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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:SFPQ-SFPQ (FusionGDB2 ID:80563)

Fusion Gene Summary for SFPQ-SFPQ

check button Fusion gene summary
Fusion gene informationFusion gene name: SFPQ-SFPQ
Fusion gene ID: 80563
HgeneTgene
Gene symbol

SFPQ

SFPQ

Gene ID

654780

654780

Gene namesplicing factor proline/glutamine-richsplicing factor proline/glutamine-rich
SynonymsSFPQSFPQ
Cytomap

16q24.1

16q24.1

Type of genencRNAncRNA
Description--
Modification date2020030320200303
UniProtAcc.

P23246

Ensembl transtripts involved in fusion geneENST00000357214, ENST00000468598, 
ENST00000357214, ENST00000468598, 
Fusion gene scores* DoF score14 X 16 X 8=179223 X 15 X 8=2760
# samples 1926
** MAII scorelog2(19/1792*10)=-3.23749931372666
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(26/2760*10)=-3.40808473863708
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SFPQ [Title/Abstract] AND SFPQ [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSFPQ(35656512)-SFPQ(35656471), # samples:3
Anticipated loss of major functional domain due to fusion event.
* 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 SFPQ (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

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
ChiTaRS5.0N/ABE276277SFPQchr1

35656512

+SFPQchr1

35656471

-
ChiTaRS5.0N/ABE385898SFPQchr1

35656512

+SFPQchr1

35656471

-
ChiTaRS5.0N/ABE408250SFPQchr1

35656512

+SFPQchr1

35656471

-
ChiTaRS5.0N/ABE926576SFPQchr1

35656449

+SFPQchr1

35652657

+
ChiTaRS5.0N/ABF089022SFPQchr1

35656157

+SFPQchr1

35654636

-
ChiTaRS5.0N/ABF359676SFPQchr1

35646587

+SFPQchr1

35647085

-


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Fusion Gene ORF analysis for SFPQ-SFPQ

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
intron-3CDSENST00000357214ENST00000357214SFPQchr1

35656512

+SFPQchr1

35656471

-
intron-intronENST00000357214ENST00000468598SFPQchr1

35656512

+SFPQchr1

35656471

-
intron-3CDSENST00000468598ENST00000357214SFPQchr1

35656512

+SFPQchr1

35656471

-
intron-intronENST00000468598ENST00000468598SFPQchr1

35656512

+SFPQchr1

35656471

-
intron-3CDSENST00000357214ENST00000357214SFPQchr1

35656449

+SFPQchr1

35652657

+
intron-intronENST00000357214ENST00000468598SFPQchr1

35656449

+SFPQchr1

35652657

+
intron-3CDSENST00000468598ENST00000357214SFPQchr1

35656449

+SFPQchr1

35652657

+
intron-intronENST00000468598ENST00000468598SFPQchr1

35656449

+SFPQchr1

35652657

+
intron-3CDSENST00000357214ENST00000357214SFPQchr1

35656157

+SFPQchr1

35654636

-
intron-intronENST00000357214ENST00000468598SFPQchr1

35656157

+SFPQchr1

35654636

-
intron-3CDSENST00000468598ENST00000357214SFPQchr1

35656157

+SFPQchr1

35654636

-
intron-intronENST00000468598ENST00000468598SFPQchr1

35656157

+SFPQchr1

35654636

-
intron-intronENST00000357214ENST00000357214SFPQchr1

35646587

+SFPQchr1

35647085

-
intron-intronENST00000357214ENST00000468598SFPQchr1

35646587

+SFPQchr1

35647085

-
intron-intronENST00000468598ENST00000357214SFPQchr1

35646587

+SFPQchr1

35647085

-
intron-intronENST00000468598ENST00000468598SFPQchr1

35646587

+SFPQchr1

35647085

-

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

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Fusion Genomic Features for SFPQ-SFPQ


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.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for SFPQ-SFPQ


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.SFPQ

P23246

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: DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer binds DNA (PubMed:25765647). The SFPQ-NONO heteromer may be involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Functions as transcriptional activator (PubMed:25765647). Transcriptional repression is mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional activity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex through histone deacetylation (By similarity). Required for the assembly of nuclear speckles (PubMed:25765647). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). {ECO:0000250|UniProtKB:Q8VIJ6, ECO:0000269|PubMed:10847580, ECO:0000269|PubMed:10858305, ECO:0000269|PubMed:10931916, ECO:0000269|PubMed:11259580, ECO:0000269|PubMed:11525732, ECO:0000269|PubMed:11897684, ECO:0000269|PubMed:15590677, ECO:0000269|PubMed:20932480, ECO:0000269|PubMed:25765647, ECO:0000269|PubMed:28712728, ECO:0000269|PubMed:8045264, ECO:0000269|PubMed:8449401}.

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


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Fusion Gene Sequence for SFPQ-SFPQ


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.

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Fusion Gene PPI Analysis for SFPQ-SFPQ


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 SFPQ-SFPQ


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneSFPQP23246DB09130CopperSmall moleculeApproved|Investigational
TgeneSFPQP23246DB09130CopperSmall moleculeApproved|Investigational

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Related Diseases for SFPQ-SFPQ


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSFPQC4518356MiT family translocation renal cell carcinoma2ORPHANET
HgeneSFPQC0019693HIV Infections1CTD_human
HgeneSFPQC0037274Dermatologic disorders1CTD_human
HgeneSFPQC0274861Arsenic Poisoning, Inorganic1CTD_human
HgeneSFPQC0274862Nervous System, Organic Arsenic Poisoning1CTD_human
HgeneSFPQC0311375Arsenic Poisoning1CTD_human
HgeneSFPQC0751851Arsenic Encephalopathy1CTD_human
HgeneSFPQC0751852Arsenic Induced Polyneuropathy1CTD_human
HgeneSFPQC4505456HIV Coinfection1CTD_human
TgeneSFPQC4518356MiT family translocation renal cell carcinoma2ORPHANET
TgeneSFPQC0019693HIV Infections1CTD_human
TgeneSFPQC0037274Dermatologic disorders1CTD_human
TgeneSFPQC0274861Arsenic Poisoning, Inorganic1CTD_human
TgeneSFPQC0274862Nervous System, Organic Arsenic Poisoning1CTD_human
TgeneSFPQC0311375Arsenic Poisoning1CTD_human
TgeneSFPQC0751851Arsenic Encephalopathy1CTD_human
TgeneSFPQC0751852Arsenic Induced Polyneuropathy1CTD_human
TgeneSFPQC4505456HIV Coinfection1CTD_human