Protein:QKI |
Protein Summary |
 Gene summary |
| Gene name: QKI | ASpdb.0 ID: 9444 | Gene | Gene symbol | QKI | Gene ID | 9444 |
| Gene name | QKI, KH domain containing RNA binding |
| Synonyms | Hqk|QK|QK1|QK3|hqkI |
| Cytomap | 6q26 |
| Type of gene | protein-coding |
| Description | KH domain-containing RNA-binding protein QKIQKI/LOC100132735 fusionRNA binding protein HQKhomolog of mouse quaking QKI (KH domain RNA binding protein)quaking homolog, KH domain RNA binding |
| Modification date | 20240403 |
| UniProtAcc | Q96PU8 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | QKI | GO:0003729 | mRNA binding | 25768908 |
| Gene | QKI | GO:0005634 | nucleus | 37379838 |
| Gene | QKI | GO:0008298 | intracellular mRNA localization | 37379838 |
| Gene | QKI | GO:0010717 | regulation of epithelial to mesenchymal transition | 25768908 |
| Gene | QKI | GO:0035886 | vascular associated smooth muscle cell differentiation | 31331967 |
| Gene | QKI | GO:0045649 | regulation of macrophage differentiation | 27029405 |
| Gene | QKI | GO:0048024 | regulation of mRNA splicing, via spliceosome | 27029405|31331967 |
| Gene | QKI | GO:0051028 | mRNA transport | 37379838 |
| Gene | QKI | GO:0160089 | internal N(7)-methylguanine-containing RNA reader activity | 37379838 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| Q96PU8-1 | Q96PU8-1_4jvh_A.pdb | 4JVH | X-ray | 3.5 | A | 12 | 204 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| Q96PU8 | QKI | Q96PU8-1 | Q96PU8-3 | 341 | 333 | 213 | 220 | Deletion | none | none | 212 | 212 |
| Q96PU8 | QKI | Q96PU8-1 | Q96PU8-5 | 341 | 317 | 213 | 220 | Deletion | none | none | 212 | 212 |
| Q96PU8 | QKI | Q96PU8-1 | Q96PU8-5 | 341 | 317 | 312 | 341 | Substitution | GAVATKVRRHDMRVHPYQRIVTADRAATGN | EWIEMPVMPDISAH | 304 | 317 |
| Q96PU8 | QKI | Q96PU8-1 | Q96PU8-6 | 341 | 325 | 312 | 341 | Substitution | GAVATKVRRHDMRVHPYQRIVTADRAATGN | EWIEMPVMPDISAH | 312 | 325 |
| Q96PU8 | QKI | Q96PU8-1 | Q96PU8-8 | 341 | 319 | 312 | 341 | Substitution | GAVATKVRRHDMRVHPYQRIVTADRAATGN | GKFFSPWG | 312 | 319 |
| Q96PU8 | QKI | Q96PU8-1 | Q96PU8-9 | 341 | 319 | 312 | 341 | Substitution | GAVATKVRRHDMRVHPYQRIVTADRAATGN | GMAFPTKG | 312 | 319 |
| Multiple sequence alignment of our canonical and alternatively spliced QKI |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of QKI |
| UniProt-id | ENSG | ENST | ENSP |
| Q96PU8-1 | ENSG00000112531.17 | ENST00000361752.8 | ENSP00000355094.3 |
| Q96PU8-3 | ENSG00000112531.17 | ENST00000361195.6 | ENSP00000354867.2 |
| Q96PU8-5 | ENSG00000112531.17 | ENST00000424802.7 | ENSP00000408382.3 |
| Q96PU8-6 | ENSG00000112531.17 | ENST00000275262.11 | ENSP00000275262.7 |
| Q96PU8-8 | ENSG00000112531.17 | ENST00000392127.6 | ENSP00000375973.2 |
| Q96PU8-9 | ENSG00000112531.17 | ENST00000361758.8 | ENSP00000354951.4 |
| Q96PU8-9 | ENSG00000112531.17 | ENST00000453779.6 | ENSP00000408775.2 |
| UniProt-id | NM ID | NP ID |
| Q96PU8-1 | NM_006775.2 | NP_006766.1 |
| Q96PU8-3 | NM_001301085.1 | NP_001288014.1 |
| Q96PU8-6 | NM_206854.2 | NP_996736.1 |
| Q96PU8-8 | NM_206855.2 | NP_996737.1 |
| Q96PU8-9 | NM_206853.2 | NP_996735.1 |
| Amino acid sequences of our canonical and alternatively spliced QKI |
| accession_id | Protein sequence |
| Q96PU8-1 | MVGEMETKEKPKPTPDYLMQLMNDKKLMSSLPNFCGIFNHLERLLDEEISRVRKDMYNDTLNGSTEKRSAELPDAVGPIVQLQEKLYVPV KEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLV PAAEGEDSLKKMQLMELAILNGTYRDANIKSPALAFSLAATAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPLIRQIQTAVMPNGTPHP |
| Q96PU8-3 | MVGEMETKEKPKPTPDYLMQLMNDKKLMSSLPNFCGIFNHLERLLDEEISRVRKDMYNDTLNGSTEKRSAELPDAVGPIVQLQEKLYVPV KEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLV PAAEGEDSLKKMQLMELAILNGTYRDANIKSPTAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPLIRQIQTAVMPNGTPHPTAAIVPPG |
| Q96PU8-5 | MVGEMETKEKPKPTPDYLMQLMNDKKLMSSLPNFCGIFNHLERLLDEEISRVRKDMYNDTLNGSTEKRSAELPDAVGPIVQLQEKLYVPV KEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLV PAAEGEDSLKKMQLMELAILNGTYRDANIKSPTAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPLIRQIQTAVMPNGTPHPTAAIVPPG |
| Q96PU8-6 | MVGEMETKEKPKPTPDYLMQLMNDKKLMSSLPNFCGIFNHLERLLDEEISRVRKDMYNDTLNGSTEKRSAELPDAVGPIVQLQEKLYVPV KEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLV PAAEGEDSLKKMQLMELAILNGTYRDANIKSPALAFSLAATAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPLIRQIQTAVMPNGTPHP |
| Q96PU8-8 | MVGEMETKEKPKPTPDYLMQLMNDKKLMSSLPNFCGIFNHLERLLDEEISRVRKDMYNDTLNGSTEKRSAELPDAVGPIVQLQEKLYVPV KEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLV PAAEGEDSLKKMQLMELAILNGTYRDANIKSPALAFSLAATAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPLIRQIQTAVMPNGTPHP |
| Q96PU8-9 | MVGEMETKEKPKPTPDYLMQLMNDKKLMSSLPNFCGIFNHLERLLDEEISRVRKDMYNDTLNGSTEKRSAELPDAVGPIVQLQEKLYVPV KEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLV PAAEGEDSLKKMQLMELAILNGTYRDANIKSPALAFSLAATAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPLIRQIQTAVMPNGTPHP |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| QKI (go to UniProt):Q96PU8 |
| Retention analysis result of 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. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q96PU8 | Region | 182 | 213 | Note=Qua2 domain%3B involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23630077;Dbxref=PMID:23630077 | Type=Deletion;Start=213;End=220 |
| Q96PU8 | Region | 182 | 213 | Note=Qua2 domain%3B involved in RNA binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23630077;Dbxref=PMID:23630077 | Type=Deletion;Start=213;End=220 |
| Q96PU8 | Motif | 324 | 330 | Note=Nuclear localization signal;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QYS9 | Type=Substitution;Start=312;End=341 |
| Q96PU8 | Motif | 324 | 330 | Note=Nuclear localization signal;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QYS9 | Type=Substitution;Start=312;End=341 |
| Q96PU8 | Motif | 324 | 330 | Note=Nuclear localization signal;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QYS9 | Type=Substitution;Start=312;End=341 |
| Q96PU8 | Motif | 324 | 330 | Note=Nuclear localization signal;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9QYS9 | Type=Substitution;Start=312;End=341 |
Gene Isoform Structures and Expression Levels for QKI |
| Gene structures of our canonical and alternative spliced genes of QKI * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of Q96PU8-1 |
| 3D view using mol* of Q96PU8-3 |
| 3D view using mol* of Q96PU8-5 |
| 3D view using mol* of Q96PU8-6 |
| 3D view using mol* of Q96PU8-8 |
| 3D view using mol* of Q96PU8-9 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of Q96PU8-1 |
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| pLDDT distribution across the protein length of Q96PU8-3 |
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| pLDDT distribution across the protein length of Q96PU8-5 |
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| pLDDT distribution across the protein length of Q96PU8-6 |
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| pLDDT distribution across the protein length of Q96PU8-8 |
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| pLDDT distribution across the protein length of Q96PU8-9 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of Q96PU8-1 |
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| Ramachandran plot of Q96PU8-3 |
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| Ramachandran plot of Q96PU8-5 |
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| Ramachandran plot of Q96PU8-9 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| Q96PU8-1 | 0.952 | 83 | 1.01 | 296.009 | 0.726 | 0.615 | 0.767 | 1.05 | 0.661 | 1.59 | 1.206 | 13,22,25,26,46,49,50,53,54,55,58,59,62,65,66,68,69 ,108,111,112,115,116,170,200 |
| Q96PU8-3 | 1.128 | 100 | 1.139 | 178.703 | 0.39 | 0.881 | 1.126 | 1.88 | 1.011 | 1.86 | 1.195 | 54,57,58,61,62,68,101,109,112,113,116,117,174,177, 178,187,189 |
| Q96PU8-5 | 1.053 | 202 | 1.1 | 490.833 | 0.549 | 0.715 | 0.919 | 0.957 | 0.825 | 1.16 | 1.041 | 54,57,58,61,62,63,64,65,67,68,69,70,72,101,109,112 ,113,116,117,167,170,173,174,177,178,180,182,187,1 88,189 |
| Q96PU8-6 | 1.052 | 181 | 1.071 | 427.035 | 0.483 | 0.767 | 1.005 | 1.008 | 1.01 | 0.998 | 0.964 | 54,55,57,58,59,61,62,64,65,67,68,69,70,101,109,112 ,113,116,117,166,170,173,174,177,178,180,182,187,1 88,189 |
| Q96PU8-8 | 1.06 | 169 | 1.079 | 363.237 | 0.446 | 0.776 | 0.993 | 1.102 | 1.004 | 1.097 | 0.942 | 54,57,58,61,62,63,64,65,67,68,69,109,112,113,116,1 17,166,170,173,174,177,178,189 |
| Q96PU8-9 | 1.089 | 169 | 1.136 | 403.368 | 0.482 | 0.762 | 0.996 | 1.559 | 0.799 | 1.951 | 0.816 | 54,57,58,60,61,62,65,68,69,72,101,109,112,113,116, 117,167,170,173,174,177,178,180,182,187,188,189,19 2 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of Q96PU8-1_Q96PU8-1_4jvh_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q96PU8-1_4jvh_A_Q96PU8-3.pdb |
| 3D view using mol* of Q96PU8-1_4jvh_A_Q96PU8-5.pdb |
| 3D view using mol* of Q96PU8-1_4jvh_A_Q96PU8-6.pdb |
| 3D view using mol* of Q96PU8-1_4jvh_A_Q96PU8-8.pdb |
| 3D view using mol* of Q96PU8-1_4jvh_A_Q96PU8-9.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q96PU8-1_Q96PU8-3.pdb |
| 3D view using mol* of Q96PU8-1_Q96PU8-5.pdb |
| 3D view using mol* of Q96PU8-1_Q96PU8-6.pdb |
| 3D view using mol* of Q96PU8-1_Q96PU8-8.pdb |
| 3D view using mol* of Q96PU8-1_Q96PU8-9.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q96PU8-1_vs_Q96PU8-3.png |
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| ./stats/secondary_structure/figure/Q96PU8-1_vs_Q96PU8-5.png |
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| ./stats/secondary_structure/figure/Q96PU8-1_vs_Q96PU8-6.png |
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| ./stats/secondary_structure/figure/Q96PU8-1_vs_Q96PU8-8.png |
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| ./stats/secondary_structure/figure/Q96PU8-1_vs_Q96PU8-9.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q96PU8-1_vs_Q96PU8-3.png |
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| ./stats/relative_asa/Q96PU8-1_vs_Q96PU8-5.png |
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| ./stats/relative_asa/Q96PU8-1_vs_Q96PU8-6.png |
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| ./stats/relative_asa/Q96PU8-1_vs_Q96PU8-8.png |
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| ./stats/relative_asa/Q96PU8-1_vs_Q96PU8-9.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to QKI |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to QKI |
| Previous studies relating to the alternative splicing of QKI and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| QKI | 11917126 | Function of quaking in myelination: regulation of alternative splicing. | Proteomic diversity is frequently achieved by alternative RNA-splicing events that can be fine-tuned in tissue-specific and developmentally regulated ways. Understanding this type of genetic regulation is compelling because of the extensive complexity of alternative splicing found in the nervous system. quaking (qk), one of the classical mouse dysmyelination mutants, is defective for the expression of myelin-associated glycoprotein (MAG), and the misregulation of MAG pre-mRNA alternative splicing is implicated as a causal factor. The qk locus encodes several RNA-binding proteins with heterogeneous nuclear ribonucleoprotein K-type homology, a characteristic of several known alternative splicing regulators. Here we test the nuclear-localized qk isoform (QKI-5) for its ability to regulate alternative splicing of MAG pre-mRNA in transient coexpression assays. QKI-5 exhibits properties of a negative regulator of MAG exon 12 alternative splicing. An intronic sequence element required for the repressive function and binding of QKI-5 is also identified. Direct evidence for irregularities in alternative splicing of MAG and other myelin protein transcripts in the qk mouse is demonstrated. | D003711 | Demyelinating Diseases |
| QKI | 23963726 | Quaking, an RNA-binding protein, is a critical regulator of vascular smooth muscle cell phenotype. | RNA-binding proteins are critical post-transcriptional regulators of RNA and can influence pre-mRNA splicing, RNA localization, and stability. The RNA-binding protein Quaking (QKI) is essential for embryonic blood vessel development. However, the role of QKI in the adult vasculature, and in particular in vascular smooth muscle cells (VSMCs), is currently unknown. | D020212 | Carotid Artery Injuries |
| QKI | 23963726 | Quaking, an RNA-binding protein, is a critical regulator of vascular smooth muscle cell phenotype. | RNA-binding proteins are critical post-transcriptional regulators of RNA and can influence pre-mRNA splicing, RNA localization, and stability. The RNA-binding protein Quaking (QKI) is essential for embryonic blood vessel development. However, the role of QKI in the adult vasculature, and in particular in vascular smooth muscle cells (VSMCs), is currently unknown. | D023903 | Coronary Restenosis |
| QKI | 23963726 | Quaking, an RNA-binding protein, is a critical regulator of vascular smooth muscle cell phenotype. | RNA-binding proteins are critical post-transcriptional regulators of RNA and can influence pre-mRNA splicing, RNA localization, and stability. The RNA-binding protein Quaking (QKI) is essential for embryonic blood vessel development. However, the role of QKI in the adult vasculature, and in particular in vascular smooth muscle cells (VSMCs), is currently unknown. | D004195 | Disease Models, Animal |
| QKI | 23963726 | Quaking, an RNA-binding protein, is a critical regulator of vascular smooth muscle cell phenotype. | RNA-binding proteins are critical post-transcriptional regulators of RNA and can influence pre-mRNA splicing, RNA localization, and stability. The RNA-binding protein Quaking (QKI) is essential for embryonic blood vessel development. However, the role of QKI in the adult vasculature, and in particular in vascular smooth muscle cells (VSMCs), is currently unknown. | D006965 | Hyperplasia |
| QKI | 23963726 | Quaking, an RNA-binding protein, is a critical regulator of vascular smooth muscle cell phenotype. | RNA-binding proteins are critical post-transcriptional regulators of RNA and can influence pre-mRNA splicing, RNA localization, and stability. The RNA-binding protein Quaking (QKI) is essential for embryonic blood vessel development. However, the role of QKI in the adult vasculature, and in particular in vascular smooth muscle cells (VSMCs), is currently unknown. | D058426 | Neointima |
| QKI | 24722255 | The RNA-binding protein QKI suppresses cancer-associated aberrant splicing. | Lung cancer is the leading cause of cancer-related death worldwide. Aberrant splicing has been implicated in lung tumorigenesis. However, the functional links between splicing regulation and lung cancer are not well understood. Here we identify the RNA-binding protein QKI as a key regulator of alternative splicing in lung cancer. We show that QKI is frequently down-regulated in lung cancer, and its down-regulation is significantly associated with a poorer prognosis. QKI-5 inhibits the proliferation and transformation of lung cancer cells both in vitro and in vivo. Our results demonstrate that QKI-5 regulates the alternative splicing of NUMB via binding to two RNA elements in its pre-mRNA, which in turn suppresses cell proliferation and prevents the activation of the Notch signaling pathway. We further show that QKI-5 inhibits splicing by selectively competing with a core splicing factor SF1 for binding to the branchpoint sequence. Taken together, our data reveal QKI as a critical regulator of splicing in lung cancer and suggest a novel tumor suppression mechanism involving QKI-mediated regulation of the Notch signaling pathway. | D002471 | Cell Transformation, Neoplastic |
| QKI | 24722255 | The RNA-binding protein QKI suppresses cancer-associated aberrant splicing. | Lung cancer is the leading cause of cancer-related death worldwide. Aberrant splicing has been implicated in lung tumorigenesis. However, the functional links between splicing regulation and lung cancer are not well understood. Here we identify the RNA-binding protein QKI as a key regulator of alternative splicing in lung cancer. We show that QKI is frequently down-regulated in lung cancer, and its down-regulation is significantly associated with a poorer prognosis. QKI-5 inhibits the proliferation and transformation of lung cancer cells both in vitro and in vivo. Our results demonstrate that QKI-5 regulates the alternative splicing of NUMB via binding to two RNA elements in its pre-mRNA, which in turn suppresses cell proliferation and prevents the activation of the Notch signaling pathway. We further show that QKI-5 inhibits splicing by selectively competing with a core splicing factor SF1 for binding to the branchpoint sequence. Taken together, our data reveal QKI as a critical regulator of splicing in lung cancer and suggest a novel tumor suppression mechanism involving QKI-mediated regulation of the Notch signaling pathway. | D008175 | Lung Neoplasms |
Clinically important variants in QKI |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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