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Fusion gene ID: 33883 |
FusionGeneSummary for SIN3A_PTPN9 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SIN3A_PTPN9 | Fusion gene ID: 33883 | Hgene | Tgene | Gene symbol | SIN3A | PTPN9 | Gene ID | 25942 | 5780 |
| Gene name | SIN3 transcription regulator family member A | protein tyrosine phosphatase, non-receptor type 9 | |
| Synonyms | WITKOS | MEG2|PTPMEG2 | |
| Cytomap | 15q24.2 | 15q24.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | paired amphipathic helix protein Sin3aSIN3 homolog A, transcription regulatorhistone deacetylase complex subunit Sin3atranscriptional co-repressor Sin3Atranscriptional corepressor Sin3atranscriptional regulator, SIN3A | tyrosine-protein phosphatase non-receptor type 9PTPase-MEG2protein-tyrosine phosphatase MEG2 | |
| Modification date | 20180523 | 20180520 | |
| UniProtAcc | Q96ST3 | P43378 | |
| Ensembl transtripts involved in fusion gene | ENST00000394947, ENST00000360439, ENST00000394949, ENST00000567289, | ENST00000306726, ENST00000564970, | |
| Fusion gene scores | * DoF score | 10 X 6 X 6=360 | 3 X 3 X 3=27 |
| # samples | 11 | 3 | |
| ** MAII score | log2(11/360*10)=-1.71049338280502 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SIN3A [Title/Abstract] AND PTPN9 [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 |
| Tgene | PTPN9 | GO:0010977 | negative regulation of neuron projection development | 27655914 |
| Tgene | PTPN9 | GO:0035335 | peptidyl-tyrosine dephosphorylation | 27655914 |
| Tgene | PTPN9 | GO:1903078 | positive regulation of protein localization to plasma membrane | 27655914 |
| 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 | RV | LGG | TCGA-CS-5396-01A | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| * 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 |
| Frame-shift | ENST00000394947 | ENST00000306726 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| 5CDS-intron | ENST00000394947 | ENST00000564970 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| Frame-shift | ENST00000360439 | ENST00000306726 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| 5CDS-intron | ENST00000360439 | ENST00000564970 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| Frame-shift | ENST00000394949 | ENST00000306726 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| 5CDS-intron | ENST00000394949 | ENST00000564970 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| Frame-shift | ENST00000567289 | ENST00000306726 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
| 5CDS-intron | ENST00000567289 | ENST00000564970 | SIN3A | chr15 | 75722528 | - | PTPN9 | chr15 | 75819602 | - |
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FusionProtFeatures for SIN3A_PTPN9 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SIN3A | PTPN9 |
| Acts as a transcriptional repressor. Corepressor forREST. Interacts with MXI1 to repress MYC responsive genes andantagonize MYC oncogenic activities. Also interacts with MXD1-MAXheterodimers to repress transcription by tethering SIN3A to DNA.Acts cooperatively with OGT to repress transcription in parallelwith histone deacetylation. Involved in he control of thecircadian rhythms. Required for the transcriptional repression ofcircadian target genes, such as PER1, mediated by the large PERcomplex through histone deacetylation. Cooperates with FOXK1 toregulate cell cycle progression probably by repressing cell cycleinhibitor genes expression (By similarity).{ECO:0000250|UniProtKB:Q60520, ECO:0000269|PubMed:12150998}. | Protein-tyrosine phosphatase that could participate inthe transfer of hydrophobic ligands or in functions of the Golgiapparatus. {ECO:0000269|PubMed:19167335}. |
| 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 SIN3A_PTPN9 |
| 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 SIN3A_PTPN9 |
| 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 |
| SIN3A | MBD3L1, HDAC9, IKZF1, HCFC1, DNMT3B, HDAC1, HDAC2, MTA2, MTA1, ARID4B, SUDS3, SAP30, SAP130, PTMA, EFCAB6, SETDB1, MORF4, PFN2, MORF4L2, RBPJ, SNW1, KDM1A, PML, NCOR1, SKI, SMARCB1, SMARCA4, SMARCA2, SMARCC1, PHB, RBBP4, RBBP7, SAP18, HBP1, MXD1, KLF11, KLF16, KLF13, KLF9, KLF10, ZBTB16, CABIN1, NCOR2, SATB1, PHF12, IKZF3, IKZF2, IKZF4, MBD2, ING1, HEY2, COPS2, BCL6, RLIM, TAL1, RUNX1T1, MNT, MXD3, OGT, MECP2, MBD4, ING2, WHSC1, SFPQ, ZBTB7A, MKX, NR4A2, GPS2, TBL1X, HDAC4, HSP90AA1, NR0B2, ADD1, ESR1, HDAC5, SAP30L, ID2, MGEA5, SAP25, NKX3-2, PRMT5, SMARCE1, MEN1, PA2G4, SMARCA5, NFX1, CBFA2T2, BCL6B, TAF1, CHD3, SMARCC2, ALL1, TAF6, TBP, MBD3, TAF9, RAN, TFCP2, CYP4V2, NKX2-2, TGIF1, ZBTB4, PFDN5, SPI1, KLF1, SP1, ETV6, SMAD3, ARID4A, SYT1, CTCF, TP53, REST, SKIL, CHD4, MYB, TRIM28, SMN1, RUNX1, CSNK2A1, TOPORS, E2F4, MAF, TADA2A, IRF5, MORF4L1, THAP11, KMT2A, NONO, SMARCAD1, SOX2, DACH1, KDM2B, HINT1, LAMTOR5, NR2C1, ISG15, BRMS1L, GRK5, AR, TAB2, SNCA, SLC9A3R2, S100A10, SEPT11, PDLIM5, ACO2, TOM1L2, SEC22B, NOTCH2, THADA, TTLL12, AHCYL1, SF1, IGBP1, EPAS1, BRMS1, BHLHE40, STAT3, MAD1L1, SHFM1, HIF1A, DDB1, CUL4B, CHFR, NXF1, HIST3H3, LOXL2, EED, EDA, LACC1, MIER2, UNK, NTRK1, GTF2E2, CAB39, CSNK2A2, DDX46, FUBP1, KHSRP, PIR, VAPA, TCF20, SIN3B, SNAI1, MAX, FOXK1, FOXK2, FBXW7, KMT2E, NANOG, POU5F1, GATAD1, FAM60A, ZNF704, PHF23, DDX41, TFAP4, MDK, TRIM25 | PTPN9 | RTN3, GHR, MYC, TP53BP1, VCP, AGTRAP, REEP6, MAL2, CMTM5, ENO1, MOV10, NXF1, NTRK1, CREB3, LZTR1, PC, EYA1, RAD51C, FAM26D, VSIG8, C5AR2, MDK, PDCD1, PTPN9, GEMIN8, FSIP1, SMN1, DDX20, GEMIN4, PMPCA, SLC39A7, STRAP, TUBA3C, AAR2, SMN2, TUBA3D, LMNA |
| - 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 SIN3A_PTPN9 |
| 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 |
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RelatedDiseases for SIN3A_PTPN9 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SIN3A | C0013336 | Dwarfism | 1 | CTD_human |
| Hgene | SIN3A | C0020255 | Hydrocephalus | 1 | CTD_human |
| Hgene | SIN3A | C0025958 | Microcephaly | 1 | CTD_human |
| Hgene | SIN3A | C0175754 | Agenesis of corpus callosum | 1 | CTD_human |
| Hgene | SIN3A | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| Hgene | SIN3A | C1510586 | Autism Spectrum Disorders | 1 | CTD_human |
| Hgene | SIN3A | C3714756 | Intellectual Disability | 1 | CTD_human;HPO |
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