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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:SPEN-FBLIM1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SPEN-FBLIM1
FusionPDB ID: 85720
FusionGDB2.0 ID: 85720
HgeneTgene
Gene symbol

SPEN

FBLIM1

Gene ID

64783

54751

Gene nameRNA binding motif protein 15filamin binding LIM protein 1
SynonymsOTT|OTT1|SPENCAL|FBLP-1|FBLP1
Cytomap

1p13.3

1p36.21

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein 15one twenty two proteinone twenty-twoone-twenty two protein 1putative RNA-binding protein 15filamin-binding LIM protein 1CSX-associated LIMMIG2-interacting proteinmigfilinmitogen-inducible 2 interacting protein
Modification date2020031320200313
UniProtAcc.

Q8WUP2

Ensembl transtripts involved in fusion geneENST idsENST00000471538, ENST00000375759, 
ENST00000332305, ENST00000375766, 
ENST00000375771, ENST00000400773, 
ENST00000441801, ENST00000509138, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score20 X 12 X 15=36005 X 7 X 6=210
# samples 318
** MAII scorelog2(31/3600*10)=-3.5376567859428
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/210*10)=-1.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SPEN [Title/Abstract] AND FBLIM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SPEN(16203173)-FBLIM1(16090991), # samples:2
SPEN(16174645)-FBLIM1(16096904), # samples:2
SPEN(16203173)-FBLIM1(16101113), # samples:2
Anticipated loss of major functional domain due to fusion event.SPEN-FBLIM1 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.
SPEN-FBLIM1 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.
SPEN-FBLIM1 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.
SPEN-FBLIM1 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.
SPEN-FBLIM1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
SPEN-FBLIM1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SPEN-FBLIM1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
SPEN-FBLIM1 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
HgeneSPEN

GO:0000381

regulation of alternative mRNA splicing, via spliceosome

26575292

HgeneSPEN

GO:0001510

RNA methylation

27602518

HgeneSPEN

GO:0009048

dosage compensation by inactivation of X chromosome

27602518

HgeneSPEN

GO:0045652

regulation of megakaryocyte differentiation

26575292

HgeneSPEN

GO:0045892

negative regulation of transcription, DNA-templated

16129689


check buttonFusion gene breakpoints across SPEN (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 FBLIM1 (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
ChimerDB4BLCATCGA-K4-A3WV-01ASPENchr1

16203173

-FBLIM1chr1

16090991

+
ChimerDB4BLCATCGA-K4-A3WV-01ASPENchr1

16203173

+FBLIM1chr1

16090991

+
ChimerDB4LIHCTCGA-5C-AAPD-01ASPENchr1

16203173

-FBLIM1chr1

16101113

+
ChimerDB4LIHCTCGA-5C-AAPDSPENchr1

16203173

+FBLIM1chr1

16101113

+
ChimerDB4LIHCTCGA-RC-A6M3-01ASPENchr1

16174645

-FBLIM1chr1

16096904

+
ChimerDB4LIHCTCGA-RC-A6M3-01ASPENchr1

16174645

+FBLIM1chr1

16096904

+


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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)
ENST00000375759SPENchr116203173+ENST00000441801FBLIM1chr116101113+17101085271184385

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
ENST00000375759ENST00000441801SPENchr116203173+FBLIM1chr116101113+0.0416411870.9583588

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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

>85720_85720_1_SPEN-FBLIM1_SPEN_chr1_16203173_ENST00000375759_FBLIM1_chr1_16101113_ENST00000441801_length(amino acids)=385AA_BP=339
MGERDGLCTGGSRRSRRRCRRHRRSRRRRRPGTRLPALTVSYEAGEGEPAAAVAGTPPSMVRETRHLWVGNLPENVREEKIIEHFKRYGR
VESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNKMGDRDLRTDYNEPGTIPSAARGLDDTVSIASRSREVSGFRGGGGGPAYGPPPS
LHAREGRYERRLDGASDNRERAYEHSAYGHHERGTGGFDRTRHYDQDYYRDPRERTLQHGLYYASRSRSPNRFDAHDPRYEPRAREQFTL
PSVVHRDIYRDDITREVRGRRPERNYQHSRSRSPHSSQSRNQSPQRLASQASRPTRSPSGSGSRSRSSSSDSISSSSSTSSDRTHWRGAA

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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/chr1:16203173/chr1:16090991)
- 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
.FBLIM1

Q8WUP2

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: Serves as an anchoring site for cell-ECM adhesion proteins and filamin-containing actin filaments. Is implicated in cell shape modulation (spreading) and motility. May participate in the regulation of filamin-mediated cross-linking and stabilization of actin filaments. May also regulate the assembly of filamin-containing signaling complexes that control actin assembly. Promotes dissociation of FLNA from ITGB3 and ITGB7. Promotes activation of integrins and regulates integrin-mediated cell-cell adhesion. {ECO:0000269|PubMed:12496242, ECO:0000269|PubMed:12679033, ECO:0000269|PubMed:18829455, ECO:0000269|PubMed:19074766}.

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
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315125_277293.66666666666673665.0Compositional biasNote=Arg-rich
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3156_81293.66666666666673665.0DomainRRM 1
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000033230515181_242140.0277.0DomainLIM zinc-binding 1
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000033230515243_300140.0277.0DomainLIM zinc-binding 2
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000033230515301_370140.0277.0DomainLIM zinc-binding 3
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000037576659243_300237.0374.0DomainLIM zinc-binding 2
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000037576659301_370237.0374.0DomainLIM zinc-binding 3
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000375771610243_300237.0374.0DomainLIM zinc-binding 2
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000375771610301_370237.0374.0DomainLIM zinc-binding 3
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000040077337181_242140.0277.0DomainLIM zinc-binding 1
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000040077337243_300140.0277.0DomainLIM zinc-binding 2
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000040077337301_370140.0277.0DomainLIM zinc-binding 3
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000044180146243_300237.0375.0DomainLIM zinc-binding 2
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000044180146301_370237.0375.0DomainLIM zinc-binding 3
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000033230515276_373140.0277.0RegionNote=FERMT2-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000037576659276_373237.0374.0RegionNote=FERMT2-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000375771610276_373237.0374.0RegionNote=FERMT2-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000040077337276_373140.0277.0RegionNote=FERMT2-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000044180146276_373237.0375.0RegionNote=FERMT2-binding

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3151170_1191293.66666666666673665.0Coiled coilOntology_term=ECO:0000255
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3151408_1428293.66666666666673665.0Coiled coilOntology_term=ECO:0000255
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3151496_1529293.66666666666673665.0Coiled coilOntology_term=ECO:0000255
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3151592_1612293.66666666666673665.0Coiled coilOntology_term=ECO:0000255
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3151928_1944293.66666666666673665.0Coiled coilOntology_term=ECO:0000255
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315688_715293.66666666666673665.0Coiled coilOntology_term=ECO:0000255
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315977_1004293.66666666666673665.0Coiled coilOntology_term=ECO:0000255
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315240_325293.66666666666673665.0Compositional biasNote=Ser-rich
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3152428_2520293.66666666666673665.0Compositional biasNote=Pro-rich
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3153220_3482293.66666666666673665.0Compositional biasNote=Pro-rich
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315616_810293.66666666666673665.0Compositional biasNote=Arg-rich
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315624_697293.66666666666673665.0Compositional biasNote=Tyr-rich
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3151_573293.66666666666673665.0DNA bindingOntology_term=ECO:0000250
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3152201_2707293.66666666666673665.0DomainNote=RID
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315335_415293.66666666666673665.0DomainRRM 2
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3153498_3664293.66666666666673665.0DomainSPOC
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315438_513293.66666666666673665.0DomainRRM 3
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+315517_589293.66666666666673665.0DomainRRM 4
TgeneFBLIM1chr1:16203173chr1:16101113ENST000003323051542_173140.0277.0Compositional biasNote=Pro-rich
TgeneFBLIM1chr1:16203173chr1:16101113ENST000003757665942_173237.0374.0Compositional biasNote=Pro-rich
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000037577161042_173237.0374.0Compositional biasNote=Pro-rich
TgeneFBLIM1chr1:16203173chr1:16101113ENST000004007733742_173140.0277.0Compositional biasNote=Pro-rich
TgeneFBLIM1chr1:16203173chr1:16101113ENST000004418014642_173237.0375.0Compositional biasNote=Pro-rich
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000037576659181_242237.0374.0DomainLIM zinc-binding 1
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000375771610181_242237.0374.0DomainLIM zinc-binding 1
TgeneFBLIM1chr1:16203173chr1:16101113ENST0000044180146181_242237.0375.0DomainLIM zinc-binding 1
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000332305151_70140.0277.0RegionNote=Filamin-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000332305151_85140.0277.0RegionNote=Intrinsically disordered
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000375766591_70237.0374.0RegionNote=Filamin-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000375766591_85237.0374.0RegionNote=Intrinsically disordered
TgeneFBLIM1chr1:16203173chr1:16101113ENST000003757716101_70237.0374.0RegionNote=Filamin-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST000003757716101_85237.0374.0RegionNote=Intrinsically disordered
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000400773371_70140.0277.0RegionNote=Filamin-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000400773371_85140.0277.0RegionNote=Intrinsically disordered
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000441801461_70237.0375.0RegionNote=Filamin-binding
TgeneFBLIM1chr1:16203173chr1:16101113ENST00000441801461_85237.0375.0RegionNote=Intrinsically disordered


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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 >>>770_SPEN_16203173_FBLIM1_16101113_ranked_0.pdbSPEN1620317316203173ENST00000441801FBLIM1chr116101113+
MGERDGLCTGGSRRSRRRCRRHRRSRRRRRPGTRLPALTVSYEAGEGEPAAAVAGTPPSMVRETRHLWVGNLPENVREEKIIEHFKRYGR
VESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNKMGDRDLRTDYNEPGTIPSAARGLDDTVSIASRSREVSGFRGGGGGPAYGPPPS
LHAREGRYERRLDGASDNRERAYEHSAYGHHERGTGGFDRTRHYDQDYYRDPRERTLQHGLYYASRSRSPNRFDAHDPRYEPRAREQFTL
PSVVHRDIYRDDITREVRGRRPERNYQHSRSRSPHSSQSRNQSPQRLASQASRPTRSPSGSGSRSRSSSSDSISSSSSTSSDRTHWRGAA
385


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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.
SPEN_pLDDT.png
all structure
all structure
FBLIM1_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
SPEN
FBLIM1


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
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3152130_2464293.66666666666673665.0MSX2
HgeneSPENchr1:16203173chr1:16101113ENST00000375759+3152709_2870293.66666666666673665.0RBPSUH


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Related Drugs to SPEN-FBLIM1


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 SPEN-FBLIM1


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