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Fusion gene ID: 33501 |
FusionGeneSummary for SFPQ_TFEB |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SFPQ_TFEB | Fusion gene ID: 33501 | Hgene | Tgene | Gene symbol | SFPQ | TFEB | Gene ID | 6421 | 7942 |
| Gene name | splicing factor proline and glutamine rich | transcription factor EB | |
| Synonyms | POMP100|PPP1R140|PSF | ALPHATFEB|BHLHE35|TCFEB | |
| Cytomap | 1p34.3 | 6p21.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | splicing factor, proline- and glutamine-rich100 kDa DNA-pairing proteinDNA-binding p52/p100 complex, 100 kDa subunitPTB-associated splicing factorpolypyrimidine tract binding protein associatedpolypyrimidine tract-binding protein-associated splicing | transcription factor EBT-cell transcription factor EBclass E basic helix-loop-helix protein 35 | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | P23246 | P19484 | |
| Ensembl transtripts involved in fusion gene | ENST00000357214, ENST00000468598, | ENST00000230323, ENST00000358871, ENST00000420312, ENST00000403298, ENST00000373033, ENST00000394283, | |
| Fusion gene scores | * DoF score | 8 X 10 X 4=320 | 3 X 2 X 3=18 |
| # samples | 19 | 4 | |
| ** MAII score | log2(19/320*10)=-0.752072486556414 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/18*10)=1.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SFPQ [Title/Abstract] AND TFEB [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | SFPQ | GO:0000122 | negative regulation of transcription by RNA polymerase II | 16731528 |
| Hgene | SFPQ | GO:0002218 | activation of innate immune response | 28712728 |
| Hgene | SFPQ | GO:1902177 | positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway | 15790595 |
| Tgene | TFEB | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19556463 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | LD | LIHC | TCGA-G3-A3CI-01A | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| TCGA | LD | LIHC | TCGA-MR-A520-01A | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 5CDS-5UTR | ENST00000357214 | ENST00000230323 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| 5CDS-5UTR | ENST00000357214 | ENST00000358871 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| 5CDS-5UTR | ENST00000357214 | ENST00000420312 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| 5CDS-5UTR | ENST00000357214 | ENST00000403298 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| 5CDS-5UTR | ENST00000357214 | ENST00000373033 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| 5CDS-5UTR | ENST00000357214 | ENST00000394283 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| intron-5UTR | ENST00000468598 | ENST00000230323 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| intron-5UTR | ENST00000468598 | ENST00000358871 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| intron-5UTR | ENST00000468598 | ENST00000420312 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| intron-5UTR | ENST00000468598 | ENST00000403298 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| intron-5UTR | ENST00000468598 | ENST00000373033 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
| intron-5UTR | ENST00000468598 | ENST00000394283 | SFPQ | chr1 | 35654604 | - | TFEB | chr6 | 41658973 | - |
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FusionProtFeatures for SFPQ_TFEB |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SFPQ | TFEB |
| DNA- and RNA binding protein, involved in severalnuclear processes. Essential pre-mRNA splicing factor requiredearly in spliceosome formation and for splicing catalytic step II,probably as a heteromer with NONO. Binds to pre-mRNA inspliceosome C complex, and specifically binds to intronicpolypyrimidine tracts. Involved in regulation of signal-inducedalternative splicing. During splicing of PTPRC/CD45, aphosphorylated form is sequestered by THRAP3 from the pre-mRNA inresting T-cells; T-cell activation and subsequent reducedphosphorylation is proposed to lead to release from THRAP3allowing binding to pre-mRNA splicing regulatotry elements whichrepresses exon inclusion. Interacts with U5 snRNA, probably bybinding to a purine-rich sequence located on the 3' side of U5snRNA stem 1b. May be involved in a pre-mRNA coupled splicing andpolyadenylation process as component of a snRNP-free complex withSNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may playa role in nuclear retention of defective RNAs. SFPQ may beinvolved in homologous DNA pairing; in vitro, promotes theinvasion of ssDNA between a duplex DNA and produces a D-loopformation. The SFPQ-NONO heteromer may be involved in DNAunwinding by modulating the function of topoisomerase I/TOP1; invitro, stimulates dissociation of TOP1 from DNA after cleavage andenhances its jumping between separate DNA helices. The SFPQ-NONOheteromer binds DNA (PubMed:25765647). The SFPQ-NONO heteromer maybe involved in DNA non-homologous end joining (NHEJ) required fordouble-strand break repair and V(D)J recombination and maystabilize paired DNA ends; in vitro, the complex stronglystimulates DNA end joining, binds directly to the DNA substratesand cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer toestablish a functional preligation complex. SFPQ is involved intranscriptional regulation. Functions as transcriptional activator(PubMed:25765647). Transcriptional repression is mediated by aninteraction of SFPQ with SIN3A and subsequent recruitment ofhistone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds tothe CYP17 promoter and regulates basal and cAMP-dependenttranscriptional activity. SFPQ isoform Long binds to the DNAbinding domains (DBD) of nuclear hormone receptors, like RXRA andprobably THRA, and acts as transcriptional corepressor in absenceof hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in theinsulin-like growth factor response element (IGFRE) and inhibitsIGF-I-stimulated transcriptional activity. Regulates the circadianclock by repressing the transcriptional activator activity of theCLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptionalrepression of circadian target genes, such as PER1, mediated bythe large PER complex through histone deacetylation (Bysimilarity). 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-RNPcomplex, a complex that serves as a platform for IRF3phosphorylation and subsequent innate immune response activationthrough 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}. | Transcription factor that specifically recognizes andbinds E-box sequences (5'-CANNTG-3'). Efficient DNA-bindingrequires dimerization with itself or with another MiT/TFE familymember such as TFE3 or MITF. In association with TFE3, activatesthe expression of CD40L in T-cells, thereby playing a role in T-cell-dependent antibody responses in activated CD4(+) T-cells andthymus-dependent humoral immunity. Specifically recognizes andbinds the CLEAR-box sequence (5'-GTCACGTGAC-3') present in theregulatory region of many lysosomal genes, leading to activatetheir expression. It thereby plays a central role in expression oflysosomal genes. Acts as a positive regulator of autophagy bypromoting expression of genes involved in autophagy. Specificallyrecognizes the gamma-E3 box, a subset of E-boxes, present in theheavy-chain immunoglobulin enhancer. Plays a role in the signaltransduction processes required for normal vascularization of theplacenta. {ECO:0000269|PubMed:19556463,ECO:0000269|PubMed:23434374}. |
| Retention 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 . * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for SFPQ_TFEB |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for SFPQ_TFEB |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| SFPQ | NONO, FHL2, EXOSC5, HN1, SFPQ, UBC, PTBP1, TOP1, CDC5L, ZMYM2, SP1, SP3, HDAC1, HDAC2, SIN3A, NR3C1, PITX3, NR4A2, RAC1, SRRM1, SRRM2, SMARCD1, SMARCA2, AR, TOPORS, MAPK1, PRKCI, TADA2A, POT1, SMN1, SNW1, STAT6, HDAC5, PPP1CA, SNRPA, U2AF2, SREK1, RAD21, CEBPA, ELAVL1, ARRB2, SIRT7, HNRNPA1, TSG101, NR2C1, CBLL1, CDK2, COPS5, AP2M1, PARK7, PPARGC1A, U2AF1, SF3B1, EFTUD2, TCERG1, HNRNPR, HNRNPC, SNRPA1, SRSF5, HNRNPM, SRSF7, SF3B3, SRSF3, SRSF4, SNRPD2, SF3A1, DDX21, PHF5A, SART1, HTATSF1, ILF3, TOP2B, HNRNPL, SLTM, SSR4, DNAJC19, TIMM10, TPR, STAG2, SON, THRAP3, SMC3, UTP14A, SMARCA5, TXN, ZC3HAV1, VTN, APEX1, UQCRFS1P1, TOMM40, TIMM9, TIMM23B, BTK, FN1, VCAM1, RNF43, CSNK2A1, SMAD5, ITGA4, PAN2, CD81, PARK2, PRPF40A, WBP4, APBB1, GAS7, PIN1, WWOX, RPA3, RPA2, RPA1, ERG, ASB3, ASB12, ASB18, STAU1, MDM2, HUWE1, FUS, MOV10, NXF1, PPARG, HIST3H3, CUL7, OBSL1, CCDC8, UBE2I, EED, ESR1, ORC6, RPS6KB2, UNK, ACAT1, CARS, COX5A, DPH5, HNRNPA2B1, HNRNPA3, HNRNPD, IMMT, KHDRBS1, LMO7, NDUFS3, NUP210, PFKM, SERBP1, DDX17, PGK1, TARS, WBP11, UQCRC2, YTHDF2, SFN, NTRK1, SCARNA22, KRAS, MUS81, AHSA1, CRY1, MCM2, MCM5, EGFR, RC3H1, ZNF746, RBMXL1, PSPC1, DIDO1, MMADHC, PRRC2A, EWSR1, LSM14A, FAM98A, DHPS, SYNCRIP, SMARCC1, PRMT5, SMARCC2, NCOA5, PRRC2C, ALYREF, SF1, RBM27, HIP1R, CYLD, CD2BP2, TRIM25, UBE2A, BRCA1, LMNA | TFEB | YWHAQ, SRPK1, XPO1, ATP5J, IFIT1, STT3A, MAPT, MITF, PPM1G, TFE3, BAG2, C10orf12, MCAT, EML4, TBC1D14, HDAC5, TFEC, TAF9, YWHAG, YWHAZ, YWHAE, YWHAB, GPNMB, TRIM16 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for SFPQ_TFEB |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | SFPQ | P23246 | DB11638 | Artenimol | Splicing factor, proline- and glutamine-rich | small molecule | approved|investigational |
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RelatedDiseases for SFPQ_TFEB |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SFPQ | C0019693 | HIV Infections | 1 | CTD_human |
| Hgene | SFPQ | C0037274 | Dermatologic disorders | 1 | CTD_human |
| Hgene | SFPQ | C0311375 | Arsenic Poisoning | 1 | CTD_human |
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