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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:NCL-SQSTM1 (FusionGDB2 ID:HG4691TG8878) |
Fusion Gene Summary for NCL-SQSTM1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NCL-SQSTM1 | Fusion gene ID: hg4691tg8878 | Hgene | Tgene | Gene symbol | NCL | SQSTM1 | Gene ID | 4691 | 8878 |
| Gene name | nucleolin | sequestosome 1 | |
| Synonyms | C23|Nsr1 | A170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62B | |
| Cytomap | ('NCL')('SQSTM1') 2q37.1 | 5q35.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nucleolin | sequestosome-1EBI3-associated protein of 60 kDaEBI3-associated protein p60EBIAPautophagy receptor p62oxidative stress induced likephosphotyrosine independent ligand for the Lck SH2 domain p62phosphotyrosine-independent ligand for the Lck SH2 domain | |
| Modification date | 20200313 | 20200327 | |
| UniProtAcc | P19338 | Q13501 | |
| Ensembl transtripts involved in fusion gene | ENST00000322723, | ||
| Fusion gene scores | * DoF score | 25 X 25 X 6=3750 | 33 X 21 X 17=11781 |
| # samples | 28 | 38 | |
| ** MAII score | log2(28/3750*10)=-3.74339186332564 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(38/11781*10)=-4.95431877505661 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: NCL [Title/Abstract] AND SQSTM1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | NCL(232319462)-SQSTM1(179250858), # 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 | NCL | GO:0001525 | angiogenesis | 16403913 |
| Tgene | SQSTM1 | GO:0006914 | autophagy | 20452972 |
| Tgene | SQSTM1 | GO:0007032 | endosome organization | 27368102 |
| Tgene | SQSTM1 | GO:0031397 | negative regulation of protein ubiquitination | 20452972 |
| Tgene | SQSTM1 | GO:0061635 | regulation of protein complex stability | 25127057 |
| Tgene | SQSTM1 | GO:1905719 | protein localization to perinuclear region of cytoplasm | 27368102 |
| 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 | LUAD | TCGA-78-7542-01A | NCL | chr2 | 232319462 | - | SQSTM1 | chr5 | 179250858 | + |
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Fusion Gene ORF analysis for NCL-SQSTM1 |
| 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 | ENST00000322723 | ENST00000376929 | NCL | chr2 | 232319462 | - | SQSTM1 | chr5 | 179250858 | + |
| intron-intron | ENST00000322723 | ENST00000360718 | NCL | chr2 | 232319462 | - | SQSTM1 | chr5 | 179250858 | + |
| intron-intron | ENST00000322723 | ENST00000389805 | NCL | chr2 | 232319462 | - | SQSTM1 | chr5 | 179250858 | + |
| intron-intron | ENST00000322723 | ENST00000402874 | NCL | chr2 | 232319462 | - | SQSTM1 | chr5 | 179250858 | + |
| intron-intron | ENST00000322723 | ENST00000506690 | NCL | chr2 | 232319462 | - | SQSTM1 | chr5 | 179250858 | + |
| intron-intron | ENST00000322723 | ENST00000510187 | NCL | chr2 | 232319462 | - | SQSTM1 | chr5 | 179250858 | + |
| 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 NCL-SQSTM1 |
| 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) |
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Fusion Protein Features for NCL-SQSTM1 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:232319462/:179250858) - 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 |
| NCL | SQSTM1 |
| FUNCTION: Nucleolin is the major nucleolar protein of growing eukaryotic cells. It is found associated with intranucleolar chromatin and pre-ribosomal particles. It induces chromatin decondensation by binding to histone H1. It is thought to play a role in pre-rRNA transcription and ribosome assembly. May play a role in the process of transcriptional elongation. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. {ECO:0000269|PubMed:10393184}. | FUNCTION: Autophagy receptor required for selective macroautophagy (aggrephagy). Functions as a bridge between polyubiquitinated cargo and autophagosomes. Interacts directly with both the cargo to become degraded and an autophagy modifier of the MAP1 LC3 family (PubMed:16286508, PubMed:20168092, PubMed:24128730, PubMed:28404643, PubMed:22622177). Along with WDFY3, involved in the formation and autophagic degradation of cytoplasmic ubiquitin-containing inclusions (p62 bodies, ALIS/aggresome-like induced structures). Along with WDFY3, required to recruit ubiquitinated proteins to PML bodies in the nucleus (PubMed:24128730, PubMed:20168092). May regulate the activation of NFKB1 by TNF-alpha, nerve growth factor (NGF) and interleukin-1. May play a role in titin/TTN downstream signaling in muscle cells. May regulate signaling cascades through ubiquitination. Adapter that mediates the interaction between TRAF6 and CYLD (By similarity). May be involved in cell differentiation, apoptosis, immune response and regulation of K(+) channels. Involved in endosome organization by retaining vesicles in the perinuclear cloud: following ubiquitination by RNF26, attracts specific vesicle-associated adapters, forming a molecular bridge that restrains cognate vesicles in the perinuclear region and organizes the endosomal pathway for efficient cargo transport (PubMed:27368102). Promotes relocalization of 'Lys-63'-linked ubiquitinated STING1 to autophagosomes (PubMed:29496741). Acts as an activator of the NFE2L2/NRF2 pathway via interaction with KEAP1: interaction inactivates the BCR(KEAP1) complex, promoting nuclear accumulation of NFE2L2/NRF2 and subsequent expression of cytoprotective genes (PubMed:20452972, PubMed:28380357, PubMed:33393215). {ECO:0000250|UniProtKB:O08623, ECO:0000250|UniProtKB:Q64337, ECO:0000269|PubMed:10356400, ECO:0000269|PubMed:10747026, ECO:0000269|PubMed:11244088, ECO:0000269|PubMed:12471037, ECO:0000269|PubMed:15340068, ECO:0000269|PubMed:15802564, ECO:0000269|PubMed:15911346, ECO:0000269|PubMed:15953362, ECO:0000269|PubMed:16079148, ECO:0000269|PubMed:16286508, ECO:0000269|PubMed:19931284, ECO:0000269|PubMed:20168092, ECO:0000269|PubMed:20452972, ECO:0000269|PubMed:22622177, ECO:0000269|PubMed:24128730, ECO:0000269|PubMed:27368102, ECO:0000269|PubMed:28380357, ECO:0000269|PubMed:28404643, ECO:0000269|PubMed:29496741, ECO:0000269|PubMed:33393215}. |
| 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 NCL-SQSTM1 |
| 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 NCL-SQSTM1 |
| 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 NCL-SQSTM1 |
| 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 NCL-SQSTM1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | NCL | C0151744 | Myocardial Ischemia | 1 | CTD_human |
| Hgene | NCL | C0152013 | Adenocarcinoma of lung (disorder) | 1 | CTD_human |
| Tgene | C4085252 | PAGET DISEASE OF BONE 3 | 9 | GENOMICS_ENGLAND;UNIPROT | |
| Tgene | C0002736 | Amyotrophic Lateral Sclerosis | 5 | CTD_human;ORPHANET | |
| Tgene | C4225326 | FRONTOTEMPORAL DEMENTIA AND/OR AMYOTROPHIC LATERAL SCLEROSIS 3 | 4 | CTD_human;UNIPROT | |
| Tgene | C0029463 | Osteosarcoma | 2 | GENOMICS_ENGLAND | |
| Tgene | C0221054 | Welander Distal Myopathy | 1 | ORPHANET | |
| Tgene | C0242383 | Age related macular degeneration | 1 | CTD_human | |
| Tgene | C0393554 | Amyotrophic Lateral Sclerosis With Dementia | 1 | CTD_human | |
| Tgene | C0543859 | Amyotrophic Lateral Sclerosis, Guam Form | 1 | CTD_human | |
| Tgene | C1853926 | NONAKA MYOPATHY | 1 | CTD_human;GENOMICS_ENGLAND | |
| Tgene | C2931290 | Welander distal myopathy, Swedish type | 1 | ORPHANET | |
| Tgene | C3888102 | Frontotemporal Dementia With Motor Neuron Disease | 1 | ORPHANET | |
| Tgene | C4011788 | Behavioral variant of frontotemporal dementia | 1 | ORPHANET |
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