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Fusion gene ID: 34831 |
FusionGeneSummary for SMARCC2_BCYRN1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SMARCC2_BCYRN1 | Fusion gene ID: 34831 | Hgene | Tgene | Gene symbol | SMARCC2 | BCYRN1 | Gene ID | 6601 | 618 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2 | brain cytoplasmic RNA 1 | |
| Synonyms | BAF170|CRACC2|Rsc8 | BC200|BC200a|LINC00004|NCRNA00004 | |
| Cytomap | 12q13.2 | 2p21 | |
| Type of gene | protein-coding | ncRNA | |
| Description | SWI/SNF complex subunit SMARCC2SWI/SNF complex 170 kDa subunitSWI3-like proteinchromatin remodeling complex BAF170 subunitmammalian chromatin remodeling complex BRG1-associated factor 170 | BC200-alphabrain cytoplasmic RNA 1 (analog of mouse Bc1)brain cytoplasmic RNA 1 (non-protein coding)brain cytoplasmic RNA 1, Bc1 analogbrain cytoplasmic RNA 200-alphalong intergenic non-protein coding RNA 4non-protein coding RNA 4 | |
| Modification date | 20180519 | 20180329 | |
| UniProtAcc | Q8TAQ2 | ||
| Ensembl transtripts involved in fusion gene | ENST00000394023, ENST00000550164, ENST00000347471, ENST00000267064, ENST00000550859, | ENST00000418539, | |
| Fusion gene scores | * DoF score | 7 X 7 X 3=147 | 8 X 9 X 1=72 |
| # samples | 7 | 9 | |
| ** MAII score | log2(7/147*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(9/72*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SMARCC2 [Title/Abstract] AND BCYRN1 [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 | SMARCC2 | GO:0006337 | nucleosome disassembly | 8895581 |
| Hgene | SMARCC2 | GO:0006338 | chromatin remodeling | 10078207|11018012|11726552 |
| Hgene | SMARCC2 | GO:0045892 | negative regulation of transcription, DNA-templated | 12192000 |
| Hgene | SMARCC2 | GO:0045893 | positive regulation of transcription, DNA-templated | 11018012 |
| 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 |
| ChiTaRS3.1 | BF376627 | SMARCC2 | chr12 | 56565518 | - | BCYRN1 | chrX | 70460360 | - |
| * 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-intron | ENST00000394023 | ENST00000418539 | SMARCC2 | chr12 | 56565518 | - | BCYRN1 | chrX | 70460360 | - |
| intron-intron | ENST00000550164 | ENST00000418539 | SMARCC2 | chr12 | 56565518 | - | BCYRN1 | chrX | 70460360 | - |
| intron-intron | ENST00000347471 | ENST00000418539 | SMARCC2 | chr12 | 56565518 | - | BCYRN1 | chrX | 70460360 | - |
| intron-intron | ENST00000267064 | ENST00000418539 | SMARCC2 | chr12 | 56565518 | - | BCYRN1 | chrX | 70460360 | - |
| intron-intron | ENST00000550859 | ENST00000418539 | SMARCC2 | chr12 | 56565518 | - | BCYRN1 | chrX | 70460360 | - |
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FusionProtFeatures for SMARCC2_BCYRN1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SMARCC2 | BCYRN1 |
| Involved in transcriptional activation and repression ofselect genes by chromatin remodeling (alteration of DNA-nucleosometopology). Component of SWI/SNF chromatin remodeling complexesthat carry out key enzymatic activities, changing chromatinstructure by altering DNA-histone contacts within a nucleosome inan ATP-dependent manner (PubMed:11018012). Can stimulate theATPase activity of the catalytic subunit of these complexes(PubMed:10078207). May be required for CoREST dependent repressionof neuronal specific gene promoters in non-neuronal cells(PubMed:12192000). Belongs to the neural progenitors-specificchromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). Duringneural development a switch from a stem/progenitor to apostmitotic chromatin remodeling mechanism occurs as neurons exitthe cell cycle and become committed to their adult state. Thetransition from proliferating neural stem/progenitor cells topostmitotic neurons requires a switch in subunit composition ofthe npBAF and nBAF complexes. As neural progenitors exit mitosisand differentiate into neurons, npBAF complexes which containACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologousalternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunitsin neuron-specific complexes (nBAF). The npBAF complex isessential for the self-renewal/proliferative capacity of themultipotent neural stem cells. The nBAF complex along with CRESTplays a role regulating the activity of genes essential fordendrite growth (By similarity). Critical regulator of myeloiddifferentiation, controlling granulocytopoiesis and the expressionof genes involved in neutrophil granule formation (By similarity).{ECO:0000250|UniProtKB:Q6PDG5, ECO:0000269|PubMed:10078207,ECO:0000269|PubMed:11018012, ECO:0000269|PubMed:12192000,ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}. | Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. |
| 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 SMARCC2_BCYRN1 |
| 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 SMARCC2_BCYRN1 |
| 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 |
| - 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 SMARCC2_BCYRN1 |
| 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 SMARCC2_BCYRN1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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