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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:RPS4Y1-ARGLU1 (FusionGDB2 ID:HG6192TG55082)

Fusion Gene Summary for RPS4Y1-ARGLU1

check button Fusion gene summary
Fusion gene informationFusion gene name: RPS4Y1-ARGLU1
Fusion gene ID: hg6192tg55082
HgeneTgene
Gene symbol

RPS4Y1

ARGLU1

Gene ID

6192

55082

Gene nameribosomal protein S4 Y-linked 1arginine and glutamate rich 1
SynonymsRPS4Y|S4-
Cytomap('RPS4Y1')('ARGLU1')

Yp11.2

13q33.3

Type of geneprotein-codingprotein-coding
Description40S ribosomal protein S4, Y isoform 140S ribosomal protein S4, Yribosomal protein S4, Y-linkedribosomal protein S4Ysmall ribosomal subunit protein eS4arginine and glutamate-rich protein 1
Modification date2020031320200313
UniProtAcc.

Q9NWB6

Ensembl transtripts involved in fusion geneENST00000477725, ENST00000250784, 
Fusion gene scores* DoF score8 X 8 X 3=1928 X 7 X 3=168
# samples 88
** MAII scorelog2(8/192*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPS4Y1 [Title/Abstract] AND ARGLU1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPS4Y1(2733176)-ARGLU1(107220075), # samples:1
Anticipated loss of major functional domain due to fusion event.RPS4Y1-ARGLU1 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.
RPS4Y1-ARGLU1 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.
RPS4Y1-ARGLU1 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.
RPS4Y1-ARGLU1 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 RPS4Y1 (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 ARGLU1 (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


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Fusion Gene ORF analysis for RPS4Y1-ARGLU1

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

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
ENST00000250784ENST00000400198RPS4Y1chrY2733176+ARGLU1chr13107220075+0.000266120.99973387

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Fusion Genomic Features for RPS4Y1-ARGLU1


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 RPS4Y1-ARGLU1


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/chrY:2733176/chr13:107220075)
- 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
.ARGLU1

Q9NWB6

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: Required for the estrogen-dependent expression of ESR1 target genes. Can act in cooperation with MED1. {ECO:0000269|PubMed:21454576}.

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
TgeneARGLU1chrY:2733176chr13:107220075ENST00000400198043_740274.0Compositional biasNote=Arg-rich
TgeneARGLU1chrY:2733176chr13:107220075ENST000004001980497_2510274.0Compositional biasNote=Glu-rich

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRPS4Y1chrY:2733176chr13:107220075ENST00000250784+1742_1040264.0DomainNote=S4 RNA-binding


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Fusion Gene Sequence for RPS4Y1-ARGLU1


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.
>77944_77944_1_RPS4Y1-ARGLU1_RPS4Y1_chrY_2733176_ENST00000250784_ARGLU1_chr13_107220075_ENST00000400198_length(transcript)=3734nt_BP=781nt
TTCCAGGATATGAACTCTACAGCGGAAGAATAAGAAACCGGAACTAAACTTCTCACTCATCTGACTTCCTGCGGTTTACGACAACAGACT
TTGGTTGCACCGGAAAAGAACAGATTCTCTTCCGTCGCAGAGTTTCGCCATGGCCCGGGGCCCCAAGAAGCACTTAAAGCGTGTTGCAGC
GCCGAAGCATTGGATGCTTGACAAACTAACGGGTGTATTTGCACCTCGTCCATCGACAGGTCCCCACAAGCTGAGGGAATGTCTTCCTCT
GATCGTCTTCCTCAGGAATAGACTCAAGTATGCGTTGACTGGAGATGAGGTAAAGAAGATATGTATGCAACGTTTCATCAAAATTGATGG
CAAGGTTCGAGTGGATGTCACATACCCTGCTGGATTCATGGATGTCATCAGCATCGAGAAGACAGGTGAACATTTCCGCCTGGTCTATGA
CACCAAGGGCCGTTTTGCTGTTCACCGCATCACAGTGGAAGAGGCAAAGTACAAGTTGTGCAAAGTGAGGAAGATTACTGTGGGAGTGAA
GGGAATCCCTCACCTGGTGACTCATGATGCTCGAACCATCCGCTACCCAGATCCTGTCATCAAGGTGAACGATACTGTGCAGATTGATTT
AGGGACTGGCAAGATAATCAACTTTATCAAATTTGATACAGTGATCACCAACAGGGAAAGACATCCTGGTTCTTTTGATGTGGTGCATGT
GAAGGATGCCAATGGCAACAGCTTTGCCACGAGGCTTTCCAACATTTTTGTCATTGGCAATGCCGAAGAACAGTTGAGAATTGTTGAAGA
ACAAAGAAAGATTCATGAGGAAAGGATGAAACTAGAACAAGAACGACAACGTCAACAAAAAGAAGAACAAAAAATTATCCTGGGCAAGGG
GAAGTCCAGGCCAAAACTGTCCTTCTCATTAAAAACCCAGGATTAAATTGCAAACTCTGAACTTTTTACAAAGAAAAATGGAAAAACTTT
GTATGGTAGCTTCATGTTGAAGTGGTTTTTTGTTTTTGTTTTTGTTTTTTTAATTTGTAAAATCTGGAAAGTTAGCTTGTTCTAATAGGG
GCTATGCTCTGCAATTCCCTTTTTTTTTTTTTTTTTCCTTCCACTAAGTCAAATCCTTATCAGATCATTGTTGTATTCTAAGGAGTGACG
TATTTTTCACCTGTTTGGATTCTATATTAGTGGTCTGAGGAAGAGCAGATCACATTGTAAAACTATGGATGGTCTGATAAGGCTTTTACT
GACCCCACTGACTTCAGAGTTATACTCTGTTTGCTACATCATAATGCTGGTTTTGCTGACTTTTTGTTTTTTTATATATTTATAAAAAAA
GAAAAAGTTGGTGATTGCATTGGGAAATTCCCAGGGTATTACTGGACCTATGTGGTGTATTGTTAAACCAGTGTCCTTGTGATACTGTTG
CTCTTGATGTTCCTGATACAGGTAAGGAAACAGTTGGTCAACTCTGATACAAAGTATATATACAGTTCAGTATTGTCTCTGTTCATTTTG
TTTTTATTTCATTGACAAAATCAAACCAGCATTCCCCATTGTGTAAATAAATGATTTTGCTGAATAAAGTAAAGTCTTAAATTCATATGT
TGAAGCAATTTTTTTTAATGTTATGTTAAGTCTTAAAGAGGGTGGTTCACTTTTTGATGGTCAACCATTTAGAAGTCTTAGAACTATATT
TCCTCTTGTTTATACTTTTAACATAGGGTTTATATGTACATTAAATATACTTGTGAATTAGTATTTAATGGCTATTTTTACAAATATCAA
CTTTATGCTGATAGAGCAAATGGCATCAGTGTTACCTTTAAGAAAGACTAACAACATCCAGAAGATTTAAATTCTCAAACCTGTGCCTCT
GTTTTAGGATATAAGTATTATCACAAAGTATACTTAATAAAGGCTAGAAAAATGCTTTTAAATTATGGAATCTGAGATCGTTTTCAGAGT
GGGCCATCAGAAAGAACTTAGCTTTATACTGTCAAAAAAAGGCTAAGATGGTCGAGTCATTTTCATTGTGTAGTGTACTTGCACGTTTAT
TTTTAGGACAAACACATTTGAACTTTATGAATTTTTTTTTTTTTTTTGCATGTGAAATCTTATGAATGGCTTTCATTTTATACACTAGAA
TCTGCCTCATTTACTCTTAACATATGTTTAAGTATACTGGTATTAAAACATTCAAGAAAAGGATATTGATCTAAAATGCTACCTGAGATG
CATAAACATGTCATCAAGTAGAGAAAATATTTTTATTTTTGCCCAATATTTTTTAGACAGTTTGATTATTCTTAAAAATTGAAAACATAA
GCTAAAGAGATGACTAAATGGTAGATTATTTTGTGTGTGCATGCTAGGAAAAATGCTGTTGCTTTAGTTTTGAGCTCTTCAATGAGTCTA
ATTGTGGTAAGGAACAATATAAAATCAGTTTAAAGATCTTTAAAGGTAGAATTTTAAATAGGCATGAAATATAGTGAGAACTTTTAGTAA
ACATACTACTTACTCTAAAATCAAACATTTTATTTTCCTAAAGAATATAGGTTGCCAAAAAATATTTTATCTCTAAATATAGGTTAGCTG
TAATTATTTCATGAATTTTTTTTTTTTTCAATGTAACTTTTTTTGGTGAAGATTCATGGTTCCTAAGTTCTGTATTCAAGTTTTTGGAAA
TGTTTATTTAAAAACTGTTCTATACAAGTGTTCAAAACATTGTATCTAAAGAGAGTAGCCTGGACTTAAAATATTTGAAATCAGCTTATG
CGTGCCTTTTAATTTTTTTTTTAAGTTTCTTACTGCCACATATGGTGTGAAGTGACAGTAAGTTGCTTAATGACATCCTGCAGTATCTGC
TTGCTTTTGGAGACTCCAGTGAGATGTTGAAATTGTTCCTGTGCTTGGTAACTACTTTCCTCTGCCAGGCTATGGGAAAGAGGATGTAAT
TGTGAATAATATACACCATCCAGTCTTTAATGTGCTGCAACAATGTAGTAATTTGTTTTTTTCATTTGTTCCCACTGCCTTTGTGTACAT
AGAAAACTTAAAAATTTCCCCCAGTCTATTAGAAGTTAAGATGTTCCCTAATTTATTAAATATGCCTTTATTCACAATTTGTTTTTTTAG
GTTATTCTTAATGCATTATAGAATTAAGTATGACTTTGTTTATTTTTATTACAGTATGTAGTTATTGACATATTGTGGTTTGCAGAATTA
TCAATTGTATAAACTAAACCTTTAAATTAGAGGAAGAACGTGCAAAACGTGAGGAGCTAGAGCGAATACTGGAAGAGAATAACCGAAAAA
TTGCAGAAGCACAAGCCAAACTGTCGACAGCAAGAAATAGAAGAAAAACTCATCGAGGAAGAAACAGCACGAAGAGTAGAAGAATTGGTA
GCAAAAAGGGTGGAGGAAGAACTGGAGAAAAGGAAGGATGAAATTGAACGAGAAGTTCTCCGAAGGGTGGAGGAAGCCAAACGCATCATG
GAAAAGCAGTTGCTCGAAGAACTCGAGCGACAGAGACAAGCTGAGCTTGCCGCACAAAAAGCTAGAGAGGTGTCCCGGCGCGAGCGGGAC
CGGGAGCGCGCCTCGTCCCCGCCCGACCGCATCGACATCTTCGGGCGCACGGTGAGCAAGCGCAGCAGCCTGGACGAGAAGCAGAAGCGA

>77944_77944_1_RPS4Y1-ARGLU1_RPS4Y1_chrY_2733176_ENST00000250784_ARGLU1_chr13_107220075_ENST00000400198_length(amino acids)=283AA_BP=
MHRKRTDSLPSQSFAMARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGK
VRVDVTYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTVQIDLG
TGKIINFIKFDTVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNAEEQLRIVEEQRKIHEERMKLEQERQRQQKEEQKIILGKGK

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Fusion Gene PPI Analysis for RPS4Y1-ARGLU1


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 RPS4Y1-ARGLU1


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 RPS4Y1-ARGLU1


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