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Fusion gene ID: 36091 |
FusionGeneSummary for SRSF3_PTCHD4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SRSF3_PTCHD4 | Fusion gene ID: 36091 | Hgene | Tgene | Gene symbol | SRSF3 | PTCHD4 | Gene ID | 6428 | 442213 |
| Gene name | serine and arginine rich splicing factor 3 | patched domain containing 4 | |
| Synonyms | SFRS3|SRp20 | C6orf138|PTCH53|dJ402H5.2 | |
| Cytomap | 6p21.31-p21.2 | 6p12.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | serine/arginine-rich splicing factor 3pre-mRNA splicing factor SRp20pre-mRNA-splicing factor SRP20splicing factor, arginine/serine-rich 3splicing factor, arginine/serine-rich, 20-kD | patched domain-containing protein 4p53-regulated patched proteinpatched domain-containing protein C6orf138 | |
| Modification date | 20180523 | 20180329 | |
| UniProtAcc | P84103 | Q6ZW05 | |
| Ensembl transtripts involved in fusion gene | ENST00000373715, ENST00000339436, | ENST00000339488, ENST00000543600, | |
| Fusion gene scores | * DoF score | 3 X 4 X 2=24 | 1 X 1 X 1=1 |
| # samples | 4 | 1 | |
| ** MAII score | log2(4/24*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: SRSF3 [Title/Abstract] AND PTCHD4 [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 | SRSF3 | GO:0048024 | regulation of mRNA splicing, via spliceosome | 26876937 |
| 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 | LD | STAD | TCGA-BR-A4PE-01A | SRSF3 | chr6 | 36566760 | + | PTCHD4 | chr6 | 47976850 | - |
| * 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 | ENST00000373715 | ENST00000339488 | SRSF3 | chr6 | 36566760 | + | PTCHD4 | chr6 | 47976850 | - |
| Frame-shift | ENST00000373715 | ENST00000543600 | SRSF3 | chr6 | 36566760 | + | PTCHD4 | chr6 | 47976850 | - |
| Frame-shift | ENST00000339436 | ENST00000339488 | SRSF3 | chr6 | 36566760 | + | PTCHD4 | chr6 | 47976850 | - |
| Frame-shift | ENST00000339436 | ENST00000543600 | SRSF3 | chr6 | 36566760 | + | PTCHD4 | chr6 | 47976850 | - |
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FusionProtFeatures for SRSF3_PTCHD4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SRSF3 | PTCHD4 |
| Splicing factor that specifically promotes exon-inclusion during alternative splicing (PubMed:26876937).Interaction with YTHDC1, a RNA-binding protein that recognizes andbinds N6-methyladenosine (m6A)-containing RNAs, promotesrecruitment of SRSF3 to its mRNA-binding elements adjacent to m6Asites, leading to exon-inclusion during alternative splicing(PubMed:26876937). Also functions as export adapter involved inmRNA nuclear export (PubMed:11336712, PubMed:18364396,PubMed:28984244). Binds mRNA which is thought to be transferred tothe NXF1-NXT1 heterodimer for export (TAP/NXF1 pathway); enhancesNXF1-NXT1 RNA-binding activity (PubMed:11336712, PubMed:18364396).Involved in nuclear export of m6A-containing mRNAs via interactionwith YTHDC1: interaction with YTHDC1 facilitates m6A-containingmRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export(PubMed:28984244). RNA-binding is semi-sequence specific(PubMed:17036044). {ECO:0000269|PubMed:11336712,ECO:0000269|PubMed:17036044, ECO:0000269|PubMed:18364396,ECO:0000269|PubMed:26876937, ECO:0000269|PubMed:28984244}. | Could act as a repressor of canonical hedgehog signalingby antagonizing the effects of SMO, as suggested by down-regulation of hedgehog target genes, including GLI1, PTCH1, andPTCH2 in PTCHD4-expressing cells. {ECO:0000269|PubMed:25296753}. |
| 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 SRSF3_PTCHD4 |
| 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 SRSF3_PTCHD4 |
| 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 |
| SRSF3 | YWHAQ, CHD1, CLK1, RBM7, SCAF11, SREK1, SRPK2, MEPCE, AIRE, SRRM1, TADA2A, POU5F1, SMN1, YWHAB, YWHAG, HDGF, SF3A2, SIRT7, NFX1, CUL3, CUL4A, CUL4B, CUL5, CUL2, CUL1, COPS5, CAND1, PCBP1, APP, DHX9, U2AF2, SRSF11, HNRNPA2B1, HNRNPM, HNRNPU, TRA2B, SYNCRIP, SFPQ, HNRNPA0, IK, SMU1, DHX15, USP39, DDX17, BUD31, EIF4A3, SAP18, ILF3, HNRNPDL, ILF2, GCN1L1, TRMT112, UTP14A, FAM3C, UQCRFS1, ZNF454, EIF4H, SFXN2, TOMM7, S100A9, VASN, TAP1, ATP6V0A1, ATP6V1E1, TIMM17A, TMEM126A, ICT1, SND1, FUBP1, UQCRFS1P1, TIA1, SEC23B, SEPT2, PGRMC1, ELAVL1, TMEM14B, TMEM177, NFIA, RBMS2, SPG7, DDX18, ESR1, MAGOH, VCP, FN1, PRPF38A, SRSF2, IL7R, PAN2, CD81, IGSF8, ICAM1, EXOSC6, SRPK3, SRPK1, PARK2, WWOX, CEP250, HUWE1, CUL7, OBSL1, EZH2, SUZ12, EED, RNF2, COPA, COPE, DDX47, HEATR1, KHDRBS1, RPL9, SLC3A2, SRSF1, MATR3, NOP2, SNRNP70, SRSF6, SRSF7, SRSF9, TRA2A, EWSR1, KATNA1, MCM2, SNW1, CRBN, ZNF746, SRSF5, NCL, CYLD, TRIM25, G3BP1, UBE2A, LMNA | PTCHD4 |
| - 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 SRSF3_PTCHD4 |
| 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 SRSF3_PTCHD4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SRSF3 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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