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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:ARPC1A-ICA1 (FusionGDB2 ID:HG10552TG3382)

Fusion Gene Summary for ARPC1A-ICA1

check button Fusion gene summary
Fusion gene informationFusion gene name: ARPC1A-ICA1
Fusion gene ID: hg10552tg3382
HgeneTgene
Gene symbol

ARPC1A

ICA1

Gene ID

10552

3382

Gene nameactin related protein 2/3 complex subunit 1Aislet cell autoantigen 1
SynonymsArc40|HEL-68|HEL-S-307|SOP2Hs|SOP2LICA69|ICAp69
Cytomap('ARPC1A')('ICA1')

7q22.1

7p21.3

Type of geneprotein-codingprotein-coding
Descriptionactin-related protein 2/3 complex subunit 1ASOP2-like proteinactin binding protein (Schizosaccharomyces pombe sop2-like)actin related protein 2/3 complex, subunit 1A, 41kDaepididymis luminal protein 68epididymis secretory protein Li 307epididymis seislet 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.

Q05084

Ensembl transtripts involved in fusion geneENST00000432884, ENST00000262942, 
ENST00000471960, 
Fusion gene scores* DoF score8 X 6 X 6=28814 X 8 X 8=896
# samples 813
** MAII scorelog2(8/288*10)=-1.84799690655495
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: ARPC1A [Title/Abstract] AND ICA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARPC1A(98983401)-ICA1(8153674), # samples:1
Anticipated loss of major functional domain due to fusion event.ARPC1A-ICA1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ARPC1A-ICA1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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

check buttonFusion gene breakpoints across ARPC1A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
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.
all structure

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
ChimerDB4Non-CancerERR315384ARPC1Achr7

98983401

+ICA1chr7

8153674

-


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Fusion Gene ORF analysis for ARPC1A-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
5CDS-intronENST00000432884ENST00000407906ARPC1Achr7

98983401

+ICA1chr7

8153674

-
5CDS-intronENST00000432884ENST00000476942ARPC1Achr7

98983401

+ICA1chr7

8153674

-
Frame-shiftENST00000432884ENST00000265577ARPC1Achr7

98983401

+ICA1chr7

8153674

-
Frame-shiftENST00000432884ENST00000396675ARPC1Achr7

98983401

+ICA1chr7

8153674

-
Frame-shiftENST00000432884ENST00000401396ARPC1Achr7

98983401

+ICA1chr7

8153674

-
Frame-shiftENST00000432884ENST00000402384ARPC1Achr7

98983401

+ICA1chr7

8153674

-
Frame-shiftENST00000432884ENST00000422063ARPC1Achr7

98983401

+ICA1chr7

8153674

-
In-frameENST00000432884ENST00000406470ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000262942ENST00000265577ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000262942ENST00000396675ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000262942ENST00000401396ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000262942ENST00000402384ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000262942ENST00000406470ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000262942ENST00000422063ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000471960ENST00000265577ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000471960ENST00000396675ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000471960ENST00000401396ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000471960ENST00000402384ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000471960ENST00000406470ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-3CDSENST00000471960ENST00000422063ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-intronENST00000262942ENST00000407906ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-intronENST00000262942ENST00000476942ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-intronENST00000471960ENST00000407906ARPC1Achr7

98983401

+ICA1chr7

8153674

-
intron-intronENST00000471960ENST00000476942ARPC1Achr7

98983401

+ICA1chr7

8153674

-

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)
ENST00000432884ARPC1Achr798983401+ENST00000406470ICA1chr78153674-232914714611480339

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
ENST00000432884ENST00000406470ARPC1Achr798983401+ICA1chr78153674-0.0184943150.9815057

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Fusion Genomic Features for ARPC1A-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.
genomic feature

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Fusion Protein Features for ARPC1A-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/chr7:98983401/chr7:8153674)
- 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
.ICA1

Q05084

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}.FUNCTION: May play a role in neurotransmitter secretion. {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
HgeneARPC1Achr7:98983401chr7:8153674ENST00000262942+110140_1790371.0RepeatNote=WD 3
HgeneARPC1Achr7:98983401chr7:8153674ENST00000262942+110202_2410371.0RepeatNote=WD 4
HgeneARPC1Achr7:98983401chr7:8153674ENST00000262942+110244_2840371.0RepeatNote=WD 5
HgeneARPC1Achr7:98983401chr7:8153674ENST00000262942+110322_3650371.0RepeatNote=WD 6
HgeneARPC1Achr7:98983401chr7:8153674ENST00000262942+11050_890371.0RepeatNote=WD 2
HgeneARPC1Achr7:98983401chr7:8153674ENST00000262942+1106_450371.0RepeatNote=WD 1
TgeneICA1chr7:98983401chr7:8153674ENST00000396675121451_254443484.0DomainAH
TgeneICA1chr7:98983401chr7:8153674ENST00000402384121451_254443484.0DomainAH
TgeneICA1chr7:98983401chr7:8153674ENST00000406470121451_254443484.0DomainAH
TgeneICA1chr7:98983401chr7:8153674ENST00000422063121451_254472513.0DomainAH


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Fusion Gene Sequence for ARPC1A-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.
>6763_6763_1_ARPC1A-ICA1_ARPC1A_chr7_98983401_ENST00000432884_ICA1_chr7_8153674_ENST00000406470_length(transcript)=2329nt_BP=1471nt
CTCTGGGCTTCCGTCCTCCGCCCGCGCCCGACGGAGCCTGTTCGCGTCGACTGCCCAGAGTCCGCGAATCCTCCGCTCCGAGCCCGTCCG
GACTCCCCCGATCCCAGCTTTCTCTCCTTTGAAAACACTAAGAATAATGTCACTGCATCAGTTTTTACTAGAGCCAATCACCTGTCATGC
CTGGAACAGGGATCGTACTCGACCAGTCTGTCTTGATTACTATAGCTTGGTGAGATTGCCCTCAGTCCCAATAATCACGAAGTGCACATC
TATAAGAAGAACGGGAGCCAGTGGGTGAAAGCTCATGAACTCAAGGAGCACAACGGACACATCACAGGGTATGCATATCTGCAGTGCAGT
GTTGCCAGGCCTCATCAGATTGCCATCATTCCCACCTGTCCTGTATGAGAGTGCTCATTTTCCCACACCCCGCCACATACTTGAGATGGG
AAGACTGAAGAATGCATGAAAGGTTCATCCATTGCTTCTGTATTGACTGGGCTCCCAAGAGCGACCGCATTGTCACTTGTGGGGCAGACC
GCAATGCCTATGTCTGGAGTCAGAAAGATGGTGTTTGGAAGCCAACCCTGGTGATCCTGAGAATTAATCGCGCAGCTACTTTTGTGAAGT
GGTCCCCCCTAGAGAACAAATTTGCTGTGGGAAGTGGAGCACGACTCATTTCTGTTTGTTACTTTGAGTCTGAAAATGACTGGTGGGTGA
GCAAGCACATTAAAAAGCCGATTCGCTCCACAGTCCTCAGCTTGGATTGGCATCCCAACAACGTTTTGCTGGCAGCAGGATCATGTGACT
TCAAATGCAGAGTGTTTTCTGCCTACATTAAAGAAGTGGATGAAAAGCCAGCCAGCACGCCCTGGGGCAGCAAGATGCCTTTTGGGCAGC
TGATGTCAGAGTTTGGTGGCAGTGGCACTGGTGGCTGGGTCCACGGGGTAAGCTTCTCTGCCAGTGGGAGCCGCCTGGCCTGGGTCAGCC
ACGACAGCACCGTGTCTGTTGCTGATGCCTCAAAAAGTGTGCAGGTCTCGACTCTGAAGACAGAGTTCCTGCCGCTCCTAAGTGTGTCAT
TTGTCTCAGAGAACAGCGTCGTGGCTGCTGGCCATGACTGCTGCCCAATGCTCTTTAACTACGATGACCGCGGCTGCCTGACCTTCGTCT
CCAAGTTAGATATTCCAAAACAGAGCATCCAACGCAACATGTCTGCCATGGAACGCTTCCGCAACATGGACAAGAGAGCCACAACTGAGG
ACCGCAACACGGCCTTGGAGACGCTGCACCAGAATAGCATCACTCAAGTCTCTATTTATGAGGTGGACAAGCAAGATTGTCGCAAATTTT
GCACTACTGGCATCGATGGAGCCATGACAATTTGGGATTTCAAGGAGCCAAGCCGCCATGGCCTACCACAGCTTCCTGGTGGAGCCCATC
AGCTGCCACGCCTGGAACAAGGACCGCACCCAACCTGCTAAGGCTGCCTCAGACCTGACTGCCTGGTTCAGCCTCTTCGCTGACCTCGAC
CCACTCTCAAATCCTGATGCTGTTGGGAAAACCGATAAAGAACACGAATTGCTCAATGCATGAATCTGTACCCTTCGGGAGGGCACTCAC
ATGCCGCCCCCAGCAGCTCCCCTGGGGGCTAGCAGAAGTATAAAGTGATCAGTATGCTGTTTTAATAATTATGTGCCATTTTAATAAAAT
GAAAGGGTCAACGGCCCTGTTTATATTGGTATAATTATTTACTCTTATTTGGTATAAAGGGTTTTCGTGTATCTCTATGTGGATCTAAAT
AATACAGGATTGTCTAGAAGCGGTTTCCAGGCCACCGCTCTCCTGCCTACATCCCATCATGGCTGCTGCGGTGTCACTGGGCTACCGTGA
GATCCAAGTTGAAATCAGAAGCCTACTTTGATGGTAGGTTTGAATGACGTGTCCTACAGCCTCAGAGGCAGCAGGAGGCTAGCAAAGCTT
AAATGCCTCCTTCTCTGCCCCCAGCCTCTGTCCCCCTTGGAGGAGGGCTGTAGGAAGATTCCCTCTTCCTGCCAAGCCACCTTCCAGTGA
GCTCTGGATGAAGCTCTGGCCAACCAAAGACACTGTCCCCACAGCAGGTGCCTGGTGGGCCACGTGTTCTCACACTGGTGGAGGAGCTGG
GCTTCTGTCCAAGGCACAAACCTTACTATGGAAAGCAGCCATATTTGCAGATACCACTGTCTCCTTTTGTCCTCTTCGTGGCTGGAATTC

>6763_6763_1_ARPC1A-ICA1_ARPC1A_chr7_98983401_ENST00000432884_ICA1_chr7_8153674_ENST00000406470_length(amino acids)=339AA_BP=
MHERFIHCFCIDWAPKSDRIVTCGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHI
KKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDST
VSVADASKSVQVSTLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAMERFRNMDKRATTEDRNT

--------------------------------------------------------------

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Fusion Gene PPI Analysis for ARPC1A-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


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Related Drugs for ARPC1A-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

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Related Diseases for ARPC1A-ICA1


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