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![]() | Fusion Gene Summary |
![]() | Fusion Gene ORF analysis |
![]() | Fusion Genomic Features |
![]() | Fusion Protein Features |
![]() | Fusion Gene Sequence |
![]() | Fusion Gene PPI analysis |
![]() | Related Drugs |
![]() | Related Diseases |
Fusion gene:CPSF6-SH3YL1 (FusionGDB2 ID:HG11052TG26751) |
Fusion Gene Summary for CPSF6-SH3YL1 |
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Fusion gene information | Fusion gene name: CPSF6-SH3YL1 | Fusion gene ID: hg11052tg26751 | Hgene | Tgene | Gene symbol | CPSF6 | SH3YL1 | Gene ID | 11052 | 26751 |
Gene name | cleavage and polyadenylation specific factor 6 | SH3 and SYLF domain containing 1 | |
Synonyms | CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7 | RAY | |
Cytomap | ('CPSF6')('SH3YL1') 12q15 | 2p25.3 | |
Type of gene | protein-coding | protein-coding | |
Description | cleavage and polyadenylation specificity factor subunit 6CPSF 68 kDa subunitcleavage and polyadenylation specific factor 6, 68kDacleavage and polyadenylation specificity factor 68 kDa subunitcleavage factor Im complex 68 kDa subunitpre-mRNA cleavage | SH3 domain-containing YSC84-like protein 1SH3 domain containing, Ysc84-like 1 | |
Modification date | 20200313 | 20200313 | |
UniProtAcc | . | . | |
Ensembl transtripts involved in fusion gene | ENST00000266679, ENST00000435070, ENST00000456847, ENST00000551516, ENST00000550987, | ||
Fusion gene scores | * DoF score | 69 X 12 X 19=15732 | 10 X 5 X 4=200 |
# samples | 71 | 10 | |
** MAII score | log2(71/15732*10)=-4.46973925655087 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(10/200*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Context | PubMed: CPSF6 [Title/Abstract] AND SH3YL1 [Title/Abstract] AND fusion [Title/Abstract] | ||
Most frequent breakpoint | CPSF6(69656342)-SH3YL1(219001), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | CPSF6-SH3YL1 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. CPSF6-SH3YL1 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. CPSF6-SH3YL1 seems lost the major protein functional domain in Hgene 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) |
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Partner | Gene | GO ID | GO term | PubMed ID |
Hgene | CPSF6 | GO:0006397 | mRNA processing | 14690600 |
Hgene | CPSF6 | GO:0051262 | protein tetramerization | 20695905 |
Hgene | CPSF6 | GO:0051290 | protein heterotetramerization | 23187700 |
Hgene | CPSF6 | GO:1990120 | messenger ribonucleoprotein complex assembly | 29276085 |
![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * 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 | LUAD | TCGA-50-5049-01A | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
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Fusion Gene ORF analysis for CPSF6-SH3YL1 |
![]() * 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 |
3UTR-3CDS | ENST00000266679 | ENST00000356150 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000266679 | ENST00000403658 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000266679 | ENST00000403712 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000266679 | ENST00000405430 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000435070 | ENST00000356150 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000435070 | ENST00000403658 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000435070 | ENST00000403712 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000435070 | ENST00000405430 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000456847 | ENST00000356150 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000456847 | ENST00000403658 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000456847 | ENST00000403712 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-3CDS | ENST00000456847 | ENST00000405430 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-5UTR | ENST00000266679 | ENST00000468321 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-5UTR | ENST00000435070 | ENST00000468321 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-5UTR | ENST00000456847 | ENST00000468321 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000266679 | ENST00000402632 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000266679 | ENST00000403657 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000266679 | ENST00000415006 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000435070 | ENST00000402632 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000435070 | ENST00000403657 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000435070 | ENST00000415006 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000456847 | ENST00000402632 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000456847 | ENST00000403657 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
3UTR-intron | ENST00000456847 | ENST00000415006 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
5CDS-5UTR | ENST00000551516 | ENST00000468321 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
5CDS-intron | ENST00000551516 | ENST00000402632 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
5CDS-intron | ENST00000551516 | ENST00000403657 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
5CDS-intron | ENST00000551516 | ENST00000415006 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
Frame-shift | ENST00000551516 | ENST00000356150 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
Frame-shift | ENST00000551516 | ENST00000403712 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
Frame-shift | ENST00000551516 | ENST00000405430 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
In-frame | ENST00000551516 | ENST00000403658 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-3CDS | ENST00000550987 | ENST00000356150 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-3CDS | ENST00000550987 | ENST00000403658 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-3CDS | ENST00000550987 | ENST00000403712 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-3CDS | ENST00000550987 | ENST00000405430 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-5UTR | ENST00000550987 | ENST00000468321 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-intron | ENST00000550987 | ENST00000402632 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-intron | ENST00000550987 | ENST00000403657 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
intron-intron | ENST00000550987 | ENST00000415006 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - |
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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) |
ENST00000551516 | CPSF6 | chr12 | 69656342 | - | ENST00000403658 | SH3YL1 | chr2 | 219001 | - | 508 | 172 | 5 | 217 | 70 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000551516 | ENST00000403658 | CPSF6 | chr12 | 69656342 | - | SH3YL1 | chr2 | 219001 | - | 0.3600307 | 0.6399692 |
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Fusion Genomic Features for CPSF6-SH3YL1 |
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Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
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Fusion Protein Features for CPSF6-SH3YL1 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:69656342/chr2:219001) - 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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Hgene | Tgene |
. | . |
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}. | FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}. |
![]() * 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 |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 208_398 | 590 | 701.3333333333334 | Compositional bias | Note=Pro-rich |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 490_551 | 590 | 701.3333333333334 | Compositional bias | Note=Arg-rich |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 208_398 | 553 | 2111.0 | Compositional bias | Note=Pro-rich |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 490_551 | 553 | 2111.0 | Compositional bias | Note=Arg-rich |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 202_206 | 590 | 701.3333333333334 | Motif | GAR |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 202_206 | 553 | 2111.0 | Motif | GAR |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 358_551 | 590 | 701.3333333333334 | Region | (Microbial infection) Binds to HIV-1 capsid protein p24 (CA) |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 404_551 | 590 | 701.3333333333334 | Region | Sufficient for nuclear speckle localization |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 405_551 | 590 | 701.3333333333334 | Region | Necessary for RNA-binding |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 510_551 | 590 | 701.3333333333334 | Region | Sufficient for nuclear targeting |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000266679 | - | 10 | 11 | 81_161 | 590 | 701.3333333333334 | Region | Necessary for nuclear paraspeckles localization |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 358_551 | 553 | 2111.0 | Region | (Microbial infection) Binds to HIV-1 capsid protein p24 (CA) |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 404_551 | 553 | 2111.0 | Region | Sufficient for nuclear speckle localization |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 405_551 | 553 | 2111.0 | Region | Necessary for RNA-binding |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 510_551 | 553 | 2111.0 | Region | Sufficient for nuclear targeting |
Hgene | CPSF6 | chr12:69656342 | chr2:219001 | ENST00000435070 | - | 9 | 10 | 81_161 | 553 | 2111.0 | Region | Necessary for nuclear paraspeckles localization |
Tgene | SH3YL1 | chr12:69656342 | chr2:219001 | ENST00000356150 | 8 | 10 | 283_342 | 279 | 343.0 | Domain | SH3 | |
Tgene | SH3YL1 | chr12:69656342 | chr2:219001 | ENST00000402632 | 0 | 7 | 283_342 | 0 | 945.3333333333334 | Domain | SH3 | |
Tgene | SH3YL1 | chr12:69656342 | chr2:219001 | ENST00000403657 | 10 | 12 | 283_342 | 164 | 228.0 | Domain | SH3 | |
Tgene | SH3YL1 | chr12:69656342 | chr2:219001 | ENST00000403658 | 9 | 11 | 283_342 | 164 | 228.0 | Domain | SH3 | |
Tgene | SH3YL1 | chr12:69656342 | chr2:219001 | ENST00000403712 | 7 | 9 | 283_342 | 260 | 324.0 | Domain | SH3 | |
Tgene | SH3YL1 | chr12:69656342 | chr2:219001 | ENST00000405430 | 10 | 12 | 283_342 | 279 | 343.0 | Domain | SH3 | |
Tgene | SH3YL1 | chr12:69656342 | chr2:219001 | ENST00000415006 | 5 | 7 | 283_342 | 183 | 247.0 | Domain | SH3 |
- 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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Fusion Gene Sequence for CPSF6-SH3YL1 |
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>19187_19187_1_CPSF6-SH3YL1_CPSF6_chr12_69656342_ENST00000551516_SH3YL1_chr2_219001_ENST00000403658_length(transcript)=508nt_BP=172nt GGAAGATGGCGGACGGCGTGGACCACATAGACATTTACGCGGATGTCGGCGAAGAGTTCAACCAGGAAGCTGAATATGAGAGAGAAGCAG AGAACGAGAGAGGCACCGGGATCGTGACCGAGACCGTGACCGAGAGCGTGACCGAGAGCGCGAATATCGTCATCGTTAGAAGGCAATTTG AATCAACCCATAGAAGTGACAGCGCTGTATTCATTTGAAGGACAGCAGCCTGGGGATTTGAATTTTCAAGCTGGAGACAGAATCACAGTT ATATCAAAAACAGATTCACATTTTGATTGGTGGGAAGGAAAACTTCGAGGTCAAACTGGCATTTTTCCAGCCAACTACGTAACCATGAAT TAAAGCGTATACTATTTTCTTCTTTGAGAATTACAAAAAAATTATTTCTACACTGACAGGATTTACTAGTTAAGCAATGTTTAATATAAA >19187_19187_1_CPSF6-SH3YL1_CPSF6_chr12_69656342_ENST00000551516_SH3YL1_chr2_219001_ENST00000403658_length(amino acids)=70AA_BP=55 -------------------------------------------------------------- |
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Fusion Gene PPI Analysis for CPSF6-SH3YL1 |
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Hgene | Hgene's interactors | Tgene | Tgene's interactors |
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Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
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Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs for CPSF6-SH3YL1 |
![]() (DrugBank Version 5.1.8 2021-05-08) |
Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for CPSF6-SH3YL1 |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |