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Fusion gene ID: 33873 |
FusionGeneSummary for SIL1_SMC1B |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SIL1_SMC1B | Fusion gene ID: 33873 | Hgene | Tgene | Gene symbol | SIL1 | SMC1B | Gene ID | 64374 | 27127 |
| Gene name | SIL1 nucleotide exchange factor | structural maintenance of chromosomes 1B | |
| Synonyms | BAP|MSS|ULG5 | SMC1BETA|SMC1L2 | |
| Cytomap | 5q31.2 | 22q13.31 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nucleotide exchange factor SIL1BiP-associated proteinSIL1 homolog, endoplasmic reticulum chaperoneSIL1-like protein endoplasmic reticulum chaperone | structural maintenance of chromosomes protein 1BSMC protein 1BSMC1 (structural maintenance of chromosomes 1, yeast)-like 1SMC1 structural maintenance of chromosomes 1-like 2mitosis-specific chromosome segregation protein like protein beta | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | Q9H173 | Q8NDV3 | |
| Ensembl transtripts involved in fusion gene | ENST00000394817, ENST00000265195, ENST00000509534, ENST00000515008, | ENST00000357450, ENST00000404354, | |
| Fusion gene scores | * DoF score | 6 X 4 X 5=120 | 4 X 3 X 4=48 |
| # samples | 7 | 4 | |
| ** MAII score | log2(7/120*10)=-0.777607578663552 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: SIL1 [Title/Abstract] AND SMC1B [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 |
| 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 | LUSC | TCGA-NC-A5HL-01A | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| * 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 |
| intron-3CDS | ENST00000394817 | ENST00000357450 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| intron-3CDS | ENST00000394817 | ENST00000404354 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| 5UTR-3CDS | ENST00000265195 | ENST00000357450 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| 5UTR-3CDS | ENST00000265195 | ENST00000404354 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| 5UTR-3CDS | ENST00000509534 | ENST00000357450 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| 5UTR-3CDS | ENST00000509534 | ENST00000404354 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| intron-3CDS | ENST00000515008 | ENST00000357450 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
| intron-3CDS | ENST00000515008 | ENST00000404354 | SIL1 | chr5 | 138532130 | - | SMC1B | chr22 | 45779493 | - |
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FusionProtFeatures for SIL1_SMC1B |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SIL1 | SMC1B |
| Required for protein translocation and folding in theendoplasmic reticulum (ER). Functions as a nucleotide exchangefactor for the ER lumenal chaperone HSPA5.{ECO:0000269|PubMed:12356756}. | Meiosis-specific component of cohesin complex. Requiredfor the maintenance of meiotic cohesion, but not, or only to aminor extent, for its establishment. Contributes to axial element(AE) formation and the organization of chromatin loops along theAE. Plays a key role in synapsis, recombination and chromosomemovements. The cohesin complex is required for the cohesion ofsister chromatids after DNA replication. The cohesin complexapparently forms a large proteinaceous ring within which sisterchromatids can be trapped. At anaphase, the complex is cleaved anddissociates from chromatin, allowing sister chromatids tosegregate. The meiosis-specific cohesin complex probably replacesmitosis specific cohesin complex when it dissociates fromchromatin during prophase I (By similarity). {ECO:0000250}. |
| 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 SIL1_SMC1B |
| 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 SIL1_SMC1B |
| 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 |
| SIL1 | HSPA5, SMAD9, CCND3, FBXO6, UBQLN1, GLB1L3, PON2, PFDN4, PSMD8, TCTN1, CEP192, POC1A, POC1B, EDRF1, CNTNAP1, ERGIC2, UBR1, TDGF1, UBR2, COL14A1, OMA1, SERPINB11, PTPRO | SMC1B | CDCA5, RAD21, STAG1, STAG2, SMC3, REC8 |
| - 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 SIL1_SMC1B |
| 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 SIL1_SMC1B |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SIL1 | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| Tgene | SMC1B | C0005695 | Bladder Neoplasm | 1 | CTD_human |
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