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Fusion Protein:SF3B3-CTCF |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: SF3B3-CTCF | FusionPDB ID: 81068 | FusionGDB2.0 ID: 81068 | Hgene | Tgene | Gene symbol | SF3B3 | CTCF | Gene ID | 23450 | 10664 |
| Gene name | splicing factor 3b subunit 3 | CCCTC-binding factor | |
| Synonyms | RSE1|SAP130|SF3b130|STAF130 | CFAP108|FAP108|MRD21 | |
| Cytomap | 16q22.1 | 16q22.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | splicing factor 3B subunit 3SAP 130pre-mRNA splicing factor SF3b, 130 kDa subunitspliceosome-associated protein 130 | transcriptional repressor CTCF11 zinc finger transcriptional repressor11-zinc finger proteinCCCTC-binding factor (zinc finger protein)CTCFL paralog | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | . | Q8NI51 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000302516, | ENST00000264010, ENST00000401394, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 13 X 15 X 9=1755 | 9 X 9 X 4=324 |
| # samples | 18 | 8 | |
| ** MAII score | log2(18/1755*10)=-3.28540221886225 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/324*10)=-2.01792190799726 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: SF3B3 [Title/Abstract] AND CTCF [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | SF3B3(70578436)-CTCF(67660458), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | SF3B3-CTCF 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. SF3B3-CTCF 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. SF3B3-CTCF 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. SF3B3-CTCF 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. SF3B3-CTCF seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. SF3B3-CTCF seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. SF3B3-CTCF seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. SF3B3-CTCF seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. SF3B3-CTCF seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. SF3B3-CTCF seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF. SF3B3-CTCF seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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) |
| 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 | SF3B3 | GO:0000398 | mRNA splicing, via spliceosome | 28781166|29360106 |
| Hgene | SF3B3 | GO:0042177 | negative regulation of protein catabolic process | 23951410 |
| Tgene | CTCF | GO:0000122 | negative regulation of transcription by RNA polymerase II | 8649389 |
| Tgene | CTCF | GO:0016584 | nucleosome positioning | 18654629 |
| Tgene | CTCF | GO:0045892 | negative regulation of transcription, DNA-templated | 8649389|18413740 |
| Tgene | CTCF | GO:0045893 | positive regulation of transcription, DNA-templated | 9407128 |
| Fusion gene breakpoints across SF3B3 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across CTCF (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | OV | TCGA-24-2289-01A | SF3B3 | chr16 | 70578436 | + | CTCF | chr16 | 67660458 | + |
| ChimerDB4 | OV | TCGA-24-2289-01A | SF3B3 | chr16 | 70578436 | + | CTCF | chr16 | 67662273 | + |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000302516 | SF3B3 | chr16 | 70578436 | + | ENST00000264010 | CTCF | chr16 | 67662273 | + | 3517 | 1540 | 109 | 2205 | 698 |
| ENST00000302516 | SF3B3 | chr16 | 70578436 | + | ENST00000401394 | CTCF | chr16 | 67662273 | + | 3517 | 1540 | 109 | 2205 | 698 |
| DeepORF 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. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000302516 | ENST00000264010 | SF3B3 | chr16 | 70578436 | + | CTCF | chr16 | 67662273 | + | 0.000765722 | 0.9992343 |
| ENST00000302516 | ENST00000401394 | SF3B3 | chr16 | 70578436 | + | CTCF | chr16 | 67662273 | + | 0.000765722 | 0.9992343 |
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Fusion Amino Acid Sequences |
| 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 >81068_81068_1_SF3B3-CTCF_SF3B3_chr16_70578436_ENST00000302516_CTCF_chr16_67662273_ENST00000264010_length(amino acids)=698AA_BP=477 MDIHTILLAAGFLGLRTVGVTKAWRSGWLRFPAAMFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTV EVFGVIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQFLAVDPKGRAVMISAIEKQKLVYILNR DAAARLTISSPLEAHKANTLVYHVVGVDVGFENPMFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLI TVPGGSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFFFLAQTEQGDIFKITLETDEDMVTEIR LKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQIAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLA NEDTPQLYVACGRGPRSSLRVLRHGLEERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRNT MARHADNCAGPDGVEGENGGETKKSKRGRKRKMRSKKEDSSDSENAEPDLDDNEDEEEPAVEIEPEPEPQPVTPAPPPAKKRRGRPPGRT -------------------------------------------------------------- >81068_81068_2_SF3B3-CTCF_SF3B3_chr16_70578436_ENST00000302516_CTCF_chr16_67662273_ENST00000401394_length(amino acids)=698AA_BP=477 MDIHTILLAAGFLGLRTVGVTKAWRSGWLRFPAAMFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTV EVFGVIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQFLAVDPKGRAVMISAIEKQKLVYILNR DAAARLTISSPLEAHKANTLVYHVVGVDVGFENPMFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLI TVPGGSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFFFLAQTEQGDIFKITLETDEDMVTEIR LKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQIAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLA NEDTPQLYVACGRGPRSSLRVLRHGLEERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRNT MARHADNCAGPDGVEGENGGETKKSKRGRKRKMRSKKEDSSDSENAEPDLDDNEDEEEPAVEIEPEPEPQPVTPAPPPAKKRRGRPPGRT -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:70578436/chr16:67660458) - 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. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | CTCF |
| 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: Testis-specific DNA binding protein responsible for insulator function, nuclear architecture and transcriptional control, which probably acts by recruiting epigenetic chromatin modifiers. Plays a key role in gene imprinting in male germline, by participating in the establishment of differential methylation at the IGF2/H19 imprinted control region (ICR). Directly binds the unmethylated H19 ICR and recruits the PRMT7 methyltransferase, leading to methylate histone H4 'Arg-3' to form H4R3sme2. This probably leads to recruit de novo DNA methyltransferases at these sites (By similarity). Seems to act as tumor suppressor. In association with DNMT1 and DNMT3B, involved in activation of BAG1 gene expression by binding to its promoter. Required for dimethylation of H3 lysine 4 (H3K4me2) of MYC and BRCA1 promoters. {ECO:0000250, ECO:0000269|PubMed:12011441, ECO:0000269|PubMed:18413740, ECO:0000269|PubMed:18765639}. |
| 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. |
| - 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 |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 523_546 | 506.0 | 728.0 | Zinc finger | C2H2-type 10 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 555_577 | 506.0 | 728.0 | Zinc finger | C2H2-type 11%3B atypical | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 266_288 | 178.0 | 400.0 | Zinc finger | C2H2-type 1 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 294_316 | 178.0 | 400.0 | Zinc finger | C2H2-type 2 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 322_345 | 178.0 | 400.0 | Zinc finger | C2H2-type 3 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 351_373 | 178.0 | 400.0 | Zinc finger | C2H2-type 4 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 379_401 | 178.0 | 400.0 | Zinc finger | C2H2-type 5 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 407_430 | 178.0 | 400.0 | Zinc finger | C2H2-type 6 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 437_460 | 178.0 | 400.0 | Zinc finger | C2H2-type 7 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 467_489 | 178.0 | 400.0 | Zinc finger | C2H2-type 8 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 495_517 | 178.0 | 400.0 | Zinc finger | C2H2-type 9 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 523_546 | 178.0 | 400.0 | Zinc finger | C2H2-type 10 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000401394 | 5 | 10 | 555_577 | 178.0 | 400.0 | Zinc finger | C2H2-type 11%3B atypical |
| - 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 |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 266_288 | 506.0 | 728.0 | Zinc finger | C2H2-type 1 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 294_316 | 506.0 | 728.0 | Zinc finger | C2H2-type 2 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 322_345 | 506.0 | 728.0 | Zinc finger | C2H2-type 3 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 351_373 | 506.0 | 728.0 | Zinc finger | C2H2-type 4 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 379_401 | 506.0 | 728.0 | Zinc finger | C2H2-type 5 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 407_430 | 506.0 | 728.0 | Zinc finger | C2H2-type 6 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 437_460 | 506.0 | 728.0 | Zinc finger | C2H2-type 7 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 467_489 | 506.0 | 728.0 | Zinc finger | C2H2-type 8 | |
| Tgene | CTCF | chr16:70578436 | chr16:67662273 | ENST00000264010 | 7 | 12 | 495_517 | 506.0 | 728.0 | Zinc finger | C2H2-type 9 |
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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| SF3B3 | |
| CTCF |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| Hgene | SF3B3 | chr16:70578436 | chr16:67662273 | ENST00000302516 | + | 10 | 26 | 786_804 | 443.0 | 1218.0 | SF3B1 and SF3B5 |
| Hgene | SF3B3 | chr16:70578436 | chr16:67662273 | ENST00000302516 | + | 10 | 26 | 1028_1049 | 443.0 | 1218.0 | SF3B1 |
| Hgene | SF3B3 | chr16:70578436 | chr16:67662273 | ENST00000302516 | + | 10 | 26 | 1100_1123 | 443.0 | 1218.0 | SF3B5 |
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Related Drugs to SF3B3-CTCF |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to SF3B3-CTCF |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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