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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:SIPA1-FRMD8

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SIPA1-FRMD8
FusionPDB ID: 81933
FusionGDB2.0 ID: 81933
HgeneTgene
Gene symbol

SIPA1

FRMD8

Gene ID

6494

83786

Gene namesignal-induced proliferation-associated 1FERM domain containing 8
SynonymsSPA1FKSG44|iTAP
Cytomap

11q13.1

11q13.1

Type of geneprotein-codingprotein-coding
Descriptionsignal-induced proliferation-associated protein 1GTPase-activating protein Spa-1p130 SPA-1signal-induced proliferation-associated gene 1sipa-1FERM domain-containing protein 8band4.1 inhibitor LRP interactorbiliiRhom Tail-Associated Protein
Modification date2020031320200313
UniProtAcc.

Q9BZ67

Ensembl transtripts involved in fusion geneENST idsENST00000394224, ENST00000394227, 
ENST00000527525, ENST00000534313, 
ENST00000355991, ENST00000416776, 
ENST00000531296, ENST00000317568, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 4 X 4=6410 X 11 X 10=1100
# samples 518
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(18/1100*10)=-2.61143471208235
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SIPA1 [Title/Abstract] AND FRMD8 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SIPA1(65412600)-FRMD8(65178713), # samples:3
Anticipated loss of major functional domain due to fusion event.SIPA1-FRMD8 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.
SIPA1-FRMD8 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
TgeneFRMD8

GO:1904469

positive regulation of tumor necrosis factor secretion

29897333


check buttonFusion gene breakpoints across SIPA1 (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 FRMD8 (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
ChimerDB4CESCTCGA-DS-A1O9-01ASIPA1chr11

65412600

-FRMD8chr11

65178713

+
ChimerDB4CESCTCGA-DS-A1O9-01ASIPA1chr11

65412600

+FRMD8chr11

65178713

+
ChimerDB4CESCTCGA-DS-A1O9SIPA1chr11

65412600

+FRMD8chr11

65178713

+
ChimerDB4SKCMTCGA-FR-A3YO-06ASIPA1chr11

65410110

+FRMD8chr11

65172335

+


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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)
ENST00000534313SIPA1chr1165412600+ENST00000317568FRMD8chr1165178713+362013361771454425
ENST00000527525SIPA1chr1165412600+ENST00000317568FRMD8chr1165178713+369014062471524425
ENST00000394224SIPA1chr1165412600+ENST00000317568FRMD8chr1165178713+373914552961573425
ENST00000394227SIPA1chr1165412600+ENST00000317568FRMD8chr1165178713+35371253941371425
ENST00000534313SIPA1chr1165410110+ENST00000317568FRMD8chr1165172335+365011611771484435
ENST00000527525SIPA1chr1165410110+ENST00000317568FRMD8chr1165172335+372012312471554435
ENST00000394224SIPA1chr1165410110+ENST00000317568FRMD8chr1165172335+376912802961603435
ENST00000394227SIPA1chr1165410110+ENST00000317568FRMD8chr1165172335+35671078941401435

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
ENST00000534313ENST00000317568SIPA1chr1165412600+FRMD8chr1165178713+0.137194280.8628057
ENST00000527525ENST00000317568SIPA1chr1165412600+FRMD8chr1165178713+0.143963580.8560364
ENST00000394224ENST00000317568SIPA1chr1165412600+FRMD8chr1165178713+0.133126480.86687356
ENST00000394227ENST00000317568SIPA1chr1165412600+FRMD8chr1165178713+0.13559610.86440396
ENST00000534313ENST00000317568SIPA1chr1165410110+FRMD8chr1165172335+0.15168460.8483154
ENST00000527525ENST00000317568SIPA1chr1165410110+FRMD8chr1165172335+0.162087250.8379128
ENST00000394224ENST00000317568SIPA1chr1165410110+FRMD8chr1165172335+0.149168370.8508317
ENST00000394227ENST00000317568SIPA1chr1165410110+FRMD8chr1165172335+0.152039480.84796053

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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

>81933_81933_1_SIPA1-FRMD8_SIPA1_chr11_65410110_ENST00000394224_FRMD8_chr11_65172335_ENST00000317568_length(amino acids)=435AA_BP=303
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVAELMSSLIEYCIELSQAAEPAGPQDSATGSPS

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

>81933_81933_2_SIPA1-FRMD8_SIPA1_chr11_65410110_ENST00000394227_FRMD8_chr11_65172335_ENST00000317568_length(amino acids)=435AA_BP=303
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVAELMSSLIEYCIELSQAAEPAGPQDSATGSPS

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

>81933_81933_3_SIPA1-FRMD8_SIPA1_chr11_65410110_ENST00000527525_FRMD8_chr11_65172335_ENST00000317568_length(amino acids)=435AA_BP=303
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVAELMSSLIEYCIELSQAAEPAGPQDSATGSPS

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

>81933_81933_4_SIPA1-FRMD8_SIPA1_chr11_65410110_ENST00000534313_FRMD8_chr11_65172335_ENST00000317568_length(amino acids)=435AA_BP=303
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVAELMSSLIEYCIELSQAAEPAGPQDSATGSPS

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

>81933_81933_5_SIPA1-FRMD8_SIPA1_chr11_65412600_ENST00000394224_FRMD8_chr11_65178713_ENST00000317568_length(amino acids)=425AA_BP=387
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVLSFQRKVGILYCRAGQGSEEEMYNNQEAGPAF

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

>81933_81933_6_SIPA1-FRMD8_SIPA1_chr11_65412600_ENST00000394227_FRMD8_chr11_65178713_ENST00000317568_length(amino acids)=425AA_BP=387
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVLSFQRKVGILYCRAGQGSEEEMYNNQEAGPAF

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

>81933_81933_7_SIPA1-FRMD8_SIPA1_chr11_65412600_ENST00000527525_FRMD8_chr11_65178713_ENST00000317568_length(amino acids)=425AA_BP=387
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVLSFQRKVGILYCRAGQGSEEEMYNNQEAGPAF

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

>81933_81933_8_SIPA1-FRMD8_SIPA1_chr11_65412600_ENST00000534313_FRMD8_chr11_65178713_ENST00000317568_length(amino acids)=425AA_BP=387
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVLSFQRKVGILYCRAGQGSEEEMYNNQEAGPAF

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

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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/chr11:65412600/chr11:65178713)
- 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
.FRMD8

Q9BZ67

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: Promotes the cell surface stability of iRhom1/RHBDF1 and iRhom2/RHBDF2 and prevents their degradation via the endolysosomal pathway. By acting on iRhoms, involved in ADAM17-mediated shedding of TNF, amphiregulin/AREG, HBEGF and TGFA from the cell surface (PubMed:29897333, PubMed:29897336). Negatively regulates Wnt signaling, possibly by antagonizing the recruitment of AXIN1 to LRP6 (PubMed:19572019). {ECO:0000269|PubMed:19572019, ECO:0000269|PubMed:29897333, ECO:0000269|PubMed:29897336}.

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

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSIPA1chr11:65410110chr11:65172335ENST00000394224+416972_1034328.01043.0Coiled coilOntology_term=ECO:0000255
HgeneSIPA1chr11:65410110chr11:65172335ENST00000534313+416972_1034328.01043.0Coiled coilOntology_term=ECO:0000255
HgeneSIPA1chr11:65412600chr11:65178713ENST00000394224+516972_1034386.33333333333331043.0Coiled coilOntology_term=ECO:0000255
HgeneSIPA1chr11:65412600chr11:65178713ENST00000534313+516972_1034386.33333333333331043.0Coiled coilOntology_term=ECO:0000255
HgeneSIPA1chr11:65410110chr11:65172335ENST00000394224+416321_539328.01043.0DomainRap-GAP
HgeneSIPA1chr11:65410110chr11:65172335ENST00000394224+416687_763328.01043.0DomainPDZ
HgeneSIPA1chr11:65410110chr11:65172335ENST00000534313+416321_539328.01043.0DomainRap-GAP
HgeneSIPA1chr11:65410110chr11:65172335ENST00000534313+416687_763328.01043.0DomainPDZ
HgeneSIPA1chr11:65412600chr11:65178713ENST00000394224+516321_539386.33333333333331043.0DomainRap-GAP
HgeneSIPA1chr11:65412600chr11:65178713ENST00000394224+516687_763386.33333333333331043.0DomainPDZ
HgeneSIPA1chr11:65412600chr11:65178713ENST00000534313+516321_539386.33333333333331043.0DomainRap-GAP
HgeneSIPA1chr11:65412600chr11:65178713ENST00000534313+516687_763386.33333333333331043.0DomainPDZ
TgeneFRMD8chr11:65410110chr11:65172335ENST0000031756881130_376357.0465.0DomainFERM
TgeneFRMD8chr11:65410110chr11:65172335ENST0000035599171030_376301.0409.0DomainFERM
TgeneFRMD8chr11:65412600chr11:65178713ENST0000031756891130_376425.3333333333333465.0DomainFERM
TgeneFRMD8chr11:65412600chr11:65178713ENST0000035599181030_376369.3333333333333409.0DomainFERM


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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 >>>887_SIPA1_65412600_FRMD8_65178713_887_SIPA1_65412600_FRMD8_65178713_ranked_0.pdbSIPA16541011065412600ENST00000317568FRMD8chr1165178713+
MPMWAGGVGSPRRGMAPASTDDLFARKLRQPARPPLTPHTFEPRPVRGPLLRSGSDAGEARPPTPASPRARAHSHEEASRPAATSTRLFT
DPLALLGLPAEEPEPAFPPVLEPRWFAHYDVQSLLFDWAPRSQGMGSHSEASSGTLASAEDQAASSDLLHGAPGFVCELGGEGELGLGGP
ASPPVPPALPNAAVSILEEPQNRTSAYSLEHADLGAGYYRKYFYGKEHQNFFGMDESLGPVAVSLRREEKEGSGGGTLHSYRVIVRTTQL
RTLRGTISEDALPPGPPRGLSPRKLLEHVAPQLSPSCLRLGSASPKVPRTLLTLDEQVLSFQRKVGILYCRAGQGSEEEMYNNQEAGPAF
425


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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.
SIPA1_pLDDT.png
all structure
all structure
FRMD8_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
SIPA1
FRMD8


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 SIPA1-FRMD8


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 SIPA1-FRMD8


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