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Fusion gene ID: 35626 |
FusionGeneSummary for SPECC1L_SMARCB1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SPECC1L_SMARCB1 | Fusion gene ID: 35626 | Hgene | Tgene | Gene symbol | SPECC1L | SMARCB1 | Gene ID | 23384 | 6598 |
| Gene name | sperm antigen with calponin homology and coiled-coil domains 1 like | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 | |
| Synonyms | CYTSA|GBBB2|OBLFC1 | BAF47|CSS3|INI1|MRD15|PPP1R144|RDT|RTPS1|SNF5|SNF5L1|SWNTS1|Sfh1p|Snr1|hSNFS | |
| Cytomap | 22q11.23 | 22q11.23|22q11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cytospin-ASPECC1-like proteincytokinesis and spindle organization Arenal carcinoma antigen NY-REN-22 | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1BRG1-associated factor 47SNF5 homologSWI/SNF-related matrix-associated proteinhSNF5integrase interactor 1 proteinmalignant rhabdoid tumor suppressorprotein | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q69YQ0 | Q12824 | |
| Ensembl transtripts involved in fusion gene | ENST00000437398, ENST00000314328, ENST00000541492, ENST00000416735, | ENST00000344921, ENST00000263121, ENST00000407422, ENST00000407082, ENST00000477836, | |
| Fusion gene scores | * DoF score | 15 X 6 X 11=990 | 3 X 7 X 3=63 |
| # samples | 15 | 14 | |
| ** MAII score | log2(15/990*10)=-2.72246602447109 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(14/63*10)=1.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SPECC1L [Title/Abstract] AND SMARCB1 [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 | SPECC1L | GO:0007155 | cell adhesion | 21703590 |
| Tgene | SMARCB1 | GO:0006337 | nucleosome disassembly | 8895581 |
| Tgene | SMARCB1 | GO:0006338 | chromatin remodeling | 11726552 |
| Tgene | SMARCB1 | GO:0039692 | single stranded viral RNA replication via double stranded DNA intermediate | 14963118 |
| Tgene | SMARCB1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 11950834 |
| Tgene | SMARCB1 | GO:0051091 | positive regulation of DNA binding transcription factor activity | 11950834 |
| Tgene | SMARCB1 | GO:1902661 | positive regulation of glucose mediated signaling pathway | 22368283 |
| 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-8678-01A | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| * 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 |
| 5UTR-3CDS | ENST00000437398 | ENST00000344921 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000437398 | ENST00000263121 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000437398 | ENST00000407422 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000437398 | ENST00000407082 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-intron | ENST00000437398 | ENST00000477836 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000314328 | ENST00000344921 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000314328 | ENST00000263121 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000314328 | ENST00000407422 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000314328 | ENST00000407082 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-intron | ENST00000314328 | ENST00000477836 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000541492 | ENST00000344921 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000541492 | ENST00000263121 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000541492 | ENST00000407422 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-3CDS | ENST00000541492 | ENST00000407082 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 5UTR-intron | ENST00000541492 | ENST00000477836 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 3UTR-3CDS | ENST00000416735 | ENST00000344921 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 3UTR-3CDS | ENST00000416735 | ENST00000263121 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 3UTR-3CDS | ENST00000416735 | ENST00000407422 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 3UTR-3CDS | ENST00000416735 | ENST00000407082 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
| 3UTR-intron | ENST00000416735 | ENST00000477836 | SPECC1L | chr22 | 24666951 | + | SMARCB1 | chr22 | 24133943 | + |
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FusionProtFeatures for SPECC1L_SMARCB1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SPECC1L | SMARCB1 |
| Involved in cytokinesis and spindle organization. Mayplay a role in actin cytoskeleton organization and microtubulestabilization and hence required for proper cell adhesion andmigration. {ECO:0000269|PubMed:21703590}. | Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles incell proliferation and differentiation, in cellular antiviralactivities and inhibition of tumor formation. The BAF complex isable to create a stable, altered form of chromatin that constrainsfewer negative supercoils than normal. This change in supercoilingwould be due to the conversion of up to one-half of thenucleosomes on polynucleosomal arrays into asymmetric structures,termed altosomes, each composed of 2 histones octamers. Stimulatesin vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involvedin activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and theneuron-specific chromatin remodeling complex (nBAF complex).During neural 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). Plays a key role in cell-cyclecontrol and causes cell cycle arrest in G0/G1.{ECO:0000250|UniProtKB:Q9Z0H3, ECO:0000269|PubMed:10078207,ECO:0000269|PubMed:12226744, ECO:0000269|PubMed:14604992,ECO:0000269|PubMed:16267391, ECO:0000269|PubMed:16314535,ECO:0000269|PubMed:9448295}. |
| 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 SPECC1L_SMARCB1 |
| 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 SPECC1L_SMARCB1 |
| 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 |
| SPECC1L | APC, UBE2I, GLIS2, FBXO25, KIAA0368, UBC, PAN2, CCDC8, LUZP4, SLC25A41, ZNF219, KCTD17, FSD1, NFKBIA, LRFN4, RCN1, OBFC1, AP2M1, CHRNA9, SLC30A6, SPC25, HERC2, CAPZA2, CDK2, DBN1, MYH9, PPP1CB, IQGAP1, PDLIM7, SYNPO, ANLN, MYO5C, MYO19, MYO18A, C10orf2, LPXN, VAV1, ATMIN, ZNF785, G2E3, DUSP22, FEZ1, CCNJ, FSCN2, RPL15, G3BP1 | SMARCB1 | RELB, TACC2, SMARCA2, SMARCA4, SMARCC1, SIN3A, HDAC1, HDAC2, RBBP4, POLR2A, KLF1, GATA1, MYC, TP53, XPO1, RAN, YEATS4, MLLT10, BRCA1, SMARCB1, HSF1, SS18, ARID1A, ARID1B, SMARCC2, SMARCE1, ACTL6A, CCNE1, NCOR1, PPP1R15A, KMT2A, CREBBP, CDK8, MED21, KAT2B, PPP1CA, PPP1CB, PPP1CC, UBQLN4, ING1, MECP2, ING2, XPC, ATM, KMT2C, KMT2B, CDYL, MCPH1, BCL7C, AKT1, ACTA1, CDX2, PRMT5, SIN3B, TAF6, NR0B2, BCL2L11, SMARCD1, NONO, CARM1, EMD, DPF2, RB1CC1, RUNX1, PBRM1, ARID2, MAPK8IP2, GADD45G, CALR, TAF1D, RPS6KA5, PDPK1, MAP1LC3B, ZAK, SMARCAD1, SOX2, DPF3, CHFR, CEBPB, TFAP4, CUL3, COPS5, CAND1, APP, SMARCD2, SMARCD3, TOP2B, SAP18, EIF4A3, NCSTN, PHF10, VTN, TRA2A, SON, DPF1, EPAS1, ZDHHC17, BCL7A, BCL7B, CHMP4A, CPSF6, TBL1X, TBL1XR1, QSOX2, JUN, NFATC1, FOXN1, C1orf131, BARD1, BRCA2, ROR1, CDK9, APC, VHL, NR3C1, AR, DLST, ABI2, AES, ARL11, ATP5A1, DPH6, BHLHE40, BLZF1, FAM208B, CAMK2D, CCDC120, CCDC33, CCDC36, CD69, CDC23, CXCL11, CYB5D2, DNAJA3, FAM154A, FAM9B, GFAP, GOLGA2, HNRNPM, HOMEZ, HOOK2, HSFY1, IKZF3, KCTD9, KLC3, KPNA6, KRT15, KRT19, KRT6A, KRT6B, KRT6C, LDOC1, LENG8, LNX2, LY96, LZTS2, MBIP, MIF4GD, MXI1, NCK2, OSGIN1, OTX2, RINT1, RXRA, TEKT5, TFIP11, TNFAIP1, TNRC6A, TRIM27, TSC22D4, VIM, ZC3H11A, ZNF398 |
| - 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 SPECC1L_SMARCB1 |
| 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 SPECC1L_SMARCB1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SPECC1L | C1801950 | Opitz-G syndrome, type 2 | 1 | ORPHANET;UNIPROT |
| Hgene | SPECC1L | C1838348 | Oculomaxillofacial dysostosis | 1 | ORPHANET;UNIPROT |
| Tgene | SMARCB1 | C0206743 | Rhabdoid Tumor | 2 | CTD_human |
| Tgene | SMARCB1 | C3553248 | MENTAL RETARDATION, AUTOSOMAL DOMINANT 15 | 2 | UNIPROT |
| Tgene | SMARCB1 | C0265338 | Coffin-Siris syndrome | 1 | CTD_human;ORPHANET |
| Tgene | SMARCB1 | C1335929 | Schwannomatosis | 1 | CTD_human;ORPHANET |
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