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Fusion gene ID: 30742 |
FusionGeneSummary for RBM38_SPO11 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RBM38_SPO11 | Fusion gene ID: 30742 | Hgene | Tgene | Gene symbol | RBM38 | SPO11 | Gene ID | 55544 | 23626 |
| Gene name | RNA binding motif protein 38 | SPO11, initiator of meiotic double stranded breaks | |
| Synonyms | HSRNASEB|RNPC1|SEB4B|SEB4D|dJ800J21.2 | CT35|SPATA43|TOPVIA | |
| Cytomap | 20q13.31 | 20q13.31 | |
| Type of gene | protein-coding | protein-coding | |
| Description | RNA-binding protein 38CLL-associated antigen KW-5RNA-binding region (RNP1, RRM) containing 1RNA-binding region-containing protein 1ssDNA-binding protein SEB4 | meiotic recombination protein SPO11SPO11 meiotic protein covalently bound to DSB homologcancer/testis antigen 35spermatogenesis associated 43 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q9H0Z9 | Q9Y5K1 | |
| Ensembl transtripts involved in fusion gene | ENST00000356208, ENST00000440234, ENST00000371219, | ENST00000371263, ENST00000345868, ENST00000371260, | |
| Fusion gene scores | * DoF score | 5 X 1 X 4=20 | 1 X 1 X 1=1 |
| # samples | 5 | 1 | |
| ** MAII score | log2(5/20*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: RBM38 [Title/Abstract] AND SPO11 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Tumor suppressor gene involved fusion gene, in-frame but not retained their domain. | ||
| * 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 | RBM38 | GO:0043484 | regulation of RNA splicing | 19285943 |
| 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 | BRCA | TCGA-BH-A0B9-01A | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| * 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 | ENST00000356208 | ENST00000371263 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| In-frame | ENST00000356208 | ENST00000345868 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| In-frame | ENST00000356208 | ENST00000371260 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| intron-3CDS | ENST00000440234 | ENST00000371263 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| intron-3CDS | ENST00000440234 | ENST00000345868 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| intron-3CDS | ENST00000440234 | ENST00000371260 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| In-frame | ENST00000371219 | ENST00000371263 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| In-frame | ENST00000371219 | ENST00000345868 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
| In-frame | ENST00000371219 | ENST00000371260 | RBM38 | chr20 | 55968389 | + | SPO11 | chr20 | 55917785 | + |
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FusionProtFeatures for RBM38_SPO11 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RBM38 | SPO11 |
| RNA-binding protein that specifically bind the 3'-UTR ofCDKN1A transcripts, leading to maintain the stability of CDKN1Atranscripts, thereby acting as a mediator of the p53/TP53 familyto regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitortranscriptionally regulated by the p53/TP53 family to induce cellcycle arrest. Isoform 1, but not isoform 2, has the ability toinduce cell cycle arrest in G1 and maintain the stability ofCDKN1A transcripts induced by p53/TP53. Also acts as a mRNAsplicing factor. Specifically regulates the expression of FGFR2-IIIb, an epithelial cell-specific isoform of FGFR2. Plays a rolein myogenic differentiation. {ECO:0000269|PubMed:17050675,ECO:0000269|PubMed:19285943}. | Component of a topoisomerase 6 complex specificallyrequired for meiotic recombination. Together with TOP6BL, mediatesDNA cleavage that forms the double-strand breaks (DSB) thatinitiate meiotic recombination. The complex promotes relaxation ofnegative and positive supercoiled DNA and DNA decatenation throughcleavage and ligation cycles. Essential for the phosphorylation ofSMC3, HORMAD1 and HORMAD2. {ECO:0000250|UniProtKB:Q9WTK8}. |
| 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 | RBM38 | chr20:55968389 | chr20:55917785 | ENST00000356208 | + | 3 | 4 | 34_111 | 138 | 240 | Domain | RRM |
| - 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 | >RBM38 | chr20:55968389 | chr20:55917785 | ENST00000440234 | + | 1 | 3 | 34_111 | -52 | 122 | Domain | RRM |
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FusionGeneSequence for RBM38_SPO11 |
| 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 RBM38_SPO11 |
| 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 |
| RBM38 | RCHY1, MDM2, RBFOX2, RBM24, TMEM184A, CLASRP, PTCD3 | SPO11 |
| - 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 RBM38_SPO11 |
| 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 RBM38_SPO11 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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