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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:CLNS1A-ABCE1 (FusionGDB2 ID:17253) |
Fusion Gene Summary for CLNS1A-ABCE1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CLNS1A-ABCE1 | Fusion gene ID: 17253 | Hgene | Tgene | Gene symbol | CLNS1A | ABCE1 | Gene ID | 1207 | 6059 |
| Gene name | chloride nucleotide-sensitive channel 1A | ATP binding cassette subfamily E member 1 | |
| Synonyms | CLCI|CLNS1B|ICln | ABC38|OABP|RLI|RLI1|RNASEL1|RNASELI|RNS4I | |
| Cytomap | 11q14.1 | 4q31.21 | |
| Type of gene | protein-coding | protein-coding | |
| Description | methylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein ICln | ATP-binding cassette sub-family E member 12'-5'-oligoadenylate-binding proteinATP-binding cassette, sub-family E (OABP), member 1RNase L inhibitor 1huHP68ribonuclease 4 inhibitorribonuclease L (2',5'-oligoisoadenylate synthetase-dependent) inhibitor | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P54105 | P61221 | |
| Ensembl transtripts involved in fusion gene | ENST00000263309, ENST00000525064, ENST00000525428, ENST00000528364, ENST00000532069, ENST00000533957, | ENST00000296577, ENST00000502803, | |
| Fusion gene scores | * DoF score | 13 X 12 X 5=780 | 3 X 2 X 3=18 |
| # samples | 16 | 3 | |
| ** MAII score | log2(16/780*10)=-2.28540221886225 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: CLNS1A [Title/Abstract] AND ABCE1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CLNS1A(77327200)-ABCE1(146021145), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | CLNS1A | GO:0000387 | spliceosomal snRNP assembly | 18984161 |
| Tgene | ABCE1 | GO:0060702 | negative regulation of endoribonuclease activity | 7539425 |
| Fusion gene breakpoints across CLNS1A (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across ABCE1 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| 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 |
| ChiTaRS5.0 | N/A | AX396659 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
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Fusion Gene ORF analysis for CLNS1A-ABCE1 |
| 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 | ENST00000263309 | ENST00000296577 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000263309 | ENST00000502803 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000525064 | ENST00000296577 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000525064 | ENST00000502803 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000525428 | ENST00000296577 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000525428 | ENST00000502803 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000528364 | ENST00000296577 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000528364 | ENST00000502803 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000532069 | ENST00000296577 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000532069 | ENST00000502803 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000533957 | ENST00000296577 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| intron-intron | ENST00000533957 | ENST00000502803 | CLNS1A | chr11 | 77327200 | - | ABCE1 | chr4 | 146021145 | + |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| 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) |
| 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 |
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Fusion Genomic Features for CLNS1A-ABCE1 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for CLNS1A-ABCE1 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:77327200/:146021145) - 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 |
| CLNS1A | ABCE1 |
| FUNCTION: Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (PubMed:21081503, PubMed:18984161). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway. {ECO:0000269|PubMed:10330151, ECO:0000269|PubMed:11713266, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:21081503}. | FUNCTION: Cotranslational quality control factor involved in the No-Go Decay (NGD) pathway (PubMed:21448132). Together with PELO and HBS1L, is required for 48S complex formation from 80S ribosomes and dissociation of vacant 80S ribosomes (PubMed:21448132). Together with PELO and HBS1L, recognizes stalled ribosomes and promotes dissociation of elongation complexes assembled on non-stop mRNAs; this triggers endonucleolytic cleavage of the mRNA, a mechanism to release non-functional ribosomes and to degrade damaged mRNAs as part of the No-Go Decay (NGD) pathway (PubMed:21448132). Plays a role in the regulation of mRNA turnover (By similarity). Plays a role in quality control of translation of mitochondrial outer membrane-localized mRNA (PubMed:29861391). As part of the PINK1-regulated signaling, ubiquitinated by CNOT4 upon mitochondria damage; this modification generates polyubiquitin signals that recruit autophagy receptors to the mitochondrial outer membrane and initiate mitophagy (PubMed:29861391). RNASEL-specific protein inhibitor which antagonizes the binding of 2-5A (5'-phosphorylated 2',5'-linked oligoadenylates) to RNASEL (PubMed:9660177). Negative regulator of the anti-viral effect of the interferon-regulated 2-5A/RNASEL pathway (PubMed:9660177, PubMed:9847332, PubMed:11585831). {ECO:0000250|UniProtKB:P61222, ECO:0000269|PubMed:11585831, ECO:0000269|PubMed:21448132, ECO:0000269|PubMed:29861391, ECO:0000269|PubMed:9660177, ECO:0000269|PubMed:9847332}.; FUNCTION: (Microbial infection) May act as a chaperone for post-translational events during HIV-1 capsid assembly. {ECO:0000269|PubMed:9847332}.; FUNCTION: (Microbial infection) Plays a role in the down-regulation of the 2-5A/RNASEL pathway during encephalomyocarditis virus (EMCV) and HIV-1 infections. {ECO:0000269|PubMed:9660177}. |
| 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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Fusion Gene Sequence for CLNS1A-ABCE1 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for CLNS1A-ABCE1 |
| 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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Related Drugs for CLNS1A-ABCE1 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for CLNS1A-ABCE1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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