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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:ACTR1A-STN1 (FusionGDB2 ID:HG10121TG79991)

Fusion Gene Summary for ACTR1A-STN1

check button Fusion gene summary
Fusion gene informationFusion gene name: ACTR1A-STN1
Fusion gene ID: hg10121tg79991
HgeneTgene
Gene symbol

ACTR1A

STN1

Gene ID

10121

79991

Gene nameactin related protein 1ASTN1 subunit of CST complex
SynonymsARP1|Arp1A|CTRN1AAF-44|AAF44|OBFC1|RPA-32|bA541N10.2
Cytomap('ACTR1A','ACTR1A')('OBFC1','STN1')

10q24.32

10q24.33

Type of geneprotein-codingprotein-coding
Descriptionalpha-centractinARP1 actin related protein 1 homolog AARP1 actin-related protein 1 homolog A, centractin alphaactin-RPVcentractincentrosome-associated actin homologepididymis secretory sperm binding proteinCST complex subunit STN1STN1, CST complex subunitalpha accessory factor 44oligonucleotide/oligosaccharide binding fold containing 1oligonucleotide/oligosaccharide-binding fold-containing protein 1replication protein A 32 kDa subunitsuppressor of cdc
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000369905, ENST00000487599, 
ENST00000446605, ENST00000545684, 
ENST00000470322, 
Fusion gene scores* DoF score9 X 6 X 6=3243 X 7 X 9=189
# samples 916
** MAII scorelog2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(16/189*10)=-0.24031432933371
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ACTR1A [Title/Abstract] AND STN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointACTR1A(104262357)-OBFC1(105642599), # samples:2
ACTR1A(104262357)-STN1(105642599), # samples:1
Anticipated loss of major functional domain due to fusion event.ACTR1A-OBFC1 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.
ACTR1A-OBFC1 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.
ACTR1A-OBFC1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ACTR1A-OBFC1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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
TgeneSTN1

GO:0032211

negative regulation of telomere maintenance via telomerase

22763445


check buttonFusion gene breakpoints across ACTR1A (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 STN1 (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
ChimerDB4PRADTCGA-VP-A87K-01AACTR1Achr10

104262357

-OBFC1chr10

105642599

-
ChimerDB4PRADTCGA-VP-A87K-01AACTR1Achr10

104262357

-STN1chr10

105642599

-
ChimerDB4PRADTCGA-VP-A87KACTR1Achr10

104262357

-OBFC1chr10

105642599

-


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Fusion Gene ORF analysis for ACTR1A-STN1

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-5UTRENST00000369905ENST00000466828ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
5CDS-5UTRENST00000487599ENST00000466828ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
5UTR-3CDSENST00000446605ENST00000224950ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
5UTR-3CDSENST00000446605ENST00000369764ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
5UTR-3CDSENST00000545684ENST00000224950ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
5UTR-3CDSENST00000545684ENST00000369764ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
5UTR-5UTRENST00000446605ENST00000466828ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
5UTR-5UTRENST00000545684ENST00000466828ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
Frame-shiftENST00000369905ENST00000224950ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
Frame-shiftENST00000487599ENST00000224950ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
In-frameENST00000369905ENST00000369764ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
In-frameENST00000487599ENST00000369764ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
intron-3CDSENST00000470322ENST00000224950ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
intron-3CDSENST00000470322ENST00000369764ACTR1Achr10

104262357

-OBFC1chr10

105642599

-
intron-5UTRENST00000470322ENST00000466828ACTR1Achr10

104262357

-OBFC1chr10

105642599

-

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)
ENST00000369905ACTR1Achr10104262357-ENST00000369764OBFC1chr10105642599-39911218739670
ENST00000487599ACTR1Achr10104262357-ENST00000369764OBFC1chr10105642599-3667915436370

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
ENST00000369905ENST00000369764ACTR1Achr10104262357-OBFC1chr10105642599-0.29541930.70458066
ENST00000487599ENST00000369764ACTR1Achr10104262357-OBFC1chr10105642599-0.543027460.45697257

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Fusion Genomic Features for ACTR1A-STN1


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 ACTR1A-STN1


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/:104262357/:105642599)
- 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
..
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: 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}.

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
TgeneOBFC1chr10:104262357chr10:105642599ENST0000022495081057_155316369.0DNA bindingNote=OB
TgeneOBFC1chr10:104262357chr10:105642599ENST000003697647957_155316369.0DNA bindingNote=OB
TgeneOBFC1chr10:104262357chr10:105642599ENST00000224950810191_295316369.0RegionNote=Winged helix-turn-helix (wHTH) 1
TgeneOBFC1chr10:104262357chr10:105642599ENST00000224950810296_368316369.0RegionNote=Winged helix-turn-helix (wHTH) 2
TgeneOBFC1chr10:104262357chr10:105642599ENST0000036976479191_295316369.0RegionNote=Winged helix-turn-helix (wHTH) 1
TgeneOBFC1chr10:104262357chr10:105642599ENST0000036976479296_368316369.0RegionNote=Winged helix-turn-helix (wHTH) 2


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Fusion Gene Sequence for ACTR1A-STN1


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.
>1822_1822_1_ACTR1A-OBFC1_ACTR1A_chr10_104262357_ENST00000369905_OBFC1_chr10_105642599_ENST00000369764_length(transcript)=399nt_BP=112nt
TCAGTGGCGCTAGCGGCGGACCCGGCTGGGCAGTTCCTTCCCCAGAAGGAGAGATTCCTCTGCCATGGAGTCCTACGATGTGATCGCCAA
CCAGCCTGTCGTGATCGACAACACATGGAGAAGGGCTGTCACTTCCTGCACATCTTGGCCTGTGCTCGCCTGAGCATCCGCCCGGGCCTG
AGCGAGGCTGTGCTGCAGCAAGTTCTGGAGCTCCTGGAGGACCAGAGTGACATTGTCAGCACAATGGAGCACTACTACACAGCGTTCTGA
GCAGAGACACGCAGACCAGCTGAGGAGGACAAAGATAAGGTGGCATTCACCCCCAGGCTCTGACTTTCAGCATCATGCAGGGGCTTATCT

>1822_1822_1_ACTR1A-OBFC1_ACTR1A_chr10_104262357_ENST00000369905_OBFC1_chr10_105642599_ENST00000369764_length(amino acids)=70AA_BP=

--------------------------------------------------------------
>1822_1822_2_ACTR1A-OBFC1_ACTR1A_chr10_104262357_ENST00000487599_OBFC1_chr10_105642599_ENST00000369764_length(transcript)=366nt_BP=79nt
TTCCTTCCCCAGAAGGAGAGATTCCTCTGCCATGGAGTCCTACGATGTGATCGCCAACCAGCCTGTCGTGATCGACAACACATGGAGAAG
GGCTGTCACTTCCTGCACATCTTGGCCTGTGCTCGCCTGAGCATCCGCCCGGGCCTGAGCGAGGCTGTGCTGCAGCAAGTTCTGGAGCTC
CTGGAGGACCAGAGTGACATTGTCAGCACAATGGAGCACTACTACACAGCGTTCTGAGCAGAGACACGCAGACCAGCTGAGGAGGACAAA
GATAAGGTGGCATTCACCCCCAGGCTCTGACTTTCAGCATCATGCAGGGGCTTATCTGTCTGGAGGCAGTTACCTCATAATAAACTATAA

>1822_1822_2_ACTR1A-OBFC1_ACTR1A_chr10_104262357_ENST00000487599_OBFC1_chr10_105642599_ENST00000369764_length(amino acids)=70AA_BP=

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

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Fusion Gene PPI Analysis for ACTR1A-STN1


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
TgeneOBFC1chr10:104262357chr10:105642599ENST000002249508101_185316.3333333333333369.0CTC1
TgeneOBFC1chr10:104262357chr10:105642599ENST00000369764791_185316.3333333333333369.0CTC1


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 ACTR1A-STN1


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 ACTR1A-STN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0085786Hamman-Rich syndrome1ORPHANET
TgeneC0242379Malignant neoplasm of lung1CTD_human
TgeneC0265965Dyskeratosis Congenita1GENOMICS_ENGLAND
TgeneC1800706Idiopathic Pulmonary Fibrosis1CTD_human;ORPHANET
TgeneC2677299CEREBRORETINAL MICROANGIOPATHY WITH CALCIFICATIONS AND CYSTS (disorder)1CTD_human;ORPHANET
TgeneC4479220CEREBRORETINAL MICROANGIOPATHY WITH CALCIFICATIONS AND CYSTS 21GENOMICS_ENGLAND;UNIPROT
TgeneC4721508Hamman-Rich Disease1CTD_human
TgeneC4721509Usual Interstitial Pneumonia1CTD_human
TgeneC4721610Carcinoma, Ovarian Epithelial1CTD_human
TgeneC4721952Familial Idiopathic Pulmonary Fibrosis1CTD_human