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Fusion gene ID: 6710 |
FusionGeneSummary for CELF1_CHMP4B |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CELF1_CHMP4B | Fusion gene ID: 6710 | Hgene | Tgene | Gene symbol | CELF1 | CHMP4B | Gene ID | 10658 | 128866 |
| Gene name | CUGBP Elav-like family member 1 | charged multivesicular body protein 4B | |
| Synonyms | BRUNOL2|CUG-BP|CUGBP|CUGBP1|EDEN-BP|NAB50|NAPOR|hNab50 | C20orf178|CHMP4A|CTPP3|CTRCT31|SNF7|SNF7-2|Shax1|VPS32B|Vps32-2|dJ553F4.4 | |
| Cytomap | 11p11.2 | 20q11.22 | |
| Type of gene | protein-coding | protein-coding | |
| Description | CUGBP Elav-like family member 150 kDa nuclear polyadenylated RNA-binding proteinCELF-1CUG RNA-binding proteinCUG triplet repeat RNA-binding protein 1CUG-BP- and ETR-3-like factor 1CUG-BP1EDEN-BP homologRNA-binding protein BRUNOL-2bruno-like 2bru | charged multivesicular body protein 4bSNF7 homolog associated with Alix 1Snf7 homologue associated with Alix 1chromatin modifying protein 4Bchromatin-modifying protein 4bhSnf7-2hVps32-2vacuolar protein-sorting-associated protein 32-2 | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | Q92879 | Q9H444 | |
| Ensembl transtripts involved in fusion gene | ENST00000395290, ENST00000358597, ENST00000395292, ENST00000310513, ENST00000361904, ENST00000539455, ENST00000531165, ENST00000532048, | ENST00000217402, | |
| Fusion gene scores | * DoF score | 13 X 11 X 11=1573 | 3 X 3 X 3=27 |
| # samples | 18 | 3 | |
| ** MAII score | log2(18/1573*10)=-3.12744985908601 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: CELF1 [Title/Abstract] AND CHMP4B [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 | CELF1 | GO:0006376 | mRNA splice site selection | 11158314 |
| Hgene | CELF1 | GO:0043484 | regulation of RNA splicing | 16946708 |
| Tgene | CHMP4B | GO:0039702 | viral budding via host ESCRT complex | 24878737 |
| Tgene | CHMP4B | GO:0051260 | protein homooligomerization | 18209100 |
| 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-43-7657-01A | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| * 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 | ENST00000395290 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| intron-3CDS | ENST00000358597 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| intron-3CDS | ENST00000395292 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| 5UTR-3CDS | ENST00000310513 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| intron-3CDS | ENST00000361904 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| intron-3CDS | ENST00000539455 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| 5UTR-3CDS | ENST00000531165 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
| intron-3CDS | ENST00000532048 | ENST00000217402 | CELF1 | chr11 | 47574544 | - | CHMP4B | chr20 | 32438758 | + |
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FusionProtFeatures for CELF1_CHMP4B |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CELF1 | CHMP4B |
| RNA-binding protein implicated in the regulation ofseveral post-transcriptional events. Involved in pre-mRNAalternative splicing, mRNA translation and stability. Mediatesexon inclusion and/or exclusion in pre-mRNA that are subject totissue-specific and developmentally regulated alternativesplicing. Specifically activates exon 5 inclusion of cardiacisoforms of TNNT2 during heart remodeling at the juvenile to adulttransition. Acts as both an activator and repressor of a pair ofcoregulated exons: promotes inclusion of the smooth muscle (SM)exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Activates SM exon 5 inclusion by antagonizing therepressive effect of PTB. Promotes exclusion of exon 11 of theINSR pre-mRNA. Inhibits, together with HNRNPH1, insulin receptor(IR) pre-mRNA exon 11 inclusion in myoblast. Increases translationand controls the choice of translation initiation codon of CEBPBmRNA. Increases mRNA translation of CEBPB in aging liver (Bysimilarity). Increases translation of CDKN1A mRNA by antagonizingthe repressive effect of CALR3. Mediates rapid cytoplasmic mRNAdeadenylation. Recruits the deadenylase PARN to the poly(A) tailof EDEN-containing mRNAs to promote their deadenylation. Requiredfor completion of spermatogenesis (By similarity). Binds to (CUG)ntriplet repeats in the 3'-UTR of transcripts such as DMPK and toBruno response elements (BREs). Binds to muscle-specific splicingenhancer (MSE) intronic sites flanking the alternative exon 5 ofTNNT2 pre-mRNA. Binds to AU-rich sequences (AREs or EDEN-like)localized in the 3'-UTR of JUN and FOS mRNAs. Binds to the IR RNA.Binds to the 5'-region of CDKN1A and CEBPB mRNAs. Binds with the5'-region of CEBPB mRNA in aging liver. May be a specificregulator of miRNA biogenesis. Binds to primary microRNA pri-MIR140 and, with CELF2, negatively regulates the processing tomature miRNA (PubMed:28431233). {ECO:0000250,ECO:0000269|PubMed:10536163, ECO:0000269|PubMed:11124939,ECO:0000269|PubMed:11158314, ECO:0000269|PubMed:12649496,ECO:0000269|PubMed:12799066, ECO:0000269|PubMed:14726956,ECO:0000269|PubMed:16601207, ECO:0000269|PubMed:16946708,ECO:0000269|PubMed:28431233}. | Probable core component of the endosomal sortingrequired for transport complex III (ESCRT-III) which is involvedin multivesicular bodies (MVBs) formation and sorting of endosomalcargo proteins into MVBs. MVBs contain intraluminal vesicles(ILVs) that are generated by invagination and scission from thelimiting membrane of the endosome and mostly are delivered tolysosomes enabling degradation of membrane proteins, such asstimulated growth factor receptors, lysosomal enzymes and lipids.The MVB pathway appears to require the sequential function ofESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostlydissociate from the invaginating membrane before the ILV isreleased (PubMed:12860994, PubMed:18209100). The ESCRT machineryalso functions in topologically equivalent membrane fissionevents, such as the terminal stages of cytokinesis(PubMed:21310966). Together with SPAST, the ESCRT-III complexpromotes nuclear envelope sealing and mitotic spindle disassemblyduring late anaphase (PubMed:26040712). Plays a role in theendosomal sorting pathway. ESCRT-III proteins are believed tomediate the necessary vesicle extrusion and/or membrane fissionactivities, possibly in conjunction with the AAA ATPase VPS4. Whenoverexpressed, membrane-assembled circular arrays of CHMP4Bfilaments can promote or stabilize negative curvature and outwardbudding. CHMP4A/B/C are required for the exosomal release ofSDCBP, CD63 and syndecan (PubMed:22660413).{ECO:0000269|PubMed:12860994, ECO:0000269|PubMed:18209100,ECO:0000269|PubMed:21310966, ECO:0000269|PubMed:22660413,ECO:0000269|PubMed:26040712}. (Microbial infection) The ESCRT machinery also functionsin topologically equivalent membrane fission events, such as thebudding of enveloped viruses (HIV-1 and other lentiviruses). Viaits interaction with PDCD6IP involved in HIV-1 p6- and p9-dependent virus release. {ECO:0000269|PubMed:14505569,ECO:0000269|PubMed:14505570, ECO:0000269|PubMed:14519844,ECO:0000269|PubMed:22422861}. |
| 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 CELF1_CHMP4B |
| 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 CELF1_CHMP4B |
| 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 |
| CELF1 | PPBP, FUBP1, TOM1L1, USP10, ELAVL1, APP, HNRNPC, RALY, TARDBP, RPA3, RPA2, RPA1, BMI1, CDK8, MKNK2, KIF2A, MAPK3, VPS26A, CCDC88A, CERK, CEP170P1, TRIM25, G3BP1 | CHMP4B | UBE2I, STAMBP, PTPN23, PDCD6IP, CHMP4C, CHMP6, NOLC1, BROX, CHMP4B, CHMP1B, CHMP4A, CHMP3, CHMP5, VPS4A, PIAS2, EXOSC9, HIPK2, ATP6V1B1, RPLP0P6, MVP, VCAM1, ITGA4, TP53, CHMP2A, CHMP2B, RNF103-CHMP3, EIF6, IMPDH2, HIST1H2BG, ATP6V1A, ATP6V1B2, ATP6V1E1, ATP6V0A1, BST2, CANX, EEF1G, FLOT2, IGF2R, MECP2, NUP98, CHMP1A, EIF2AK2, RPL6, SPAST, TAF1, TARBP1, TCEB1, TSG101, UGCG, EVI5, HERC2, ATP6V0D1, VPS9D1, IST1, FLOT1, TM9SF1, CTCF, CAPN7, ZNF281, KPNA6, PVRL3, FBXO5, SLC25A24, SARAF, KDM3B, SLC38A2, NLE1, CC2D1A, DNAAF5, TMEM63B, CDK5RAP2, TTC7A, NBEAL1, DCTPP1, ZMYM1, RNF170, TLN2, MVB12A, OSBPL9, CAPZA2, CLTC, DAXX, DBN1, FLNA, RAB5C, VCP, RAB7A, SMC3, TFG, GOLT1B, MYO19, MITD1, C1orf52, CC2D1B, METRNL, NF2, PCGF1, CDH1, COQ2, COX15, DLST, SOAT1, VDAC1, BIN1 |
| - 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 CELF1_CHMP4B |
| 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 CELF1_CHMP4B |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | CHMP4B | C1854311 | Cataract, posterior polar, 3 | 1 | CTD_human;UNIPROT |
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