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Fusion Protein:CDK6-SEMA3D |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: CDK6-SEMA3D | FusionPDB ID: 15297 | FusionGDB2.0 ID: 15297 | Hgene | Tgene | Gene symbol | CDK6 | SEMA3D | Gene ID | 1021 | 223117 |
| Gene name | cyclin dependent kinase 6 | semaphorin 3D | |
| Synonyms | MCPH12|PLSTIRE | Sema-Z2|coll-2 | |
| Cytomap | 7q21.2 | 7q21.11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cyclin-dependent kinase 6cell division protein kinase 6serine/threonine-protein kinase PLSTIRE | semaphorin-3Dcollapsin 2sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D | |
| Modification date | 20200329 | 20200313 | |
| UniProtAcc | Q00534 | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000265734, ENST00000424848, ENST00000491250, | ENST00000484038, ENST00000284136, ENST00000444867, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 12 X 9 X 7=756 | 3 X 3 X 3=27 |
| # samples | 17 | 3 | |
| ** MAII score | log2(17/756*10)=-2.15285148808337 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 (manual curation of fusion genes in FusionPDB) | PubMed: CDK6 [Title/Abstract] AND SEMA3D [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CDK6(92404010)-SEMA3D(84685175), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | CDK6-SEMA3D 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. CDK6-SEMA3D 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. CDK6-SEMA3D 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. CDK6-SEMA3D 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. CDK6-SEMA3D seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. CDK6-SEMA3D seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. CDK6-SEMA3D seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. CDK6-SEMA3D seems lost the major protein functional domain in Hgene 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 | CDK6 | GO:0001954 | positive regulation of cell-matrix adhesion | 10205165 |
| Hgene | CDK6 | GO:0003323 | type B pancreatic cell development | 20668294 |
| Hgene | CDK6 | GO:0006468 | protein phosphorylation | 8114739 |
| Hgene | CDK6 | GO:0010468 | regulation of gene expression | 15254224 |
| Hgene | CDK6 | GO:0045638 | negative regulation of myeloid cell differentiation | 17431401 |
| Hgene | CDK6 | GO:0045656 | negative regulation of monocyte differentiation | 26542173 |
| Hgene | CDK6 | GO:0045668 | negative regulation of osteoblast differentiation | 15254224 |
| Hgene | CDK6 | GO:0045786 | negative regulation of cell cycle | 14985467 |
| Hgene | CDK6 | GO:2000773 | negative regulation of cellular senescence | 17420273 |
| Fusion gene breakpoints across CDK6 (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 SEMA3D (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 | STAD | TCGA-D7-A6EX-01A | CDK6 | chr7 | 92404010 | - | SEMA3D | chr7 | 84685175 | - |
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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) |
| ENST00000265734 | CDK6 | chr7 | 92404010 | - | ENST00000284136 | SEMA3D | chr7 | 84685175 | - | 6284 | 781 | 948 | 2396 | 482 |
| ENST00000265734 | CDK6 | chr7 | 92404010 | - | ENST00000444867 | SEMA3D | chr7 | 84685175 | - | 1318 | 781 | 412 | 1005 | 197 |
| 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 |
| ENST00000265734 | ENST00000284136 | CDK6 | chr7 | 92404010 | - | SEMA3D | chr7 | 84685175 | - | 0.000169315 | 0.9998306 |
| ENST00000265734 | ENST00000444867 | CDK6 | chr7 | 92404010 | - | SEMA3D | chr7 | 84685175 | - | 0.002360693 | 0.9976393 |
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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 >15297_15297_1_CDK6-SEMA3D_CDK6_chr7_92404010_ENST00000265734_SEMA3D_chr7_84685175_ENST00000284136_length(amino acids)=482AA_BP= MINKWTTFLKARLICSIPGSDGADTYFDELQDIYLLPTRDERNPVVYGVFTTTSSIFKGSAVCVYSMADIRAVFNGPYAHKESADHRWVQ YDGRIPYPRPGTCPSKTYDPLIKSTRDFPDDVISFIKRHSVMYKSVYPVAGGPTFKRINVDYRLTQIVVDHVIAEDGQYDVMFLGTDIGT VLKVVSISKEKWNMEEVVLEELQIFKHSSIILNMELSLKQQQLYIGSRDGLVQLSLHRCDTYGKACADCCLARDPYCAWDGNACSRYAPT SKRRARRQDVKYGDPITQCWDIEDSISHETADEKVIFGIEFNSTFLECIPKSQQATIKWYIQRSGDEHREELKPDERIIKTEYGLLIRSL QKKDSGMYYCKAQEHTFIHTIVKLTLNVIENEQMENTQRAEHEEGKVKDLLAESRLRYKDYIQILSSPNFSLDQYCEQMWHREKRRQRNK -------------------------------------------------------------- >15297_15297_2_CDK6-SEMA3D_CDK6_chr7_92404010_ENST00000265734_SEMA3D_chr7_84685175_ENST00000444867_length(amino acids)=197AA_BP=123 MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDR ETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKEQNLLELSSYQTPTIQMMIKYISSFVNHLKKAVPPIKPSFLELEEFVRRICALKIDL -------------------------------------------------------------- |
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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/chr7:92404010/chr7:84685175) - 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 |
| CDK6 | . |
| FUNCTION: Serine/threonine-protein kinase involved in the control of the cell cycle and differentiation; promotes G1/S transition. Phosphorylates pRB/RB1 and NPM1. Interacts with D-type G1 cyclins during interphase at G1 to form a pRB/RB1 kinase and controls the entrance into the cell cycle. Involved in initiation and maintenance of cell cycle exit during cell differentiation; prevents cell proliferation and regulates negatively cell differentiation, but is required for the proliferation of specific cell types (e.g. erythroid and hematopoietic cells). Essential for cell proliferation within the dentate gyrus of the hippocampus and the subventricular zone of the lateral ventricles. Required during thymocyte development. Promotes the production of newborn neurons, probably by modulating G1 length. Promotes, at least in astrocytes, changes in patterns of gene expression, changes in the actin cytoskeleton including loss of stress fibers, and enhanced motility during cell differentiation. Prevents myeloid differentiation by interfering with RUNX1 and reducing its transcription transactivation activity, but promotes proliferation of normal myeloid progenitors. Delays senescence. Promotes the proliferation of beta-cells in pancreatic islets of Langerhans. May play a role in the centrosome organization during the cell cycle phases (PubMed:23918663). {ECO:0000269|PubMed:12833137, ECO:0000269|PubMed:14985467, ECO:0000269|PubMed:15254224, ECO:0000269|PubMed:15809340, ECO:0000269|PubMed:17420273, ECO:0000269|PubMed:17431401, ECO:0000269|PubMed:20333249, ECO:0000269|PubMed:20668294, ECO:0000269|PubMed:23918663, ECO:0000269|PubMed:8114739}. | 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. |
| 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 |
| Hgene | CDK6 | chr7:92404010 | chr7:84685175 | ENST00000265734 | - | 3 | 8 | 19_27 | 123.0 | 327.0 | Nucleotide binding | ATP |
| Hgene | CDK6 | chr7:92404010 | chr7:84685175 | ENST00000424848 | - | 3 | 8 | 19_27 | 123.0 | 327.0 | Nucleotide binding | ATP |
| Tgene | SEMA3D | chr7:92404010 | chr7:84685175 | ENST00000284136 | 5 | 17 | 739_773 | 239.33333333333334 | 778.0 | Compositional bias | Note=Arg/Lys-rich (basic) | |
| Tgene | SEMA3D | chr7:92404010 | chr7:84685175 | ENST00000284136 | 5 | 17 | 533_585 | 239.33333333333334 | 778.0 | Domain | Note=PSI | |
| Tgene | SEMA3D | chr7:92404010 | chr7:84685175 | ENST00000284136 | 5 | 17 | 592_680 | 239.33333333333334 | 778.0 | Domain | Note=Ig-like C2-type |
| - 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 |
| Hgene | CDK6 | chr7:92404010 | chr7:84685175 | ENST00000265734 | - | 3 | 8 | 13_300 | 123.0 | 327.0 | Domain | Protein kinase |
| Hgene | CDK6 | chr7:92404010 | chr7:84685175 | ENST00000424848 | - | 3 | 8 | 13_300 | 123.0 | 327.0 | Domain | Protein kinase |
| Tgene | SEMA3D | chr7:92404010 | chr7:84685175 | ENST00000284136 | 5 | 17 | 44_531 | 239.33333333333334 | 778.0 | Domain | Sema |
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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 |
| CDK6 | CDKN2C, CDKN2A, CCND1, CDKN2D, PPP2CA, PPM1B, CDK2, CCND2, CCND3, CDKN1B, CDC37, FBXO7, CDKN1A, UHRF2, CDK5R1, ELAVL1, CCNE1, CCNA2, KIF26B, RB1, CDK7, ATXN1, HIST1H1A, PML, HSP90AA1, FOXM1, ZSCAN1, SYNPO2, DEDD2, SRSF12, ZNF101, SNIP1, ZNF335, PRX, EBF4, EIF4ENIF1, RBM23, BCL11A, TCEB3B, PPHLN1, TRA2A, SENP3, NIPBL, CBY1, SSBP2, SIRT1, POGZ, LPIN1, ANKRD12, TPX2, TRAK1, CASC3, CLASRP, PPARGC1A, MSL3, SORBS1, ABI2, N4BP1, VGLL4, TJP2, SRSF11, ZMYM3, ZNF174, SLBP, ZFP36, MZF1, KLF10, TFDP1, ZEB1, SOX5, SOX10, SRSF1, SRSF2, SRSF7, TRA2B, RBL1, RBL2, NUMA1, NFATC3, MYC, MEF2D, MLLT3, ISL1, HSF1, EZH2, FOXO3, ELK1, ATF6B, DDIT3, CDC6, MCM2, MCM10, UCHL1, CDKN2B, WDR33, CDKL3, CDK6, DMBT1, AMY2A, PIGR, CDK4, DAB1, PSMA3, RTFDC1, HSP90AA5P, UBE2W, CCNT2, CCNT1, RCHY1, EIF2AK1, CDKN1C, NTRK1, RUNX1, CTNNB1, AR, VHL, FGFR3, USP17L2, MCF2L2, PAK4, FKBP5, FAM26E, TRIM25, HHV8GK18_gp82, EGLN2, RBPMS, HEXIM1, LARP7, KIAA1429, GBF1, SUMO1, UBE2I, ARNT, BECN1, AKT1, CD44, EPHA2, FGFR4, LATS2, STK11, FZR1, GLIS2, MAP2K3, MAP2K5, NF2, RAF1, RASSF1, ARAF, CBLC, KEAP1, MAP3K5, TEAD2, TERT, TSC1, ERBB2, GLIS1, GRM1, HGF, HIF1A, KAT2A, KDELR2, MAPK14, MET, PDGFRA, TNFRSF1A, TP53, TRIM28, APOBEC1, CCNI, CCNH, OTP, TRIM15, UBE2N, FASN, ACACA, NUPR1, USP51, ATG7, BSPRY, KLC3, CA4, NEU2, METTL21B, PPM1M, FAM96A, EPB41L5, HSP90AB1, PCNA, MAP1LC3B, CALCOCO2, |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| CDK6 |  |
| SEMA3D |
| - 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 |
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Related Drugs to CDK6-SEMA3D |
| 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 CDK6-SEMA3D |
| 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 |
| Hgene | CDK6 | C0004238 | Atrial Fibrillation | 2 | CTD_human |
| Hgene | CDK6 | C0025149 | Medulloblastoma | 2 | CTD_human |
| Hgene | CDK6 | C0205833 | Medullomyoblastoma | 2 | CTD_human |
| Hgene | CDK6 | C0235480 | Paroxysmal atrial fibrillation | 2 | CTD_human |
| Hgene | CDK6 | C0278510 | Childhood Medulloblastoma | 2 | CTD_human |
| Hgene | CDK6 | C0278876 | Adult Medulloblastoma | 2 | CTD_human |
| Hgene | CDK6 | C0751291 | Desmoplastic Medulloblastoma | 2 | CTD_human |
| Hgene | CDK6 | C1275668 | Melanotic medulloblastoma | 2 | CTD_human |
| Hgene | CDK6 | C2585653 | Persistent atrial fibrillation | 2 | CTD_human |
| Hgene | CDK6 | C3468561 | familial atrial fibrillation | 2 | CTD_human |
| Hgene | CDK6 | C0002871 | Anemia | 1 | CTD_human |
| Hgene | CDK6 | C0003873 | Rheumatoid Arthritis | 1 | CTD_human |
| Hgene | CDK6 | C0004403 | Autosome Abnormalities | 1 | CTD_human |
| Hgene | CDK6 | C0008625 | Chromosome Aberrations | 1 | CTD_human |
| Hgene | CDK6 | C0017636 | Glioblastoma | 1 | CTD_human |
| Hgene | CDK6 | C0023452 | Childhood Acute Lymphoblastic Leukemia | 1 | CTD_human |
| Hgene | CDK6 | C0023453 | L2 Acute Lymphoblastic Leukemia | 1 | CTD_human |
| Hgene | CDK6 | C0023467 | Leukemia, Myelocytic, Acute | 1 | CTD_human |
| Hgene | CDK6 | C0024668 | Mammary Neoplasms, Experimental | 1 | CTD_human |
| Hgene | CDK6 | C0026998 | Acute Myeloid Leukemia, M1 | 1 | CTD_human |
| Hgene | CDK6 | C0038454 | Cerebrovascular accident | 1 | CTD_human |
| Hgene | CDK6 | C0263454 | Chloracne | 1 | CTD_human |
| Hgene | CDK6 | C0334588 | Giant Cell Glioblastoma | 1 | CTD_human |
| Hgene | CDK6 | C0345967 | Malignant mesothelioma | 1 | CTD_human |
| Hgene | CDK6 | C0677866 | Brain Stem Neoplasms | 1 | CTD_human |
| Hgene | CDK6 | C0751886 | Brain Stem Neoplasms, Primary | 1 | CTD_human |
| Hgene | CDK6 | C0751887 | Medullary Neoplasms | 1 | CTD_human |
| Hgene | CDK6 | C0751888 | Mesencephalic Neoplasms | 1 | CTD_human |
| Hgene | CDK6 | C0751889 | Pontine Tumors | 1 | CTD_human |
| Hgene | CDK6 | C0751956 | Acute Cerebrovascular Accidents | 1 | CTD_human |
| Hgene | CDK6 | C1168401 | Squamous cell carcinoma of the head and neck | 1 | CTD_human |
| Hgene | CDK6 | C1621958 | Glioblastoma Multiforme | 1 | CTD_human |
| Hgene | CDK6 | C1879321 | Acute Myeloid Leukemia (AML-M2) | 1 | CTD_human |
| Hgene | CDK6 | C1961102 | Precursor Cell Lymphoblastic Leukemia Lymphoma | 1 | CTD_human |
| Hgene | CDK6 | C3711387 | Autosomal Recessive Primary Microcephaly | 1 | ORPHANET |
| Hgene | CDK6 | C4015156 | MICROCEPHALY 12, PRIMARY, AUTOSOMAL RECESSIVE | 1 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
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