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Fusion gene ID: 28886 |
FusionGeneSummary for PRPF6_SDC4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: PRPF6_SDC4 | Fusion gene ID: 28886 | Hgene | Tgene | Gene symbol | PRPF6 | SDC4 | Gene ID | 24148 | 6385 |
| Gene name | pre-mRNA processing factor 6 | syndecan 4 | |
| Synonyms | ANT-1|ANT1|C20orf14|Prp6|RP60|SNRNP102|TOM|U5-102K|hPrp6 | SYND4 | |
| Cytomap | 20q13.33 | 20q13.12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | pre-mRNA-processing factor 6PRP6 homologPRP6 pre-mRNA processing factor 6 homologU5 snRNP-associated 102 kDa proteinU5-102 kDa proteinandrogen receptor N-terminal domain transactivating protein-1p102 U5 small nuclear ribonucleoprotein particle-bindi | syndecan-4amphiglycanryudocan amphiglycanryudocan core proteinsyndecan 4 (amphiglycan, ryudocan)syndecan proteoglycan 4 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | O94906 | P31431 | |
| Ensembl transtripts involved in fusion gene | ENST00000535781, | ENST00000372733, ENST00000537976, | |
| Fusion gene scores | * DoF score | 6 X 6 X 5=180 | 5 X 6 X 3=90 |
| # samples | 6 | 6 | |
| ** MAII score | log2(6/180*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/90*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: PRPF6 [Title/Abstract] AND SDC4 [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 | PRPF6 | GO:0000398 | mRNA splicing, via spliceosome | 28781166 |
| Hgene | PRPF6 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 16414017 |
| 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 | BRCA | TCGA-C8-A8HP-01A | PRPF6 | chr20 | 62626445 | + | SDC4 | chr20 | 43964560 | - |
| * 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 |
| In-frame | ENST00000535781 | ENST00000372733 | PRPF6 | chr20 | 62626445 | + | SDC4 | chr20 | 43964560 | - |
| 5CDS-intron | ENST00000535781 | ENST00000537976 | PRPF6 | chr20 | 62626445 | + | SDC4 | chr20 | 43964560 | - |
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FusionProtFeatures for PRPF6_SDC4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| PRPF6 | SDC4 |
| Cell surface proteoglycan that bears heparan sulfate.Regulates exosome biogenesis in concert with SDCBP and PDCD6IP(PubMed:22660413). {ECO:0000269|PubMed:22660413}. |
| 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 |
| Hgene | PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 67_72 | 205 | 902 | Compositional bias | Note=Poly-Asp |
| Tgene | >SDC4 | chr20:62626445 | chr20:43964560 | ENST00000372733 | - | 0 | 5 | 171_198 | 20 | 199 | Topological domain | Cytoplasmic |
| Tgene | >SDC4 | chr20:62626445 | chr20:43964560 | ENST00000372733 | - | 0 | 5 | 19_145 | 20 | 199 | Topological domain | Extracellular |
| Tgene | >SDC4 | chr20:62626445 | chr20:43964560 | ENST00000372733 | - | 0 | 5 | 146_170 | 20 | 199 | Transmembrane | Helical |
| - 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 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 384_416 | 205 | 902 | Repeat | Note=HAT 1 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 418_444 | 205 | 902 | Repeat | Note=HAT 2 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 445_476 | 205 | 902 | Repeat | Note=HAT 3 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 554_586 | 205 | 902 | Repeat | Note=HAT 4 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 588_620 | 205 | 902 | Repeat | Note=HAT 5 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 622_654 | 205 | 902 | Repeat | Note=HAT 6 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 689_721 | 205 | 902 | Repeat | Note=HAT 7 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 723_755 | 205 | 902 | Repeat | Note=HAT 8 |
| Hgene | >PRPF6 | chr20:62626445 | chr20:43964560 | ENST00000535781 | + | 5 | 20 | 855_887 | 205 | 902 | Repeat | Note=HAT 9 |
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FusionGeneSequence for PRPF6_SDC4 |
| 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. |
| >In-frame_PRPF6_ENST00000535781_chr20_62626445_+_SDC4_ENST00000372733_chr20_43964560_-_384aa MNKKKKPFLGMPAPLGYVPGLGRGATGFTTRSDIGPARDANDPVDDRHAPPGKRTVGDQMKKNQAADDDDEDLNDTNYDEFNGYAGSLFS SGPYEKDDEEADAIYAALDKRMDERRKERREQREKEEIEKYRMERPKIQQQFSDLKRKLAEVTEEEWLSIPEVGDARNKRQRNPRYEKLT PVPDSFFAKHLQTGENHTSVDPRQTIRETEVIDPQDLLEGRYFSGALPDDEDVVGPGQESDDFELSGSGDLDDLEDSMIGPEVVHPLVPL DNHIPERAGSGSQVPTEPKKLEENEVIPKRISPVEESEDVSNKVSMSSTVQGSNIFERTEVLAALIVGGIVGILFAVFLILLLMYRMKKK |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| >In-frame_PRPF6_ENST00000535781_chr20_62626445_+_SDC4_ENST00000372733_chr20_43964560_-_1152nt ATGAACAAGAAGAAGAAACCGTTCCTAGGGATGCCCGCGCCCCTCGGCTACGTGCCGGGGCTGGGCCGGGGCGCCACTGGCTTCACCACG CGGTCAGACATTGGGCCCGCCCGTGATGCAAATGACCCTGTGGATGATCGCCATGCACCCCCAGGCAAGAGAACCGTTGGGGACCAGATG AAGAAAAATCAGGCTGCTGACGATGACGACGAGGATCTAAATGACACCAATTACGATGAGTTTAATGGCTATGCTGGGAGCCTCTTCTCA AGTGGACCCTACGAGAAAGATGATGAGGAAGCAGATGCTATCTATGCAGCCCTGGATAAAAGGATGGATGAAAGAAGAAAAGAAAGACGG GAGCAAAGGGAGAAAGAAGAAATAGAGAAATATCGTATGGAACGCCCCAAAATCCAACAGCAGTTCTCAGACCTCAAGAGGAAGTTGGCA GAAGTCACAGAAGAAGAGTGGCTGAGCATCCCCGAGGTTGGCGATGCCAGAAATAAACGTCAGCGGAACCCACGCTATGAGAAGCTGACC CCTGTTCCTGACAGTTTCTTTGCCAAACATTTACAGACCGGAGAGAACCATACCTCAGTGGATCCCCGACAAACTATCCGAGAGACTGAG GTCATCGACCCCCAGGACCTCCTAGAAGGCCGATACTTCTCCGGAGCCCTACCAGACGATGAGGATGTAGTGGGGCCCGGGCAGGAATCT GATGACTTTGAGCTGTCTGGCTCTGGAGATCTGGATGACTTGGAAGACTCCATGATCGGCCCTGAAGTTGTCCATCCCTTGGTGCCTCTA GATAACCATATCCCTGAGAGGGCAGGGTCTGGGAGCCAAGTCCCCACCGAACCCAAGAAACTAGAGGAGAATGAGGTTATCCCCAAGAGA ATCTCACCCGTTGAAGAGAGTGAGGATGTGTCCAACAAGGTGTCAATGTCCAGCACTGTGCAGGGCAGCAACATCTTTGAGAGAACGGAG GTCCTGGCAGCTCTGATTGTGGGTGGCATCGTGGGCATCCTCTTTGCCGTCTTCCTGATCCTACTGCTCATGTACCGTATGAAGAAGAAG |
| * Fusion transcript sequences (Full-length transcript). |
| >In-frame_PRPF6_ENST00000535781_chr20_62626445_+_SDC4_ENST00000372733_chr20_43964560_-_3239nt GGCGACACTTTGCTACGGAGTGCATCGGACGTCGAAGCCTAGAGTCTCTGCGTCTTTCCCTCTTCCGCTGCCTCATTCCTTTCCTTCCTA GCCTTGGTCGTCGCCGCCACCATGAACAAGAAGAAGAAACCGTTCCTAGGGATGCCCGCGCCCCTCGGCTACGTGCCGGGGCTGGGCCGG GGCGCCACTGGCTTCACCACGCGGTCAGACATTGGGCCCGCCCGTGATGCAAATGACCCTGTGGATGATCGCCATGCACCCCCAGGCAAG AGAACCGTTGGGGACCAGATGAAGAAAAATCAGGCTGCTGACGATGACGACGAGGATCTAAATGACACCAATTACGATGAGTTTAATGGC TATGCTGGGAGCCTCTTCTCAAGTGGACCCTACGAGAAAGATGATGAGGAAGCAGATGCTATCTATGCAGCCCTGGATAAAAGGATGGAT GAAAGAAGAAAAGAAAGACGGGAGCAAAGGGAGAAAGAAGAAATAGAGAAATATCGTATGGAACGCCCCAAAATCCAACAGCAGTTCTCA GACCTCAAGAGGAAGTTGGCAGAAGTCACAGAAGAAGAGTGGCTGAGCATCCCCGAGGTTGGCGATGCCAGAAATAAACGTCAGCGGAAC CCACGCTATGAGAAGCTGACCCCTGTTCCTGACAGTTTCTTTGCCAAACATTTACAGACCGGAGAGAACCATACCTCAGTGGATCCCCGA CAAACTATCCGAGAGACTGAGGTCATCGACCCCCAGGACCTCCTAGAAGGCCGATACTTCTCCGGAGCCCTACCAGACGATGAGGATGTA GTGGGGCCCGGGCAGGAATCTGATGACTTTGAGCTGTCTGGCTCTGGAGATCTGGATGACTTGGAAGACTCCATGATCGGCCCTGAAGTT GTCCATCCCTTGGTGCCTCTAGATAACCATATCCCTGAGAGGGCAGGGTCTGGGAGCCAAGTCCCCACCGAACCCAAGAAACTAGAGGAG AATGAGGTTATCCCCAAGAGAATCTCACCCGTTGAAGAGAGTGAGGATGTGTCCAACAAGGTGTCAATGTCCAGCACTGTGCAGGGCAGC AACATCTTTGAGAGAACGGAGGTCCTGGCAGCTCTGATTGTGGGTGGCATCGTGGGCATCCTCTTTGCCGTCTTCCTGATCCTACTGCTC ATGTACCGTATGAAGAAGAAGGATGAAGGCAGCTATGACCTGGGCAAGAAACCCATCTACAAGAAAGCCCCCACCAATGAGTTCTACGCG TGAAGCTTGCTTGTGGGCACTGGCTTGGACTTTAGCGGGGAGGGAAGCCAGGGGATTTTGAAGGGTGGACATTAGGGTAGGGTGAGGTCA ACCTAATACTGACTTGTCAGTATCTCCAGCTCTGATTACCTTTGAAGTGTTCAGAAGAGACATTGTCTTCTACTGTTCTGCCAGGTTCTT CTTGAGCTTTGGGCCTCAGTTGCCCTGGCAGAAAAATGGATTCAACTTGGCCTTTCTGAAGGCAAGACTGGGATTGGATCACTTCTTAAA CTTCCAGTTAAGAATCTAGGTCCGCCCTCAAGCCCATACTGACCATGCCTCATCCAGAGCTCCTCTGAAGCCAGGGGGCTAACGGATGTT GTGTGGAGTCCTGGCTGGAGGTCCTCCCCCAGTGGCCTTCCTCCCTTCCTTTCACAGCCGGTCTCTCTGCCAGGAAATGGGGGAAGGAAC TAGAACCACCTGCACCTTGAGATGTTTCTGTAAATGGGTACTTGTGATCACACTACGGGAATCTCTGTGGTATATACCTGGGGCCATTCT AGGCTCTTTCAAGTGACTTTTGGAAATCAACCTTTTTTATTTGGGGGGGAGGATGGGGAAAAGAGCTGAGAGTTTATGCTGAAATGGATT TATAGAATATTTGTAAATCTATTTTTAGTGTTTGTTCGTTTTTTTAACTGTTCATTCCTTTGTGCAGAGTGTATATCTCTGCCTGGGCAA GAGTGTGGAGGTGCCGAGGTGTCTTCATTCTCTCGCACATTTCCACAGCACCTGCTAAGTTTGTATTTAATGGTTTTTGTTTTTGTTTTT GTTTGTTTCTTGAAAATGAGAGAAGAGCCGGAGAGATGATTTTTATTAATTTTTTTTTTTTTTTTTTTTTTTTACTATTTATAGCTTTAG ATAGGGCCTCCCTTCCCCTCTTCTTTCTTTGTTCTCTTTCATTAAACCCCTTCCCCAGTTTTTTTTTTATACTTTAAACCCCGCTCCTCA TGGCCTTGGCCCTTTCTGAAGCTGCTTCCTCTTATAAAATAGCTTTTGCCGAAACATAGTTTTTTTTTAGCAGATCCCAAAATATAATGA AGGGGATGGTGGGATATTTGTGTCTGTGTTCTTATAATATATTATTATTCTTCCTTGGTTCTAGAAAAATAGATAAATATATTTTTTTCA GGAAATAGTGTGGTGTTTCCAGTTTGATGTTGCTGGGTGGTTGAGTGAGTGAATTTTCATGTGGCTGGGTGGGTTTTTGCCTTTTTCTCT TGCCCTGTTCCTGGTGCCTTCTGATGGGGCTGGAATAGTTGAGGTGGATGGTTCTACCCTTTCTGCCTTCTGTTTGGGACCCAGCTGGTG TTCTTTGGTTTGCTTTCTTCAGGCTCTAGGGCTGTGCTATCCAATACAGTAACCACATGCGGCTGTTTAAAGTTAAGCCAATTAAAATCA CATAAGATTAAAAATTCCTTCCTCAGTTGCACTAACCACGTTTCTAGAGGCGTCACTGTATGTAGTTCATGGCTACTGTACTGACAGCGA GAGCATGTCCATCTGTTGGACAGCACTATTCTAGAGAACTAAACTGGCTTAACGAGTCACAGCCTCAGCTGTGCTGGGACGACCCTTGTC TCCCTGGGTAGGGGGGGGGGAATGGGGGAGGGCTGATGAGGCCCCAGCTGGGGCCTGTTGTCTGGGACCCTCCCTCTCCTGAGAGGGGAG GCCTGGTGGCTTAGCCTGGGCAGGTCGTGTCTCCTCCTGACCCCAGTGGCTGCGGTGAGGGGAACCACCCTCCCTTGCTGCACCAGTGGC CATTAGCTCCCGTCACCACTGCAACCCAGGGTCCCAGCTGGCTGGGTCCTCTTCTGCCCCCAGTGCCCTTCCCCTTGGGCTGTGTTGGAG |
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FusionGenePPI for PRPF6_SDC4 |
| 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 |
| PRPF6 | TXNL4B, CD2BP2, SNRNP40, RNPS1, RNU11, ARAF, RAF1, TIMM44, PRPF6, YWHAB, AR, USP39, PRPF4, MEPCE, GIGYF2, SMARCA2, TADA2A, MYC, SF3A2, SIRT7, PRPF31, SART1, TXNL4A, EFTUD2, SNRNP200, PRPF8, PRPF3, SNRPD1, SNRPD3, SF3B3, SNRPD2, SNRPA1, SRSF7, NHP2L1, HNRNPM, U2AF1, SRSF5, U2AF2, PRPF19, EIF4A3, ACIN1, SRRM2, SAP18, SON, TPBG, THRAP3, NCSTN, NPM1, RPS13, RPS24, DDX18, RBM14, SUPT16H, TRA2A, ZNF326, NOTCH1, IK, CTNNB1, MMS19, HDAC11, PRPF4B, PARK2, RPA1, RPA2, RPA3, PASK, CUL7, OBSL1, CCDC8, EED, GCFC2, DDX23, TSSC4, BSG, LUC7L2, SF3A1, SNRPA, SF3A3, RNU12, NTRK1, SCARNA22, TP53, KIF21B, RAB4B, SNW1, CDC5L, MEX3C, RC3H1, ZNF746, SNRPG, SNRPE, SNRPN, SNRPF, KIAA1143, GPR156, RBM42, SMU1, RIOK1, ZNHIT2, AAR2, EAPP, DLST, PDHA1, FOXA1, TRIM25, BRCA1, LMNA | SDC4 | FGF2, CCL5, GIPC1, DVL1, ELAVL1, MYC, TGFB3, TANK, SGTA, FGF1, PTEN, DBN1, RARRES3, CYLD, GPR183, UBC |
| - 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 PRPF6_SDC4 |
| 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 PRPF6_SDC4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | PRPF6 | C3151434 | RETINITIS PIGMENTOSA 60 | 1 | UNIPROT |
| Tgene | SDC4 | C0007131 | Non-Small Cell Lung Carcinoma | 1 | CTD_human |
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