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Fusion Protein:KHSRP-TFE3 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: KHSRP-TFE3 | FusionPDB ID: 41986 | FusionGDB2.0 ID: 41986 | Hgene | Tgene | Gene symbol | KHSRP | TFE3 | Gene ID | 8570 | 7030 |
| Gene name | KH-type splicing regulatory protein | transcription factor binding to IGHM enhancer 3 | |
| Synonyms | FBP2|FUBP2|KSRP|p75 | RCCP2|RCCX1|TFEA|bHLHe33 | |
| Cytomap | 19p13.3 | Xp11.23 | |
| Type of gene | protein-coding | protein-coding | |
| Description | far upstream element-binding protein 2FUSE-binding protein 2epididymis secretory sperm binding protein | transcription factor E3class E basic helix-loop-helix protein 33transcription factor E family, member Atranscription factor for IgH enhancertranscription factor for immunoglobulin heavy-chain enhancer 3 | |
| Modification date | 20200329 | 20200327 | |
| UniProtAcc | Q92945 | P19532 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000398148, | ENST00000487451, ENST00000315869, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 8 X 8 X 5=320 | 14 X 15 X 6=1260 |
| # samples | 8 | 15 | |
| ** MAII score | log2(8/320*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(15/1260*10)=-3.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: KHSRP [Title/Abstract] AND TFE3 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | KHSRP(6415150)-TFE3(48895857), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | KHSRP-TFE3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. KHSRP-TFE3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. | ||
| * 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 | KHSRP | GO:0043488 | regulation of mRNA stability | 16126846 |
| Hgene | KHSRP | GO:0045019 | negative regulation of nitric oxide biosynthetic process | 16126846 |
| Hgene | KHSRP | GO:0061014 | positive regulation of mRNA catabolic process | 16126846 |
| Hgene | KHSRP | GO:0061158 | 3'-UTR-mediated mRNA destabilization | 16126846 |
| Fusion gene breakpoints across KHSRP (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across TFE3 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | KIRC | TCGA-CJ-5681-01A | KHSRP | chr19 | 6415150 | - | TFE3 | chrX | 48895857 | - |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000398148 | KHSRP | chr19 | 6415150 | - | ENST00000315869 | TFE3 | chrX | 48895857 | - | 4731 | 2220 | 93 | 2663 | 856 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000398148 | ENST00000315869 | KHSRP | chr19 | 6415150 | - | TFE3 | chrX | 48895857 | - | 0.009606976 | 0.990393 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >41986_41986_1_KHSRP-TFE3_KHSRP_chr19_6415150_ENST00000398148_TFE3_chrX_48895857_ENST00000315869_length(amino acids)=856AA_BP= MSDYSTGGPPPGPPPPAGGGGGAGGAGGGPPPGPPGAGDRGGGGPGGGGPGGGSAGGPSQPPGGGGPGIRKDAFADAVQRARQIAAKIGG DAATTVNNSTPDFGFGGQKRQLEDGDQPESKKLASQGDSISSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQI SPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILI QDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQ DDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRGGENVKAI NQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPGPFNQGPPGAPPHAGGPPPH QYPPQGWGNTYPQWQPPAPHDPSKAAAAAADPNAAWAAYYSHYYQQPPGPVPGPAPAPAAPPAQGEPPQPPPTGQSDYTKAWEEYYKKIG QQPQQPGAPPQQDYTKAWEEYYKKQAQVATGGGPGAPPGSQPDYSAAWAEYYRQQAAYYGQTPGPGGPQPPPTQQGQQQELELQAQIHGL PVPPTPGLLSLATTSASDSLKPEQLDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEE -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:6415150/chrX:48895857) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| KHSRP | TFE3 |
| FUNCTION: Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs. {ECO:0000250, ECO:0000269|PubMed:11003644, ECO:0000269|PubMed:8940189, ECO:0000269|PubMed:9136930}. | FUNCTION: Transcription factor that acts as a master regulator of lysosomal biogenesis and immune response (PubMed:2338243, PubMed:29146937, PubMed:30733432, PubMed:31672913). Specifically recognizes and binds E-box sequences (5'-CANNTG-3'); efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFEB or MITF (By similarity). Involved in the cellular response to amino acid availability by acting downstream of MTOR: in the presence of nutrients, TFE3 phosphorylation by MTOR promotes its cytosolic retention and subsequent inactivation (PubMed:31672913). Upon starvation or lysosomal stress, inhibition of MTOR induces TFE3 dephosphorylation, resulting in nuclear localization and transcription factor activity (PubMed:31672913). In association with TFEB, activates the expression of CD40L in T-cells, thereby playing a role in T-cell-dependent antibody responses in activated CD4(+) T-cells and thymus-dependent humoral immunity (By similarity). Specifically recognizes the MUE3 box, a subset of E-boxes, present in the immunoglobulin enhancer (PubMed:2338243). It also binds very well to a USF/MLTF site (PubMed:2338243). May regulate lysosomal positioning in response to nutrient deprivation by promoting the expression of PIP4P1 (PubMed:29146937). Acts as a positive regulator of browning of adipose tissue by promoting expression of target genes; mTOR-dependent phosphorylation promotes cytoplasmic retention of TFE3 and inhibits browning of adipose tissue (By similarity). Maintains the pluripotent state of embryonic stem cells by promoting the expression of genes such as ESRRB; mTOR-dependent nuclear exclusion promotes exit from pluripotency (By similarity). Required to maintain the naive pluripotent state of hematopoietic stem cell; mTOR-dependent cytoplasmic retention of TFE3 promotes the exit of hematopoietic stem cell from pluripotency (PubMed:30733432). {ECO:0000250|UniProtKB:Q64092, ECO:0000269|PubMed:2338243, ECO:0000269|PubMed:29146937, ECO:0000269|PubMed:30733432, ECO:0000269|PubMed:31672913}. |
| 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. |
| - 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 | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 498_612 | 709.0 | 712.0 | Compositional bias | Note=Ala/Gly/Pro-rich |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 68_496 | 709.0 | 712.0 | Compositional bias | Note=Gly-rich |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 7_67 | 709.0 | 712.0 | Compositional bias | Note=Gly/Pro-rich |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 144_208 | 709.0 | 712.0 | Domain | KH 1 |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 233_299 | 709.0 | 712.0 | Domain | KH 2 |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 322_386 | 709.0 | 712.0 | Domain | KH 3 |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 424_491 | 709.0 | 712.0 | Domain | KH 4 |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 571_684 | 709.0 | 712.0 | Region | Note=4 X 12 AA imperfect repeats |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 571_582 | 709.0 | 712.0 | Repeat | Note=1 |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 617_628 | 709.0 | 712.0 | Repeat | Note=2 |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 643_654 | 709.0 | 712.0 | Repeat | Note=3 |
| Hgene | KHSRP | chr19:6415150 | chrX:48895857 | ENST00000398148 | - | 19 | 20 | 673_684 | 709.0 | 712.0 | Repeat | Note=4 |
| Tgene | TFE3 | chr19:6415150 | chrX:48895857 | ENST00000315869 | 0 | 10 | 346_399 | 0 | 576.0 | Domain | bHLH | |
| Tgene | TFE3 | chr19:6415150 | chrX:48895857 | ENST00000315869 | 0 | 10 | 260_271 | 0 | 576.0 | Region | Strong transcription activation domain | |
| Tgene | TFE3 | chr19:6415150 | chrX:48895857 | ENST00000315869 | 0 | 10 | 409_430 | 0 | 576.0 | Region | Note=Leucine-zipper |
| - 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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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| TFE3 | AKR1B1, CLTC, PHB2, ACLY, CUL2, EPRS, PFAS, VARS, NEDD8, RPL38, TRIM28, EIF3A, RPA3, E2F3, SMARCE1, MITF, TFE3, SMAD3, SMAD4, TFEC, EWSR1, XPO1, TFEB, Arrb2, TARDBP, HIST1H4A, LAMTOR3, nsp2, nsp7, AIM2, NR3C1, DDX58, YWHAG, YWHAQ, HDAC5, BTF3, nsp16, IRF8, KLF12, KLF16, KLF3, KLF5, KLF8, SOX2, TLX3, VSX1, |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| KHSRP | |
| TFE3 |  |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to KHSRP-TFE3 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to KHSRP-TFE3 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | TFE3 | C4518356 | MiT family translocation renal cell carcinoma | 2 | ORPHANET |
| Tgene | TFE3 | C0206657 | Alveolar Soft Part Sarcoma | 1 | ORPHANET |
| Tgene | TFE3 | C0206732 | Epithelioid hemangioendothelioma | 1 | ORPHANET |
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