-ICA1


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/:153606819/:8196844)
- 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
CHTOP

Q9Y3Y2

ICA1

Q8NDH6

FUNCTION: Plays an important role in the ligand-dependent activation of estrogen receptor target genes (PubMed:19858291). May play a role in the silencing of fetal globin genes (PubMed:20688955). Recruits the 5FMC complex to ZNF148, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (By similarity). Plays an important role in the tumorigenicity of glioblastoma cells. Binds to 5-hydroxymethylcytosine (5hmC) and associates with the methylosome complex containing PRMT1, PRMT5, MEP50 and ERH. The CHTOP-methylosome complex associated with 5hmC is recruited to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis (PubMed:25284789). {ECO:0000250|UniProtKB:Q9CY57, ECO:0000269|PubMed:19858291, ECO:0000269|PubMed:20688955, ECO:0000269|PubMed:25284789}.; FUNCTION: Required for effective mRNA nuclear export and is a component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. Stimulates DDX39B ATPase and helicase activities. In cooperation with ALYREF/THOC4 enhances NXF1 RNA binding activity (PubMed:23299939). {ECO:0000269|PubMed:23299939}.

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 CHTOP-ICA1


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 CHTOP-ICA1


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 CHTOP-ICA1


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 CHTOP-ICA1


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