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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SHROOM4-ARID3A

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SHROOM4-ARID3A
FusionPDB ID: 81796
FusionGDB2.0 ID: 81796
HgeneTgene
Gene symbol

SHROOM4

ARID3A

Gene ID

57477

1820

Gene nameshroom family member 4AT-rich interaction domain 3A
SynonymsSHAP|shrm4BRIGHT|DRIL1|DRIL3|E2FBP1
Cytomap

Xp11.22

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionprotein Shroom4second homolog of apical proteinAT-rich interactive domain-containing protein 3AARID domain-containing 3AARID domain-containing protein 3AAT rich interactive domain 3A (BRIGHT- like) proteinAT rich interactive domain 3A (BRIGHT-like)B-cell regulator of IgH transcriptionE2F-binding
Modification date2020031320200313
UniProtAcc.

Q99856

Ensembl transtripts involved in fusion geneENST idsENST00000289292, ENST00000376020, 
ENST00000460112, ENST00000483955, 
ENST00000592216, ENST00000263620, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 4 X 6=1448 X 9 X 5=360
# samples 710
** MAII scorelog2(7/144*10)=-1.04064198449735
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SHROOM4 [Title/Abstract] AND ARID3A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SHROOM4(50556902)-ARID3A(960092), # samples:4
Anticipated loss of major functional domain due to fusion event.SHROOM4-ARID3A 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.
SHROOM4-ARID3A 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.
SHROOM4-ARID3A 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.
SHROOM4-ARID3A 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
HgeneSHROOM4

GO:0000902

cell morphogenesis

16684770

HgeneSHROOM4

GO:0007420

brain development

16249884

HgeneSHROOM4

GO:0050890

cognition

16249884


check buttonFusion gene breakpoints across SHROOM4 (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 ARID3A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4UCECTCGA-BK-A0CC-01ASHROOM4chrX

50556902

-ARID3Achr19

960092

+
ChimerDB4UCECTCGA-BK-A0CC-01BSHROOM4chrX

50556902

-ARID3Achr19

960092

+
ChimerDB4UCECTCGA-BK-A0CCSHROOM4chrX

50556901

-ARID3Achr19

960091

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000376020SHROOM4chrX50556902-ENST00000263620ARID3Achr19960092+5106143261231401
ENST00000289292SHROOM4chrX50556902-ENST00000263620ARID3Achr19960092+53644012841489401
ENST00000376020SHROOM4chrX50556901-ENST00000263620ARID3Achr19960091+5106143261231401
ENST00000289292SHROOM4chrX50556901-ENST00000263620ARID3Achr19960091+53644012841489401

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
ENST00000376020ENST00000263620SHROOM4chrX50556902-ARID3Achr19960092+0.0024555230.99754447
ENST00000289292ENST00000263620SHROOM4chrX50556902-ARID3Achr19960092+0.0026123330.9973877
ENST00000376020ENST00000263620SHROOM4chrX50556901-ARID3Achr19960091+0.0024555230.99754447
ENST00000289292ENST00000263620SHROOM4chrX50556901-ARID3Achr19960091+0.0026123330.9973877

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>81796_81796_1_SHROOM4-ARID3A_SHROOM4_chrX_50556901_ENST00000289292_ARID3A_chr19_960091_ENST00000263620_length(amino acids)=401AA_BP=37
MENRPGSFQYVPVQLQGGAPWGFTLKGGLEHCEPLTVSKLYELDGDPKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEK
GGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQAAIDSNRREGRRQSFGGSLFAYSPGGAHGMLSS
PKLPVSSLGLAASTNGSSITPAPKIKKEEDSAIPITVPGRLPVSLAGHPVVAAQAAAVQAAAAQAAVAAQAAALEQLREKLESAEPPEKK
MALVADEQQRLMQRALQQNFLAMAAQLPMSIRINSQASESRQDSAVNLTGTNGSNSISMSVEINGIMYTGVLFAQPPAPTPTSAPNKGGG

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

>81796_81796_2_SHROOM4-ARID3A_SHROOM4_chrX_50556901_ENST00000376020_ARID3A_chr19_960091_ENST00000263620_length(amino acids)=401AA_BP=37
MENRPGSFQYVPVQLQGGAPWGFTLKGGLEHCEPLTVSKLYELDGDPKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEK
GGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQAAIDSNRREGRRQSFGGSLFAYSPGGAHGMLSS
PKLPVSSLGLAASTNGSSITPAPKIKKEEDSAIPITVPGRLPVSLAGHPVVAAQAAAVQAAAAQAAVAAQAAALEQLREKLESAEPPEKK
MALVADEQQRLMQRALQQNFLAMAAQLPMSIRINSQASESRQDSAVNLTGTNGSNSISMSVEINGIMYTGVLFAQPPAPTPTSAPNKGGG

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

>81796_81796_3_SHROOM4-ARID3A_SHROOM4_chrX_50556902_ENST00000289292_ARID3A_chr19_960092_ENST00000263620_length(amino acids)=401AA_BP=37
MENRPGSFQYVPVQLQGGAPWGFTLKGGLEHCEPLTVSKLYELDGDPKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEK
GGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQAAIDSNRREGRRQSFGGSLFAYSPGGAHGMLSS
PKLPVSSLGLAASTNGSSITPAPKIKKEEDSAIPITVPGRLPVSLAGHPVVAAQAAAVQAAAAQAAVAAQAAALEQLREKLESAEPPEKK
MALVADEQQRLMQRALQQNFLAMAAQLPMSIRINSQASESRQDSAVNLTGTNGSNSISMSVEINGIMYTGVLFAQPPAPTPTSAPNKGGG

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

>81796_81796_4_SHROOM4-ARID3A_SHROOM4_chrX_50556902_ENST00000376020_ARID3A_chr19_960092_ENST00000263620_length(amino acids)=401AA_BP=37
MENRPGSFQYVPVQLQGGAPWGFTLKGGLEHCEPLTVSKLYELDGDPKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEK
GGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQAAIDSNRREGRRQSFGGSLFAYSPGGAHGMLSS
PKLPVSSLGLAASTNGSSITPAPKIKKEEDSAIPITVPGRLPVSLAGHPVVAAQAAAVQAAAAQAAVAAQAAALEQLREKLESAEPPEKK
MALVADEQQRLMQRALQQNFLAMAAQLPMSIRINSQASESRQDSAVNLTGTNGSNSISMSVEINGIMYTGVLFAQPPAPTPTSAPNKGGG

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

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Fusion Protein Functional Features


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/chrX:50556902/chr19:960092)
- 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
.ARID3A

Q99856

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Transcription factor which may be involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation. {ECO:0000269|PubMed:11812999, ECO:0000269|PubMed:12692263}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029424_445231.0594.0Compositional biasNote=Ala-rich
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029550_579231.0594.0Compositional biasNote=Gly-rich
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029424_445231.0594.0Compositional biasNote=Ala-rich
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029550_579231.0594.0Compositional biasNote=Gly-rich
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029238_330231.0594.0DomainARID
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029444_541231.0594.0DomainREKLES
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029238_330231.0594.0DomainARID
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029444_541231.0594.0DomainREKLES
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029445_488231.0594.0RegionImportant for nuclear localization
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029490_513231.0594.0RegionNote=Homodimerization
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029537_557231.0594.0RegionImportant for cytoplasmic localization
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029445_488231.0594.0RegionImportant for nuclear localization
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029490_513231.0594.0RegionNote=Homodimerization
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029537_557231.0594.0RegionImportant for cytoplasmic localization

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSHROOM4chrX:50556901chr19:960091ENST00000289292-1101382_148839.01898.0Coiled coilOntology_term=ECO:0000255
HgeneSHROOM4chrX:50556901chr19:960091ENST00000376020-191382_148839.01494.0Coiled coilOntology_term=ECO:0000255
HgeneSHROOM4chrX:50556901chr19:960091ENST00000460112-181382_148801378.0Coiled coilOntology_term=ECO:0000255
HgeneSHROOM4chrX:50556902chr19:960092ENST00000289292-1101382_148839.01898.0Coiled coilOntology_term=ECO:0000255
HgeneSHROOM4chrX:50556902chr19:960092ENST00000376020-191382_148839.01494.0Coiled coilOntology_term=ECO:0000255
HgeneSHROOM4chrX:50556902chr19:960092ENST00000460112-181382_148801378.0Coiled coilOntology_term=ECO:0000255
HgeneSHROOM4chrX:50556901chr19:960091ENST00000289292-1101100_110739.01898.0Compositional biasNote=Poly-Pro
HgeneSHROOM4chrX:50556901chr19:960091ENST00000289292-1101119_113539.01898.0Compositional biasNote=Gln-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000289292-1101136_118139.01898.0Compositional biasNote=Glu-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000289292-110871_93739.01898.0Compositional biasNote=Cys-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000376020-191100_110739.01494.0Compositional biasNote=Poly-Pro
HgeneSHROOM4chrX:50556901chr19:960091ENST00000376020-191119_113539.01494.0Compositional biasNote=Gln-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000376020-191136_118139.01494.0Compositional biasNote=Glu-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000376020-19871_93739.01494.0Compositional biasNote=Cys-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000460112-181100_110701378.0Compositional biasNote=Poly-Pro
HgeneSHROOM4chrX:50556901chr19:960091ENST00000460112-181119_113501378.0Compositional biasNote=Gln-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000460112-181136_118101378.0Compositional biasNote=Glu-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000460112-18871_93701378.0Compositional biasNote=Cys-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000289292-1101100_110739.01898.0Compositional biasNote=Poly-Pro
HgeneSHROOM4chrX:50556902chr19:960092ENST00000289292-1101119_113539.01898.0Compositional biasNote=Gln-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000289292-1101136_118139.01898.0Compositional biasNote=Glu-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000289292-110871_93739.01898.0Compositional biasNote=Cys-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000376020-191100_110739.01494.0Compositional biasNote=Poly-Pro
HgeneSHROOM4chrX:50556902chr19:960092ENST00000376020-191119_113539.01494.0Compositional biasNote=Gln-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000376020-191136_118139.01494.0Compositional biasNote=Glu-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000376020-19871_93739.01494.0Compositional biasNote=Cys-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000460112-181100_110701378.0Compositional biasNote=Poly-Pro
HgeneSHROOM4chrX:50556902chr19:960092ENST00000460112-181119_113501378.0Compositional biasNote=Gln-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000460112-181136_118101378.0Compositional biasNote=Glu-rich
HgeneSHROOM4chrX:50556902chr19:960092ENST00000460112-18871_93701378.0Compositional biasNote=Cys-rich
HgeneSHROOM4chrX:50556901chr19:960091ENST00000289292-11010_9239.01898.0DomainPDZ
HgeneSHROOM4chrX:50556901chr19:960091ENST00000289292-1101213_149239.01898.0DomainASD2
HgeneSHROOM4chrX:50556901chr19:960091ENST00000376020-1910_9239.01494.0DomainPDZ
HgeneSHROOM4chrX:50556901chr19:960091ENST00000376020-191213_149239.01494.0DomainASD2
HgeneSHROOM4chrX:50556901chr19:960091ENST00000460112-1810_9201378.0DomainPDZ
HgeneSHROOM4chrX:50556901chr19:960091ENST00000460112-181213_149201378.0DomainASD2
HgeneSHROOM4chrX:50556902chr19:960092ENST00000289292-11010_9239.01898.0DomainPDZ
HgeneSHROOM4chrX:50556902chr19:960092ENST00000289292-1101213_149239.01898.0DomainASD2
HgeneSHROOM4chrX:50556902chr19:960092ENST00000376020-1910_9239.01494.0DomainPDZ
HgeneSHROOM4chrX:50556902chr19:960092ENST00000376020-191213_149239.01494.0DomainASD2
HgeneSHROOM4chrX:50556902chr19:960092ENST00000460112-1810_9201378.0DomainPDZ
HgeneSHROOM4chrX:50556902chr19:960092ENST00000460112-181213_149201378.0DomainASD2
TgeneARID3AchrX:50556901chr19:960091ENST000002636202967_70231.0594.0Compositional biasNote=Poly-Ala
TgeneARID3AchrX:50556901chr19:960091ENST000002636202989_157231.0594.0Compositional biasNote=Glu-rich
TgeneARID3AchrX:50556902chr19:960092ENST000002636202967_70231.0594.0Compositional biasNote=Poly-Ala
TgeneARID3AchrX:50556902chr19:960092ENST000002636202989_157231.0594.0Compositional biasNote=Glu-rich
TgeneARID3AchrX:50556901chr19:960091ENST0000026362029119_156231.0594.0RegionNote=Acidic
TgeneARID3AchrX:50556902chr19:960092ENST0000026362029119_156231.0594.0RegionNote=Acidic


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>805_SHROOM4_50556902_ARID3A_960092_ranked_0.pdbSHROOM45055690150556902ENST00000263620ARID3Achr19960092+
MENRPGSFQYVPVQLQGGAPWGFTLKGGLEHCEPLTVSKLYELDGDPKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEK
GGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQAAIDSNRREGRRQSFGGSLFAYSPGGAHGMLSS
PKLPVSSLGLAASTNGSSITPAPKIKKEEDSAIPITVPGRLPVSLAGHPVVAAQAAAVQAAAAQAAVAAQAAALEQLREKLESAEPPEKK
MALVADEQQRLMQRALQQNFLAMAAQLPMSIRINSQASESRQDSAVNLTGTNGSNSISMSVEINGIMYTGVLFAQPPAPTPTSAPNKGGG
401


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
SHROOM4_pLDDT.png
all structure
all structure
ARID3A_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SHROOM4
ARID3A


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to SHROOM4-ARID3A


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to SHROOM4-ARID3A


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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