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Fusion gene ID: 33495 |
FusionGeneSummary for SFPQ_ITGB7 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SFPQ_ITGB7 | Fusion gene ID: 33495 | Hgene | Tgene | Gene symbol | SFPQ | ITGB7 | Gene ID | 6421 | 3695 |
| Gene name | splicing factor proline and glutamine rich | integrin subunit beta 7 | |
| Synonyms | POMP100|PPP1R140|PSF | - | |
| Cytomap | 1p34.3 | 12q13.13 | |
| Type of gene | protein-coding | protein-coding | |
| Description | splicing factor, proline- and glutamine-rich100 kDa DNA-pairing proteinDNA-binding p52/p100 complex, 100 kDa subunitPTB-associated splicing factorpolypyrimidine tract binding protein associatedpolypyrimidine tract-binding protein-associated splicing | integrin beta-7gut homing receptor beta subunitintegrin beta 7 subunit | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P23246 | P26010 | |
| Ensembl transtripts involved in fusion gene | ENST00000357214, ENST00000468598, | ENST00000267082, ENST00000422257, ENST00000338737, ENST00000550743, | |
| Fusion gene scores | * DoF score | 8 X 10 X 4=320 | 4 X 4 X 4=64 |
| # samples | 19 | 4 | |
| ** MAII score | log2(19/320*10)=-0.752072486556414 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/64*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: SFPQ [Title/Abstract] AND ITGB7 [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 | SFPQ | GO:0000122 | negative regulation of transcription by RNA polymerase II | 16731528 |
| Hgene | SFPQ | GO:0002218 | activation of innate immune response | 28712728 |
| Hgene | SFPQ | GO:1902177 | positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway | 15790595 |
| 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 | BM149731 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| * 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 | ENST00000357214 | ENST00000267082 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| intron-3CDS | ENST00000357214 | ENST00000422257 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| intron-3CDS | ENST00000357214 | ENST00000338737 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| intron-3CDS | ENST00000357214 | ENST00000550743 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| intron-3CDS | ENST00000468598 | ENST00000267082 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| intron-3CDS | ENST00000468598 | ENST00000422257 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| intron-3CDS | ENST00000468598 | ENST00000338737 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
| intron-3CDS | ENST00000468598 | ENST00000550743 | SFPQ | chr1 | 35658612 | - | ITGB7 | chr12 | 53585689 | + |
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FusionProtFeatures for SFPQ_ITGB7 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SFPQ | ITGB7 |
| DNA- and RNA binding protein, involved in severalnuclear processes. Essential pre-mRNA splicing factor requiredearly in spliceosome formation and for splicing catalytic step II,probably as a heteromer with NONO. Binds to pre-mRNA inspliceosome C complex, and specifically binds to intronicpolypyrimidine tracts. Involved in regulation of signal-inducedalternative splicing. During splicing of PTPRC/CD45, aphosphorylated form is sequestered by THRAP3 from the pre-mRNA inresting T-cells; T-cell activation and subsequent reducedphosphorylation is proposed to lead to release from THRAP3allowing binding to pre-mRNA splicing regulatotry elements whichrepresses exon inclusion. Interacts with U5 snRNA, probably bybinding to a purine-rich sequence located on the 3' side of U5snRNA stem 1b. May be involved in a pre-mRNA coupled splicing andpolyadenylation process as component of a snRNP-free complex withSNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may playa role in nuclear retention of defective RNAs. SFPQ may beinvolved in homologous DNA pairing; in vitro, promotes theinvasion of ssDNA between a duplex DNA and produces a D-loopformation. The SFPQ-NONO heteromer may be involved in DNAunwinding by modulating the function of topoisomerase I/TOP1; invitro, stimulates dissociation of TOP1 from DNA after cleavage andenhances its jumping between separate DNA helices. The SFPQ-NONOheteromer binds DNA (PubMed:25765647). The SFPQ-NONO heteromer maybe involved in DNA non-homologous end joining (NHEJ) required fordouble-strand break repair and V(D)J recombination and maystabilize paired DNA ends; in vitro, the complex stronglystimulates DNA end joining, binds directly to the DNA substratesand cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer toestablish a functional preligation complex. SFPQ is involved intranscriptional regulation. Functions as transcriptional activator(PubMed:25765647). Transcriptional repression is mediated by aninteraction of SFPQ with SIN3A and subsequent recruitment ofhistone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds tothe CYP17 promoter and regulates basal and cAMP-dependenttranscriptional activity. SFPQ isoform Long binds to the DNAbinding domains (DBD) of nuclear hormone receptors, like RXRA andprobably THRA, and acts as transcriptional corepressor in absenceof hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in theinsulin-like growth factor response element (IGFRE) and inhibitsIGF-I-stimulated transcriptional activity. Regulates the circadianclock by repressing the transcriptional activator activity of theCLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptionalrepression of circadian target genes, such as PER1, mediated bythe large PER complex through histone deacetylation (Bysimilarity). Required for the assembly of nuclear speckles(PubMed:25765647). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNPcomplex, a complex that serves as a platform for IRF3phosphorylation and subsequent innate immune response activationthrough the cGAS-STING pathway (PubMed:28712728).{ECO:0000250|UniProtKB:Q8VIJ6, ECO:0000269|PubMed:10847580,ECO:0000269|PubMed:10858305, ECO:0000269|PubMed:10931916,ECO:0000269|PubMed:11259580, ECO:0000269|PubMed:11525732,ECO:0000269|PubMed:11897684, ECO:0000269|PubMed:15590677,ECO:0000269|PubMed:20932480, ECO:0000269|PubMed:25765647,ECO:0000269|PubMed:28712728, ECO:0000269|PubMed:8045264,ECO:0000269|PubMed:8449401}. | Integrin alpha-4/beta-7 (Peyer patches-specific homingreceptor LPAM-1) is an adhesion molecule that mediates lymphocytemigration and homing to gut-associated lymphoid tissue (GALT).Integrin alpha-4/beta-7 interacts with the cell surface adhesionmolecules MADCAM1 which is normally expressed by the vascularendothelium of the gastrointestinal tract. Interacts also withVCAM1 and fibronectin, an extracellular matrix component. Itrecognizes one or more domains within the alternatively splicedCS-1 region of fibronectin. Interactions involves the tripeptideL-D-T in MADCAM1, and L-D-V in fibronectin. Binds to HIV-1 gp120,thereby allowing the virus to enter GALT, which is thought to bethe major trigger of AIDS disease. Interaction would involve atripeptide L-D-I in HIV-1 gp120. Integrin alpha-E/beta-7 (HML-1)is a receptor for E-cadherin. |
| 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 SFPQ_ITGB7 |
| 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 SFPQ_ITGB7 |
| 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 SFPQ_ITGB7 |
| 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 |
| Hgene | SFPQ | P23246 | DB11638 | Artenimol | Splicing factor, proline- and glutamine-rich | small molecule | approved|investigational |
| Tgene | ITGB7 | P26010 | DB09033 | Vedolizumab | Integrin beta-7 | biotech | approved |
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RelatedDiseases for SFPQ_ITGB7 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SFPQ | C0019693 | HIV Infections | 1 | CTD_human |
| Hgene | SFPQ | C0037274 | Dermatologic disorders | 1 | CTD_human |
| Hgene | SFPQ | C0311375 | Arsenic Poisoning | 1 | CTD_human |
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